key: cord- - jnkki z authors: mohammad, fahim; theisen-toupal, jesse c.; arnaout, ramy title: advantages and limitations of anticipating laboratory test results from regression- and tree-based rules derived from electronic health-record data date: - - journal: plos one doi: . /journal.pone. sha: doc_id: cord_uid: jnkki z laboratory testing is the single highest-volume medical activity, making it useful to ask how well one can anticipate whether a given test result will be high, low, or within the reference interval (“normal”). we analyzed years of electronic health records—a total of . million blood tests—to see how well standard rule-mining techniques can anticipate test results based on patient age and gender, recent diagnoses, and recent laboratory test results. we evaluated rules according to their positive and negative predictive value (ppv and npv) and area under the receiver-operator characteristic curve (roc aucs). using a stringent cutoff of ppv and/or npv≥ . , standard techniques yield few rules for sendout tests but several for in-house tests, mostly for repeat laboratory tests that are part of the complete blood count and basic metabolic panel. most rules were clinically and pathophysiologically plausible, and several seemed clinically useful for informing pre-test probability of a given result. but overall, rules were unlikely to be able to function as a general substitute for actually ordering a test. improving laboratory utilization will likely require different input data and/or alternative methods. laboratory testing is the single highest-volume medical activity [ ] . its main role is to help adjust the level of clinical suspicion of a diagnosis to help rule it in or out; it is also used for disease monitoring. in practice, the level of clinical suspicion and the probability of a given test result can be correlated: the higher the suspicion, the more likely it is that the result will confirm the diagnosis. information that feeds into the clinical suspicionincluding the age and gender of the patient, prior diagnoses, and prior laboratory results-thus may also influence the test result. in principle, this relationship can be used to improve laboratory testing by making it possible to estimate the pre-test probability of getting a given test result before ordering the test, and, in the limit, to reduce test utilization without adversely affecting patient outcomes. indeed, ordering fewer tests, where warranted, might benefit outcomes by saving the patient the burden of following up false positives (or negatives) [ ] [ ] [ ] . conceptually, the relationship between clinical suspicion and pre-test probability is used routinely to help set guidelines regarding when and when not to order a given test. for example, the pre-test probability of lyme serology being positive given a targetoid rash is high enough that, given the test's sensitivity and specificity, ordering the test is contraindicated [ ] . because of the large number of tests and clinical scenarios that exist, and in light of evidence from across medicine that utilization of laboratory testing can be improved [ , ] , it is of interest to understand whether analyzing large clinical databases using the robust application of standard statistical techniques can turn this relationship into actionable decision-support rules-or whether progress toward better laboratory utilization might instead lie elsewhere. we sought to test the limits of rule-mining for this purpose. to what extent can laboratory results be anticipated computationally based on data available to the clinician, or a clinical decision support system, at the time of the order? we addressed this question using generalized linear modeling (glm), a generalized form of linear regression [ ] , and, for comparison, classification trees (ct) [ , ] . we used four types of input-age, gender, diagnoses (three-digit icd- codes), and results of laboratory tests on blood samples added to the record in the seven days before a given test was ordered-to build simple, robust models for whether the result of a test would be within the reference interval (''normal'') or outside of it in a given direction (''abnormal''), treating high and low results separately. we based our study on years of records from the beth israel deaconess medical center (bidmc), a -bed tertiary care center in boston, ma. we first anonymized records and reconciled test names (work approved by bidmc committee on clinical investigation's institutional review board for research involving human subjects, protocol -p- / ). informed consent was not obtained because patient records/ information was anonymized prior to analysis. each blood test (the test of interest), over . million in all, was marked as an in-house test (performed at the hospital) or a sendout (performed off-site). for each test, we compiled a list of all instances in which the test was ordered and performed. for each instance, we recorded the patient's age, gender, and any diagnoses or other blood-test test results from the seven days prior to the result of interest. when a test was ordered multiple times within a seven-day period, we considered only the most recent one (i.e., the one closest in time to the sendout order) as input data. for relevance, we considered only those tests that were ordered at least , times over the entire -year period, for an average of at least twice a week. we randomly divided the resulting instances into a training set and a test set (see below for details). all tests had either two (reference vs. abnormal) or three (low, normal, or high) possible response values. for tests with three values, we performed two separate rule searches: one for high vs. not high-i.e., grouping normal and low-and one for low vs. not low. we sought to identify simple, robust subsets of our input data to evaluate as linear predictors (''rules'') for whether a test result would be normal or abnormal. to do this, we used glm twice: first to find rules based on a particular training set and a second time to find rules based on just those items that were common to rules found from a number of different training sets (to avoid overfitting any one training set). we did this as follows, for each test of interest (the response variable or ''response''). we first excluded those input variables (''features'') that appeared with fewer than percent of the response. we then temporarily set aside the most common features (those of the complete blood count and basic metabolic panel) as well as age and gender, and searched the remaining items for frequent featuresets (using the apriori algorithm [ , ] ). we then added back to each resulting featureset the common features, age, and gender (which are frequent items by definition, since they appear in all instances) with a support threshold of . (i.e., itemsets for which all items were present with at least percent of instances of the response variable). this set-aside/add-back approach sped the search for featuresets without loss of comprehensiveness. we used each featureset to create a model for the test of interest using r's glm function (with the family argument set to ''binomial''). we used backward feature elimination to remove non-significant features one at a time from the featureset (using a significance threshold p-value of ; see below) until the only features that remained were all significantly correlated with the response. we also removed features that are used to calculate the result for the test of interest-e.g., cd and cd count for t-cell count, which is the sum of cd and cd -for all but proof-ofprinciple runs. the significance threshold was corrected for multiple comparisons by dividing the traditional threshold of p = . by the product of the total number of tests considered and the average number of rules generated for each test. the combined total number of features (in-house tests plus sendout tests plus diagnoses) was + + = . the average number of rules after application of glm for the first time for each test is . thus our threshold p-value was . /( * ) = . , which we rounded to . we constructed a model for the result by running glm a second time on a training set (see below) based on this reduced featureset. of note, there was no guarantee that any feature would be significantly correlated (p# ) or that there would be enough instances (glm's threshold was ) of the test appearing with all features of even the reduced featureset for glm to produce a model. when feature elimination resulted in no significant features or too few instances, no model was constructed. we scored models using ppv, npv, and roc auc. we were interested only in models that were robust to the size and choice of training set. therefore we repeated the above process for a range of training set-test set splits ( - , - , - , - , - , - , and - percent). for each split, we ran the above process times and found the number of rules with auc$ . . we decided on using a - split for downstream analyses as this split generated a total number of rules comparable to - and - splits but with less training data (fig. ) . finally, for each test of interest, we selected features that appeared in a strict majority of rules for that test and reran glm using only those features. this made rules both simpler and more robust by removing features whose presence was contingent on a particular choice of training or test set. for each of the inhouse and sendout tests we used cart, implemented as rpart in r (rpart v . - ; cran.r-project.org/ package = rpart), to predict the response from all input features, using : training:test-set splits. we fixed some of the metrics (see below) that were used in building the final tree. the cart grows classification tree in two stages. in stage one, a tree is grown by finding a feature which best splits the data into two groups. splitting is done only if the overall ''impurity,'' the number of outcomes different from the majority (e.g., a ''low'' response alongside many ''normal'' responses), decreases, above some threshold (the ''complexity parameter;'' . ). then, in top-down fashion, these two subgroups are further divided in a recursive manner until the subgroups reach a minimum size (minsplit = records) or until no further improvement can be made. the resulting tree may overfit the training data. to avoid this, crossvalidation (xval = ; -fold cross-validation) was used in the second stage by pruning the tree. we fixed the maximum depth (maxdepth) of the tree, i.e., the maximum number of branchings from stem to leaf, to be . the final models were tested on the test data and performance statistics are found. we repeated modelbuilding times for each test and summarized the statistics. data-processing was performed in python (enthought canopy python version . . . r (version . . ) was used for statistical analysis and reports generation. to determine how well sendout and in-house test results can be anticipated based on basic information available in the medical record, we used two independent methods-generalized linear modeling (glm) and classification and regression trees (cart)to build simple, robust test-result predictors and then evaluated the performance of these predictors according to the standard clinical metrics of positive predictive value (ppv) and negative predictive value (npv), as well as sensitivity and specificity via the receiveroperator curve (roc) area under the curve (auc). as proof of principle for glm, we first tested it on the anion gap, a result calculated by subtracting the serum concentrations of the anions chloride and bicarbonate from those of the cations sodium and potassium, and confirmed that our methods found a rule for elevated anion gap based on these four items. we next applied glm to sendout tests ordered regularly at our hospital. glm generated rules for just of these tests. for the remaining tests, either no recent diagnosis or in-house test result (or age or gender) was sufficiently correlated with the sendout test result, or there were not enough instances in which correlated items appeared with the result, to generate a rule. only two tests-for high corticotropin (acth) and for low ceruloplasmin-had npv$ . . of these, ceruloplasmin had a ppv$ . . the mean auc for all rules was . , with models for only three tests having an average auc$ . over repeat runs. removal of features that did not appear in a majority of rules had essentially no effect on these aucs (difference in mean auc# . ). cart generated rules for tests. however, the auc for most of these rules was low, with only five tests having auc$ . : free t , alpha-macroglobulin, ca - , hyaluronic acid, and alpha fetoprotein (auc . - . ). we next applied glm to in-house tests. a total of in-house tests were analyzed. a number of rules exhibited a high ppv (the probability of seeing an abnormal value given a prediction of an abnormal value by the rule) or npv (the probability of seeing a normal value given prediction of a normal value). these were mostly components of the complete blood count (cbc) and metabolic panels. interestingly, the predictive power of these rules was almost exclusively based on a previous measurement of the test in question: in other words, the best rules were for repeat tests, and the best predictor of a result being normal or abnormal was whether it had been normal or abnormal within the previous seven days. for example, the npv for a low red blood cell count was . (with ppv = . ), with a rule that depended most on the previous red blood cell count also having been low, and the ppv for high total calcium was . (npv = . ) and based exclusively on the previous total calcium having been high. for comparison, we applied cart to in-house tests, again including in the input data the most recent result for that test if performed within a week of the order. again, a number of rules exhibited a high ppv ($ . ), and again these were often tests of the cbc and metabolic panels, with rules based almost exclusively on a previous abnormal value. examples included low white blood cell count (wbc; ppv = . , npv = . ), platelet count ( . , . ), and serum sodium ( . , . ), and high total calcium ( . , . ), mean corpuscular volume ( . , . ), and iron ( . , . ) all of which were determined almost exclusively from the previous value being low or high (table ) . overall, there was good agreement in ppv between glm and cart for tests for which both methods found rules, but cart outperformed glm noticeably in npv (fig. ). the growing availability of large clinical databases has raised interest in the possibility of using systematic rule-mining for clinical decision support [ ] [ ] [ ] [ ] . one popular and well characterized approach has been logistic regression [ ] [ ] [ ] , a special case of generalized linear modeling (glm). researchers have applied these approaches for diverse health-related purposes including prediction of cardiovascular risk [ ] , mortality in head trauma [ ] , texture analysis of magnetic resonance images [ ] , and many other applications [ , , ] . however, we note that glm does not easily incorporate missing values, as it removes records with missing features; a feature will be ''missing'' for any record in which that test (the feature) was not performed. other methods, such as classification and regression trees (cart) and artificial neural networks [ ] , have also been applied. most of these studies were limited in scope to predicting risk of a particular diagnosis. harper [ ] compared four classification techniques (regression, cart, artificial neural networks, and discriminant analysis) on four different datasets and concluded that there was no obvious best choice for their data; while cart performed best, regression was fastest and nearly as good. similar comparative studies on coronary artery disease [ ] and alzheimer disease [ ] indicated that newer algorithms such as ann and random forests [ ] have little advantage over simpler, more traditional approaches. also, the utility and limitations of these approaches for predicting laboratory results (as opposed to diagnoses) are unclear. however, while cart is both a top performer and overcomes glm's problem with missing values, it is also more computationally intensive and potentially less sensitive to simple algebraic relationships among features (e.g., among sodium, chloride and bicarbonate and the anion gap). therefore we chose glm as a well-understood approach with strong performance and excellent speed, and cart as the bestperforming complementary approach for purposes of comparison. given the importance of laboratory testing, we asked how much information regression-or classification tree-based rules could provide in assessing the pre-test probability of a test result being abnormal for commonly ordered in-house and sendout tests at our hospital. data-mining can sometimes find spurious correlations, artifacts of the particular partitioning of the data into training and test set. to avoid such artifacts, we repeated our regression on multiple independent partitions of the data and kept only items that appeared in a majority of the resulting rules. this safeguard also had the effect of simplifying rules by making each rule dependent on a smaller number of items. as expected, the effect on performance was negligible and dependence on the resulting items was more often clinically and pathophysiologically plausible than rules derived from each run. when data-mining it is also important to consider the setting. the rules we found do not exist in a vacuum but are ''contingent'' in the sense that they depend on current clinical practice. certain tests and panels are ordered in patterns. in a sense, contingency is a form of selection bias: there may well be other diagnoses or test result results that correlate with the result for the test of interest that are not routinely measured according to current best practices. however, as long as the setting in which such rules would be applied is the substantially similar to that in which they were found, selection bias would have little if any effect on finding rules. as long as one is clear that one is looking for relationships in a current practice process, and not among all things that could possibly be measured, any rules that are discovered will by construction be setting-appropriate. but while our rules appear to be plausible and settingappropriate, the motivating question behind this study is whether the rules we found could be useful clinically. one way to approach this question is by considering the positive and negative predictive value of each rule (ppv and npv). these metrics are in contrast to sensitivity and specificity, by which rules are often measured but which do not incorporate disease prevalence in spite of its importance to clinical decision-making. a ppv of . means that when a rule suggests that the test result will be abnormal, the result actually will be abnormal percent of the time. a npv of . means that when a rule suggests that the test result will be normal, the result actually will be normal percent of the time. we found rules with ppv and/or npv$ . (by glm) for only two tests that are sendouts at our hospital-one of which is ceruloplasmin, which we have previously suggested is overordered via chart review [ ] . in contrast, for in-house tests we found over a dozen such rules. interestingly, the main determinant for rules for in-house tests was a normal or abnormal result for the same test within the previous seven days. although in this study we did not set out explicitly to make a statement about repeat laboratory testing, the appropriateness of which has been investigated elsewhere [ ] , these results suggest that repeat laboratory testing within one week does not always add information that could not have been anticipated from the previous result. refining this observation using the same unbiased approach we have followed here is potentially an area for future investigation. our results should not be taken as a categorical criticism of repeat testing. first, while the ppv was $ . in several cases, the npv was more typically . - . . thus, while prediction that a result will be abnormal may be correct percent of the time, which may be good enough to discourage repeat ordering, prediction that a result will be normal may not be so dependable. therefore use of a rule depends on the subtle distinction of whether the clinical question is ''will the result be abnormal'' vs. ''will the result be normal.'' second, we note that no rules with such strong performance were found for the majority of our sendout or in-house tests by either of our two complementary approaches. thus while the rules we found can inform clinical decision-makers, the information they provide rarely replaces the information obtained from actually performing these tests. it is interesting to note that on average, our simple rules yielded a ppv of . and an npv of . . this means that on average, rules will correctly predict an abnormal laboratory result times out of ( / < . ) and correctly predict a normal result times out of . while not good enough to replace testing (especially for rules that depend on previous test results), these observations raise the question of how much better prediction can get. integration of information not considered in the present study, including vital signs, chief complaints, and physical findings, may improve prediction by these methods. the ulysses syndrome the dangers of false-positive and false-negative test results: false-positive results as a function of pretest probability the landscape of inappropriate laboratory testing: a -year systematic review and meta-analysis laboratory evaluation in the diagnosis of lyme disease elementary, my dear doctor watson generalized linear models electronic health record surveillance algorithms facilitate the detection of transfusion-related pulmonary complications using classification trees to assess low birth weight outcomes fast algorithms for mining association rules fast discovery of association rules data mining and clinical data repositories: insights from a , patient data set mining association rules from clinical databases: an intelligent diagnostic process in healthcare machine learning for personalized medicine: predicting primary myocardial infarction from electronic health records predictive data mining in clinical medicine: current issues and guidelines textural analysis of contrast-enhanced mr images of the breast establishing a clinical decision rule of severe acute respiratory syndrome at the emergency department comparison of artificial neural network and logistic regression models for prediction of mortality in head trauma based on initial clinical data improved cardiovascular risk prediction using nonparametric regression and electronic health record data comparing performances of logistic regression, classification and regression tree, and neural networks for predicting coronary artery disease predicting improvement in urinary and bowel incontinence for home health patients using electronic health record data a review and comparison of classification algorithms for medical decision making application and comparison of classification algorithms for recognition of alzheimer's disease in electrical brain activity (eeg) random forests the overuse of serum ceruloplasmin measurement key: cord- -zr bo el authors: pfannschmidt, karlson; hüllermeier, eyke; held, susanne; neiger, reto title: evaluating tests in medical diagnosis: combining machine learning with game-theoretical concepts date: - - journal: information processing and management of uncertainty in knowledge-based systems doi: . / - - - - _ sha: doc_id: cord_uid: zr bo el in medical diagnosis, information about the health state of a patient can often be obtained through different tests, which may perhaps be combined into an overall decision rule. practically, this leads to several important questions. for example, which test or which subset of tests should be selected, taking into account the effectiveness of individual tests, synergies and redundancies between them, as well as their cost. how to produce an optimal decision rule on the basis of the data given, which typically consists of test results for patients with or without confirmed health condition. to address questions of this kind, we develop an approach that combines (semi-supervised) machine learning methodology with concepts from (cooperative) game theory. roughly speaking, while the former is responsible for optimally combining single tests into decision rules, the latter is used to judge the influence and importance of individual tests as well as the interaction between them. our approach is motivated and illustrated by a concrete case study in veterinary medicine, namely the diagnosis of a disease in cats called feline infectious peritonitis. different types of tests, such as measuring serum antibody concentrations, are commonly used in medical diagnostics in order to reveal the health condition of an individual. the effectiveness of a single test is typically determined by correlating the test outcome with the true condition. moreover, classical statistical hypothesis testing can be used to compare different test procedures in terms of their effectiveness. in this paper, we tackle the problem of evaluating or selecting a test procedure from a slightly different perspective using methods of (semi-)supervised machine learning. roughly speaking, the idea is that, by learning a model in which various candidate tests play the role of predictor variables, information about the usefulness of individual tests as well as their combination is provided by properties of that model. an approach of that kind has at least two important advantages: -first, it not only allows for judging the usefulness of single tests but also of combined tests, i.e., the combination of different tests into one overall (diagnostic) decision rule. thus, it informs about possible synergies (as well as redundancies) between individual tests and the potential to improve diagnostic accuracy thanks to a suitable combination of these tests. -second, going beyond the standard setting of supervised learning, a machine learning approach suggests various ways of improving the selection of tests by taking advantage of additional sources of information. an important special case is the use of semi-supervised learning to exploit "unlabeled" data coming from individuals for which tests have been made but the true health condition is unknown. this situation is highly relevant in medical practice, because tests can often be conducted quite easily, whereas determining the true health condition is very difficult or expensive. our approach is motivated by a concrete case study in veterinary medicine, namely the diagnosis of a disease in cats called feline infectious peritonitis (fip). complete certainty about whether or not a cat is fip-positive, and eventually will die from the disease, requires a necropsy [ , ] ; unfortunately, no test performed in a cat while still alive has a % sensitivity or % specificity. consequently, while different tests can be applied to cats quite easily, "labeling" a cat in the sense of supervised learning is expensive, difficult and time-consuming. in addition to the use of (semi-supervised) machine learning methodology in medical diagnosis, we propose a game-theoretical approach for measuring the usefulness of individual tests as well as model-based combinations of such tests. roughly speaking, the idea is to consider a combination of tests as a "coalition" in the sense of cooperative game theory, and the "payoff" of the coalition as the diagnostic accuracy achieved by the test combination. this approach will be detailed in the next section, prior to elaborating more closely on our case study in sect. , presenting experimental results in sect. and concluding the paper in sect. . suppose a set of tests x , . . . , x k to be available. we consider the outcome of each test as a random variable x k : Ω −→ r, where Ω is the population of individuals to which the test can be applied. jointly, the k tests thus define a random vector the health state is a dichotomous variable y ∈ y = {− , + }. typically, each test is a positive indicator in the sense that p(y = + | x k ) increases with x k , i.e., the larger x k , the larger the probability of the positive class. using machine learning terminology, each test corresponds to a feature or predictor variable. moreover, x is the instance space, each x ∈ x is an instance, and y is the (binary) output or response variable. if a diagnostic decisionŷ ∈ {− , + } is not necessarily based on a single test x k alone, but possibly uses a combination of several tests, a first question concerns the way in which such a combination is realized. from a machine learning point of view, this question is related to the choice of an underlying models class (hypothesis space) where j ≤ k is the number of tests included in the decision rule. formally, we specify a combined test in terms of the subset the model class h could be defined, for example, as the class of linear threshold functions of the form where w , . . . , w j , t ∈ r + and · maps true predicates to + and false predicates to − ; moreover, σ(j) is the j-th test included in the combination, i.e., i.e., a decision rule that minimizes the loss in expectation. we denote the expected loss of this model, which corresponds to the bayes predictors in h |a| , by e * (a) = l y, h * a (x) d p(x, y).( ) in practice, of course, neither the bayes predictor h * a nor the ideal generalization performance e * (a) are known. instead, we only assume a data set d = d l ∪ d u to be given, which consists of a set of labeled instances and possibly another set of unlabeled instances (test results without ground truth) d u = {x j } u j= ⊂ x . from a machine learning point of view, it is then natural to estimate the generalization performance on the basis of d for each a ⊆ [k] . to this end, models ( ) can be fitted and their generalization performance can be estimated, for example, using cross-validation techniques or the bootstrap. more specifically, what can be estimated in this way is the generalization performance of a model that is trained on a combination a and data in the form of l labeled and u unlabeled examples. therefore, we shall denote a corresponding estimate byê(a, l, u ) or simplyê(a) (assuming the underlying data to be given). needless to say, the estimatesê(a) thus obtained are not necessarily monotone in the sense thatê(b) ≤ê(a) for a ⊆ b. in fact, while e * (a) is the generalization performance of the bayes predictor, i.e., the model that is obtained in the limit of an infinite sample size (provided the underlying learner is consistent), the estimatesê(a) are obtained from models trained on a finite (and possibly small) data set. therefore, practical problems such as overfitting become an issue, i.e., including additional tests may deteriorate instead of improve generalization performance. how can the ideal generalization performances be estimated? starting with the finite-sample estimates our proposal is to correct these estimates so as to assure monotonicity. in fact, monotonicity is the main difference between the ideal and finite-sample scores. apart from that, the ideal scores ( ) should not differ too much from the estimates ( ), i.e., e * (a) ≈ê(a), at least if the training data is not too small. these considerations suggest the following estimation principle: find a set of values ( ) that satisfy monotonicity while remaining as close as possible to the corresponding scores ( ). this principle can be formalized as an optimization problem of the following kind: the above problem can be tackled by means of methods for isotonic regression. more specifically, since the inclusion relation on subsets induces a partial order on [k] , methods for isotonic regression on partially ordered structures are needed [ , ] . consider the set function ν : obviously, ν is a monotone measure (of the usefulness of combined tests). moreover, this measure can be normalized by setting where ν (∅) is the performance of the best (default) decision rule that does not use any test, i.e., which either always predictsŷ = + or alwaysŷ = − . the measure ν * (·) thus defined satisfies the following properties: thus, ν * is a normalized, monotone (but not necessarily additive) set function, referred to as fuzzy measure or capacity in the literature [ ] . for each combined test a, ν * (a) is a reasonable measure of the usefulness of this test. in a similar way, a measure v • can be defined on the basis of the finite-sample scores ( ), that is, by normalizing ν where ν min = − max b⊆[k]ê (b) and ν max = − min b⊆[k]ê (b). note, however, that this measure is not necessarily monotone. which of the two measures is more meaningful, ν * or ν • ? the answer to this question depends on practical considerations and what the measure is actually supposed to capture. when being interested in the potential asymptotic usefulness of a test combination, then ν * is the right measure. otherwise, if a model induced from a concrete set of training data is supposed to be put into (medical) practice, ν • is arguably more relevant. from the point of view of (cooperative) game theory, each (test) combination a ⊆ [k] can be seen as a coalition and ν ∈ {ν * , ν • } as the characteristic function, i.e., v(a) is the payoff achieved by the coalition a. thanks to this view, we can take advantage of various established game-theoretical concepts for analyzing the importance of individual players, which correspond to tests in our case, as well as the interaction between them. in particular, the shapley value, also called importance index, is defined as follows [ ] : the shapley value of ν is the vector ϕ(ν) = (ϕ( ), . . . , ϕ(k)). for monotone measures (such as ν = ν * ), one can show that ≤ ϕ(k) ≤ and k k= ϕ(k) = ; thus, ϕ(k) is a measure of the relative importance of the test x k . the interaction index, as proposed by [ ] , is defined as follows: this index ranges between − and + and indicates a positive (negative) interaction between the tests x i and x j if i i,j > (i i,j < ). it is worth mentioning that the approach put forward in this section is quite in line with the idea of shapley value regression [ ] , which makes use of the shapley value in order to quantify the contribution of predictor variables in (linear) regression analysis (quantifying the value of a set of variables in terms of the r measure on the training data). feline infectious peritonitis (fip) is a disease with an affinity to young cats, a predisposition to involve cats living in larger groups. as it exhibits typical physical examination and clinical laboratory findings, it appears to be easy to diagnose. however, while a presumptive diagnosis is quickly established, a definite diagnosis is difficult to impossible to obtain without gross and histopathological evaluation including immunohistochemistry [ , ] . the seroprevalence is high, especially in catteries where up to % of the cats are positive [ ] , but also up to % of cats living in single-cat households have coronavirus-specific antibodies [ ] . of these, - % will develop the deadly form of fip. a characteristic symptom of fip is body cavity effusion, which also appears in other diseases [ ] . several treatment options exist for some of these diseases while fip is deadly and no reliable effective therapy is known so far [ ] . therefore, it is important to diagnose the correct disease early. several diagnostic tests are available that diagnose fip, for which sensitivity, specificity, positive and negative predictive value vary between different studies, presumably because different forms of fip (effusive and dry) were investigated and because various clinical signs, geographic locations, years of investigation, prevalence and combination of tests were used [ , , , , , ] . in studies so far, no cat had all available tests performed. the data underlying our study includes the following diagnostic tests: -albumin to globulin ratio, plasma (x ) and effusion (x ) -rivalta test (x ) -presence of antibodies against feline coronavirus (fcov, x ) -reverse transcriptase nested polymerase chain reaction (rt-npcr) to detect fcov-rna in edta-blood (x ) and in the effusion (x ) -immunofluorescence staining (ifa) of fcov antigen in macrophages in the effusion (x ) our dataset consists of cats in total. for of these cats, a necropsy was performed to establish the gold standard diagnosis; of the cats were diagnosed with feline infectious peritonitis (fip). additionally, the above diagnostic tests were performed on all cats (i.e., k = , l = and u = ). to estimate the generalization accuracy (in terms of the simple / loss function) of each of the = combined diagnostic tests, we employ a semisupervised classification technique called maximum contrastive pessimistic likelihood estimation (mcpl) [ ] . logistic regression with l penalization is used as the base learner in mcpl, i.e., individual tests are combined using a linear model of the form ( ). estimatesê(a) of the (finite-sample) classification errors are obtained as follows: we resample the set of labelled cats and split the resulting sample into training and test examples. the remaining cats without label information are added to the training set. this procedure is repeated times for each of the combinations of tests, and the results are averaged. to obtain estimates e * (a) of the ideal generalization performances, the finite-sample estimates are subsequently corrected using isotonic regression [ , ] as described in sect. . . to further illustrate the importance of the diagnostic test rt-npcr, fig. shows the mean validated classification accuracy for all test combinations. the % empirical percentiles are indicated by the vertical lines, and the subsets are sorted in decreasing order of their mean validated accuracy. moreover, the results for those subsets including rt-npcr (measured in blood) are highlighted in blue. evidently, the concentration of subsets containing rt-npcr (blood) is systematically higher to the left of the plot, which confirms that the inclusion of the test improves diagnostic accuracy. the effect of isotonic regression on the finite-sample estimates is shown in fig. . here, each blue dot corresponds to an estimateê(a) for a particular subset a of diagnostic tests. since partial monotonicity, which is assured by isotonic regression, cannot be visualized in a two-dimensional plot, the data points are sorted by their corrected classification accuracy (and ties are broken at random). the green line shows the isotonic regression fit. the corrected performance estimates ν * (a) can subsequently be used to calculate the shapley values for each diagnostic test. the results are shown in fig. . due to the monotonicity of ν * , all values are now positive. again, the rt-npcr tests achieve the highest shapley values, but fcov antibody titer and ifa (effusion) obtain values > . , too. note that the relative order of the rt-npcr tests changed from the one in fig. , probably due to their accuracy being very similar and the random nature of the bootstrap validation. figure shows the accuracy estimates for all subsets. the dots indicate the corrected accuracies ν * (a) and are used to sort subsets in decreasing order, while fig. ) , the subsets containing rt-npcr (blood) can mostly be found on the left side of the plot; this trend is now even more pronounced. an important question for a veterinary physician is which combination a of tests to perform, taking into account both diagnostic accuracy and effort. figure shows the corrected accuracies ν * (a) (green dots) of all subsets of tests and their combined monetary cost in euro. the pareto set, consisting of those combinations that are not outperformed by any other combination in terms of both accuracy and cost at the same time, is indicated as a blue line. from a practical point of view, the result suggests to use a single diagnostic test, namely rt-npcr (blood or effusion), because the inclusion of more tests yields only minor improvements. this is confirmed by the pairwise interaction indices shown for both measures ν • and ν * in table . all these measures are negative, suggesting that the tests are more redundant than complementary. note that, once a decision in favor of using a single test is made, the shapley value, as a measure of average improvement achieved by adding a test, is no longer the best indicator of the usefulness of a test. instead, a selection should be made based on the tests' individual performance. with a validated accuracy of %, rt-npcr (effusion) appears to be the best choice in this regard. in this paper, we proposed a method for measuring the importance and usefulness of predictor variables in (semi-/supervised) machine learning, which makes use of concepts from cooperative game theory: subsets of variables are considered as coalitions, and their predictive performance plays the role of the payoff. although our approach is motivated by a concrete application in veterinary medicine, namely the diagnosis of feline infectious peritonitis in cats, it is completely general and can obviously be used for other learning problems as well. for the case study just mentioned, our method produces results that appear to be plausible and agree with the medical experts' experience. roughly speaking, there are two strong diagnostic tests that are significantly more accurate than others; practically, it suffices to use one of them, since a combination with other tests yields only minor improvements. there are several directions for future work. for example, the principle we proposed in sect. . for inducing ideal generalization performances e * (a) from finite-sample estimatesê(a) is clearly plausible and, moreover, seems to be indeed able to calibrate the original estimates thanks to an ensemble effect. nevertheless, it calls for a more thorough analysis and theoretical justification. recommendations from workshops of the second international feline coronavirus/feline infectious peritonitis symposium prevalence of feline coronavirus types i and ii in cats with histopathologically verified feline infectious peritonitis structure algorithms for partially ordered isotonic regression performances of different diagnostic tests for feline infectious peritonitis in challenging clinical cases fundamentals of uncertainty calculi with applications to fuzzy inference comparison of different tests to diagnose feline infectious peritonitis using direct immunofluorescence to detect coronaviruses in peritoneal in peritoneal and pleural effusions sensitivity and specificity of cytologic evaluation in the diagnosis of neoplasia in body fluids from dogs and cats positive predictive value of albumin: globulin ratio for feline infectious peritonitis in a mid-western referral hospital population a comparison of lymphatic tissues from cats with spontaneous feline infectious peritonitis (fip), cats with fip virus infection but no fip, and cats with no infection analysis of regression in game theory approach contrastive pessimistic likelihood estimation for semi-supervised classification techniques for reading fuzzy measures (iii): interaction index algorithms for a class of isotonic regression problems using direct immunofluorescence to detect coronaviruses in peritoneal and pleural effusions effect of feline interferon-omega on the survival time and quality of life of cats with feline infectious peritonitis a value for n-person games detection of ascitic feline coronavirus rna from cats with clinically suspected feline infectious peritonitis key: cord- - xaynf authors: werner, linda l.; turnwald, grant h.; willard, michael d. title: immunologic and plasma protein disorders date: - - journal: small animal clinical diagnosis by laboratory methods doi: . /b - - - / - sha: doc_id: cord_uid: xaynf nan occurs in glomerular disease (and may be severe; see chapter ). albuminuria as the result of glomerulopathy is rarely associated with significant globulin loss. decreased production is due to chronic hepatic insufficiency or hyperglobulinemia. the latter may cause mild hypoalbuminemia, whereas chronic hepatic insufficiency can cause moderate to severe decreases. in hyperglobulinemia, albumin synthesis may be decreased (i.e., "down regulation"). when inflammation is associated with hypoalbuminemia and hyperglobulinemia, albumin is sometimes called a negative acute phase protein. inadequate protein intake (including poorly digestible protein), maldigestion, and malabsorption are rare causes of mild hypoalbuminemia; however, occasionally they accompany other conditions causing hepatic insufficiency or increased protein loss. significant hypoalbuminemia (i.e., albumin < . g/dl) should never be attributed solely to decreased nutrition until hepatic insufficiency and proteinlosing disorders have been eliminated by definitive tests (not just by history and physical examination). decreased intake very rarely causes serum albumin concentrations less than . g/dl, except perhaps in very young animals. plasma total protein . - . . - . serum total protein . - . . - . serum albumin . - . . - . serum globulin . - . . - . sequestration may occur in pleural or peritoneal cavities or subcutaneous (sc) tissues. thus patients with effusion caused by hypoalbuminemia may further lower their serum albumin concentration via sequestration. alternatively, sequestration can be secondary to increased hydrostatic pressure (e.g., portal hypertension, right-sided cardiac failure). immune-mediated or infectious vasculopathies (e.g., endotoxemia and bacteremia, ehrlichiosis, rocky mountain spotted fever [rmsf] ) also allow loss from the vascular compartment. hypoalbuminemia as the result of sequestration or vasculopathy is usually mild. a diagnostic approach to hypoalbuminemic patients is outlined in figure - . a urinalysis (sometimes including urine protein:creatinine ratio; see chapter ) and measurement of serum bile acids (see chapter ) are indicated. severe cutaneous exudative lesions may be diagnosed by physical examination, but the possibility of renal, hepatic, and alimentary disease should still be investigated. hypercholesterolemia plus hypoalbuminemia suggests protein-losing nephropathy. significant proteinuria indicates a diagnostic workup for protein-losing nephropathy (pln) (see chapter ). hypocholesterolemia plus hypoalbuminemia is suggestive of hepatic insufficiency or ple. hypoalbuminemia associated with hepatomegaly; microhepatia; neurologic signs; icterus; decreased blood urea nitrogen (bun) with or without increased alanine aminotransferase (alt), serum alkaline phosphatase (sap), or both; or abnormal hepatic function test results (e.g., serum bile acids) requires a diagnostic workup for hepatic insufficiency (see chapter ). note: alt and sap are normal in many patients with severe hepatic disease. a portosystemic shunt is more likely in young animals; however, congenital shunts can be diagnosed in animals more than years old. acquired hepatic disease is more common in adults and requires hepatic biopsy for diagnosis; however, some dogs less than year old have severe, acquired hepatic disease. hypoalbuminemia with normal liver function tests and absence of proteinuria or cutaneous lesions allows one to diagnose ple by exclusion (see chapter ), even if feces are normal. if the patient has renal or hepatic disease and ple is still a concern, then measurement of fecal alpha- protease inhibitor concentrations (chapter ) may allow diagnosis of ple by inclusion. intestinal biopsy may then provide a definitive diagnosis of which intestinal disease is causing ple. endoscopic biopsies are safer, but it is critical that excellent quality tissue samples be obtained (many endoscopically-obtained samples are nondiagnostic). exploratory laparotomy is acceptable. if laparotomy is performed, hepatic biopsy should generally be performed along with intestinal biopsies. it is important to small animal clinical diagnosis by laboratory methods obtain biopsy specimens at several sites along the small intestine, even when no apparent gross lesions are found. edematous sc fluid accumulations associated with hypoalbuminemia are usually transudates: pln or ple, chronic hepatic insufficiency, and immune-mediated or infectious vasculitis may be responsible. however, one should always sample fluid accumulations to be sure that they are in fact transudates, as opposed to unexpected modified transudates or exudates. • see following discussion of protein electrophoresis. occasionally indicated • protein electrophoresis is performed when hyperglobulinemia is not caused by hemoconcentration and either ( ) the globulin concentration is high enough to make monoclonal gammopathy a reasonable possibility or ( ) humoral immunodeficiencies are suspected. a paleblue background on stained blood or bone marrow smears can represent increased plasma protein and may be an indication for protein electrophoresis. disadvantages • specific diagnosis is seldom obtained. although a specific diagnosis is seldom obtained from electrophoresis, electrophoretic patterns can be valuable when interpreted with clinical signs and other laboratory data. electrophoresis is quantitative. immunoelectrophoresis is qualitative, identifying specific proteins (e.g., immunoglobulins) but not detecting slight increases or decreases. immunoelectrophoresis is the method of choice to detect urinary and serum bence jones protein, a monoclonal protein equivalent to immunoglobulin light chains which occasionally occurs in multiple myeloma and macroglobulinemia. a routine protein electrophoresis performed on a concentrated urine sample occasionally detects an isolated monoclonal peak in the urine (e.g., bence jones protein). finding a urine electrophoresis pattern mimicking that of serum indicates a glomerular lesion substantial enough to allow leakage of most serum proteins, including the serum monoclonal heavy chain peak; therefore, it is not evidence of bence jones light chains. canine bence jones proteinuria is only rarely detected by heat precipitation. positive results for bence jones proteins by an acid precipitation screening test should be confirmed by concentrated urine electrophoresis or immunoelectrophoresis because of the possibility of false-positive results. analysis • serum or urine may be analyzed, and it may be refrigerated or frozen. analysis • the cellulose acetate technique is the method of choice. interpretation of electrophoretograms is based on densitometric measurements of intensity of staining of protein bands on cellulose acetate strips. the serum separates into four fractions: ( ) albumin, ( ) alpha (α) globulins, ( ) beta (β) globulins, and ( ) gamma (γ) globulins. canine and feline α-, β-, and γ-globulins are usually divided into two subfractions each: α , α ; β , β ; and γ , γ (table - ). normal-appearing electrophoretograms from dogs and cats are presented in figures - and - . artifacts • albumin concentration is usually underestimated by electrophoresis compared with a chemical determination. therefore the albumin:globulin ratio (a:g) is usually higher by chemical determinations than by electrophoretic determination. analysis • after electrophoresis in agar gel, polyclonal antiserum to specific proteins (including immunoglobulins) is added to a trough parallel with the separated serum proteins. the reagents are allowed to diffuse. to obtain quantitation of the individual immunoglobulins, radial immunodiffusion (rid), electroimmunodiffusion (i.e., rocket electrophoresis), or laser nephelometry is performed. these procedures, when available, can also be used to quantitate immunoglobulin subclasses. (feldsburg, ) . it is likely that breedspecific variations also occur. staining are overestimated. igg migrates in βand γ-globulin regions; therefore, igg concentrations determined by rid are usually higher than the γ-globulin fraction determined by electrophoresis. this discrepancy increases when igg hyperproduction occurs, such as in some myelomas, canine ehrlichiosis, feline infectious peritonitis [fip] , and other chronic infections. causes of hyperglobulinemia • polyclonal hyperglobulinemias, also called gammopathies, have a broad-based peak encompassing β and γ regions and suggest persistent antigenic stimulation and inflammation (chronic bacterial, viral, fungal, protozoal, rickettsial, or parasitic disorders), neoplasia, or immune-mediated disease (see table - ). the most common causes in dogs are cutaneous parasitism, pyoderma, dirofilariasis, and ehrlichiosis, depending on geographic location (see figure - and table - ). increases are commonly in the β and γ regions. in cats the most common cause of severe polyclonal gammopathy is fip (see figure - ). increases in feline globulins are commonly in the γ region. a concurrent mild decrease in albumin synthesis may occur in patients with hyperglobulinemia, perhaps to maintain oncotic pressure or viscosity. in hypoalbuminemic states, globulin may increase secondarily. monoclonal hyperglobulinemias have a narrow-based electrophoretic peak (i.e., "spike") in the β or γ region, normally no wider than the albumin peak. monoclonal immunoglobulin elevations are also called paraproteins or m proteins and are usually the result of lymphocyte and plasma cell neoplasias (e.g., multiple myeloma, macroglobulinemia, lymphosarcoma; see table - ). monoclonal or oligoclonal spikes are occasionally caused by infectious (e.g., ehrlichiosis; see figure - ) or idiopathic disorders. both multiple myeloma and ehrlichiosis can have monoclonal electrophoretic patterns and bone marrow plasmacytosis. in ehrlichiosis, however, the electrophoretic pattern is often a monoclonal or oligoclonal pattern superimposed on or arising within a broader-based globulin peak (see figure - , top). in such cases, examination of the stained electrophoretogram bands shows a clearly restricted monoclonal band with sharper edges within a paler, broader background band. in contrast, monoclonal spikes associated with neoplastic disorders are frequently accompanied by normal to decreased nonparaprotein globulin fractions, often reflecting impaired production of other immunoglobulins. a suggested diagnostic approach to hyperglobulinemia is outlined in figure - . in dogs with hyperglobulinemia and severe pruritic dermatitis, diagnostic evaluation may involve only a physical examination to identify fleas and ticks or skin scrapings to detect mites. demodex canis mites are usually detected easily, whereas sarcoptes scabiei are often difficult to find. for canine heartworm disease, the enzyme-linked immunosorbent assay (elisa) antigen test is the preferred screening procedure. in areas endemic for ehrlichiosis or rmsf, titers are indicated (see chapter ), particularly if the patient has anemia, thrombocytopenia, leukopenia (or a combination thereof). testing for other infectious disorders, such as canine brucellosis, blastomycosis, histoplasmosis, coccidioidomycosis, or feline cryptococcosis, is dictated by geographic location and other physical, laboratory, or radiographic abnormalities. the possibility of more than one cause of hyperglobulinemia should be considered. gammopathies associated with immune-mediated disease and nonlymphocytic and plasmacytic neoplasia are usually mild and rarely require extensive evaluation of the gammopathy. feline corona virus (i.e., fip) titers are generally not useful in cats with signs consistent with fip. if an exudative effusion is present, fluid:serum γ-globulin ratios can be determined (see chapter ). confirmatory testing for fip can be performed on affected tissue biopsies, usually liver, using an immunohistochemical stain for fip virus. hyperglobulinemia can be the result of dirofilariasis in cats, but the disease is less common than in dogs. hyperglobulinemia can also be present in chronic feline leukemia virus (felv) and feline immunodeficiency virus (fiv) infections. if joint pain, stiff gait, or increased joint fluid volume accompanies hyperglobulinemia, radiographs and joint fluid analysis (see chapter ) are indicated. rheumatoid factor (rf) testing, ana testing, rickettsial titers, or a borreliosis titer (or a combination of these tests) may be helpful if the joint fluid is a nonseptic exudate. if a diagnosis is not obtained at this stage, if a patient appears inappropriately ill, if the hyperglobulinemia seems excessive (e.g., globulin > g/dl), or if any signs consistent with hyperviscosity are present (see serum viscosity), one should differentiate monoclonal from polyclonal gammopathies by serum protein electrophoresis. if monoclonal gammopathy is detected in a patient with multiple myeloma or lymphosarcoma, immunoelectrophoresis or quantitation of immunoglobulins by rid (or rocket electrophoresis) identifies the class of immunoglobulin composing the paraprotein. these tests also detect nonparaprotein immunoglobulin deficiencies, which are common in patients with lymphocytic or plasmacytic neoplasias (see causes of hypoglobulinemia). polyclonal gammopathies may be caused by infectious, immune-mediated, or neoplastic disorders. if the cause of polyclonal gammopathy is unknown, thoracic and abdominal immunologic and plasma protein disorders figure - . diagnostic evaluation of moderate to severe hyperglobulinemia (globulin ≥ . g/dl) in dogs and cats. cbc, complete blood count; elisa, enzyme-linked immunosorbent assay; fip, feline infectious peritonitis; felv, feline leukemia virus; fiv, feline immunodeficiency virus. imaging, various titers, and/or exploratory surgery plus biopsy may be indicated. monoclonal gammopathies are usually caused by lymphoproliferative (e.g., plasma cell) neoplasia. evaluation of patients with monoclonal gammopathy may include skeletal radiographs, serum and urine immunoelectrophoresis, and bone marrow biopsy with cytologic and histologic evaluation. diagnosis of multiple myeloma in dogs requires finding at least two of the following: lytic skeletal lesions, bone marrow plasmacytosis, bence jones proteinuria, or a monoclonal spike on serum protein electrophoresis. skeletal lesions are uncommon in feline multiple myeloma. in areas endemic for ehrlichiosis, an ehrlichia canis titer should be performed in dogs with a monoclonal gammopathy. ehrlichiosis commonly causes proteinuria and bone marrow plasmacytosis, closely resembling multiple myeloma. fip rarely causes monoclonal spikes. serum viscosity can be measured. causes of hypoglobulinemia • newborn animals are physiologically hypogammaglobulinemic and have serum total protein concentrations % to % of adult values. congenital combined or selective immunodeficiencies occur but are rarely diagnosed, probably because immunodeficient puppies or kittens rapidly succumb to infections. in dogs these infections are usually distemper or parvovirus, and they occur in the postnatal period after maternal immunity wanes. immunodeficiency should be suspected when more than one pup in a properly cared for litter dies of infection in the first to months of life. complete blood count (cbc), serum chemistry profile, serum protein electrophoresis, and immunoelectrophoresis are typical initial tests in such situations. immunoglobulin quantitation by rid or rocket electrophoresis is recommended for confirmation and characterization of the type of immunoglobulin deficiency present. immunoglobulin quantitation techniques are more precise than qualitative methods (i.e., immunoelectrophoresis). selective (single class or subclass) and partial immunoglobulin deficiencies may not be readily detectable via serum electrophoresis and immunoelectrophoresis; all immunoglobulin classes (and igg subclasses when available) should be quantitated when a humoral immunodeficiency is suspected. humoral immunodeficiency is usually detected by finding decreased igg and iga and normal to decreased igm concentrations. selective iga deficiency and transient hypogammaglobulinemia occur in dogs; patients with selective iga deficiency may show chronic problems involving mucosal immunity (e.g., antibiotic responsive enteropathy) or be asymptomatic. serum electrophoresis in cases of selective or partial immunoglobulin deficiency may yield normal results or even show polyclonal elevations in globulins. immunoelectrophoresis of normal canine serum may show a low or absent stainable iga precipitation band because of iga's relatively low concentration or the result of quality assurance problems involving antisera or technique. when selective iga deficiency is suspected, the best diagnostic test is quantitative rid or rocket electrophoresis. iga deficiency is sometimes accompanied by elevated concentrations of igm or igg. the relationship between certain types of chronic inflammatory enteropathy (e.g., lymphocytic plasmacytic enteritis) and serum iga deficiency is unclear at this time. it is likely that deficiency of local secretory iga is not always reflected by serum iga values. in addition, low concentrations of serum iga have been associated with canine allergic and parasitic disorders, with return to normal after successful therapy. this finding suggests that those disease processes may lead to down regulation of iga as an immunomodulation event, and low iga probably has no causative role in the underlying chronic inflammatory bowel disease (hill, moriello, and deboer, ) . breed-specific normal ranges for immunoglobulins may provide a clearer picture of the role of selective iga deficiency in chronic enteropathies. the most common causes of hypoglobulinemia are external blood loss and ple. less common causes are pln and hepatic insufficiency (see chapters and , respectively). in patients with paraproteinemias (e.g., multiple myeloma, macroglobulinemia, lymphosarcoma), remaining immunoglobulins are usually depressed. a complement measurement and evaluations of lymphocyte and phagocyte functions may also be indicated for patients with suspected congenital immunodeficiency (see testing for cellular immunity). rarely indicated • monoclonal gammopathy, hyperglobulinemic patients with signs of hyperviscosity (i.e., poor tissue perfusion, dilated retinal vessels, retinal hemorrhage or retinal detachment, renal disease, central nervous system (cns) dysfunction, bleeding problems), and monitoring of treatment of diseases causing hyperviscosity. hyperviscosity may be suspected based on finding high serum protein (usually > g/dl) or on physical characteristics of serum (i.e., viscous). polycythemia should be included as a cause of increased blood viscosity to be eliminated in patients showing clinical signs of hyperviscosity. advantages • simple and diagnostically significant. ostwald viscosimeter or a . ml capillary pipette. time for a given volume of serum to flow from the pipette is compared with that for the same volume of water. artifacts • volume depletion causing increased serum protein concentration may increase serum viscosity but is unlikely to be clinically significant. markedly increased blood viscosity can interfere with tests using flow through devices (e.g., hematology autoanalyzers). viscosity • any drug causing volume depletion can increase serum viscosity. a relative viscosity greater than or equal to is abnormal in people and probably abnormal for dogs. because of the relatively large size of igm, it has the greatest potential to cause hyperviscosity. iga (which can exist as a polymer or dimer) and very high concentrations of igg can also cause hyperviscosity. clinically significant serum hyperviscosity is almost invariably caused by lymphocyte and plasma cell neoplastic disorders (e.g., multiple myeloma, macroglobulinemia, lymphosarcoma; see table - ). hyperviscosity syndrome rarely occurs in monoclonal gammopathy caused by ehrlichiosis. diagnostic approach is described in figure - under monoclonal gammopathy. because lymphosarcoma and plasma cell myeloma are the major causes of serum hyperviscosity, aspiration of bone marrow, involved lymph nodes, masses, or other abnormal lymphoreticular organs is indicated. if results are equivocal, biopsy and histopathologic evaluation of bone marrow or involved tissues are indicated. cytologic or histologic evaluation of spleen and liver occasionally helps diagnose lymphocytic or plasmacytic neoplasia when samples from lymph nodes, bone marrow, or solid masses are not diagnostic. cryoglobulins are usually monoclonal or complexed immunoglobulins that reversibly precipitate or gel at low temperatures but dissolve when heated. cryoglobulins are rarely found in canine multiple myeloma and macroglobulinemia. rarely indicated • paraproteins that precipitate or gel when blood or serum is refrigerated at °c. advantage • detection of cryoglobulins is important, because failing to detect them may cause false-negative tests for hyperglobulinemia or monoclonal paraproteinemia in patients with clinical or laboratory evidence of hyperviscosity. analysis • the clinician should contact a reference lab about assaying for cryoglobulins. causes of cryoglobulinemia • macroglobulinemia or multiple myeloma of igm and iga classes may cause canine cryoglobulinemia. finding cryoglobulinemia indicates diagnostic evaluation for lymphocyte and plasma cell neoplasia as described for monoclonal gammopathies. occasionally indicated • abnormalities suggestive of systemic lupus erythematosus (sle), such as symmetric dermatitis principally distributed on the head and mucous membranes, hemolytic anemia, thrombocytopenia, nonseptic polyarthritis, myositis, proteinuria, or fever of unknown origin. less common are neuromuscular, cardiac, note: cryoglobulins are not cold agglutinins (i.e., antibodies binding antigen reversibly at temperatures < °c). or pulmonary abnormalities. the test can be used to monitor patients being treated for sle. advantages • simple and indicative of immune-mediated disease when positive with a relatively high titer in conjunction with compatible clinical abnormalities. disadvantages • not a disease-specific test (i.e., many diseases besides sle may be associated with a low titer; table - ). analysis • measured in serum by indirect immunofluorescence testing (iit). the result should be reported as the highest dilution of a patient's serum causing definite staining of nuclei. several patterns of nuclear fluorescence are recognized: homogeneous (diffuse), rim (peripheral), speckled (fine or large speckles), and nucleolar. normal values • values vary among laboratories owing to different substrates, controls, and procedures used. accuracy requires procedural consistency and experience. fetal and newborn sera do not stain nuclei. most veterinary laboratories use tissue culture monolayers of human epithelial- (hep- ) cells as substrate, which allows improved discernment of fluorescent patterns of staining and more standardized procedural consistency. when this test method was used in a comparative study involving canine serum samples, a significant positive titer was established at a screening dilution of : for greater than % specificity, whereas a minimum significant ana titer of : was established as the corresponding significant titer using rat liver sections, which identified the identical group of ana-positive dogs at the same specificity of greater than % (hansson, turnwald-wigh, and karlsson-parra, ) . drug therapy that may alter antinuclear antibody titer • anything decreasing antibody synthesis (e.g., cytotoxic drugs, chronic or high-dose corticosteroid therapy) can decrease the titer. positive ana titers have been attributed to treatment with griseofulvin, hydralazine, procainamide, sulfonamides, and tetracyclines. positive ana titers can occur in cats treated with propylthiouracil or methimazole (peterson, kintzer, and hurvitz, ) . some of these cats develop drug-induced, immune-mediated hemolytic anemia (imha) and immunemediated thrombocytopenia (imt). artifacts • improper reagent preparation, storage, or application; inadequate controls. • a positive titer may occur in a number of infectious, inflammatory, and neoplastic disorders. a partial list of diseases (in addition to sle, in which a positive ana titer can be found) is given in table - . normal dogs and cats can also have detectable ana; however, these tend to be low titers. positive titers obtained in disorders other than sle are generally not markedly elevated; therefore, it is important to consider values established by the laboratory for low, moderate, and high titers. equally important is consideration of other clinical and clinicopathologic changes consistent with a diagnosis of sle. suggested criteria for diagnosis of canine and feline sle are a positive ana titer plus one or more of the following: skin or oral cavity lesions with histopathologic and immunopathologic changes consistent with sle, polyarthritis, coombs'-positive hemolytic anemia, idiopathic or imt, pln, myositis, or (particularly in cats) neurologic disturbances. a positive ana titer is the most important criterion for diagnosis of sle, providing small animal clinical diagnosis by laboratory methods established clinical criteria are met and exclusionary diagnoses are not made (e.g., felv or fip infection, cholangiohepatitis, rickettsial or systemic parasitic diseases). no well-established patterns of ana fluorescence in cats and dogs distinguish sle from other (i.e., non-sle) immune-mediated diseases or other conditions associated with positive ana titers (see table - ). although ana titers in sle are frequently higher than in other disorders, there can be some overlap. magnitude of titer does not parallel severity of disease. periodic ana titers may be useful in monitoring a lupus patient's response to therapy. a positive ana titer can be an indication for performing additional tests to distinguish sle from non-sle disease: dermatitis favoring mucocutaneous junctions is an indication for biopsy, histopathologic examination, and immunohistochemical or direct immunofluorescent testing (dit; see immunostaining of tissues); hemolytic anemia is an indication for an antiglobulin (i.e., coombs') test (see chapter ) and tests for hemoparasites; swollen, painful joints are an indication for arthrocentesis, fluid analysis (see chapter ), and rf test (see later discussion). occasionally indicated • suspected sle (see antinuclear antibody). advantages • specific; does not require species-specific reagents, therefore more widely available. disdvantages • time-consuming and much less sensitive than the ana test; requires very fresh blood sample. analysis • depending on the laboratory, heparinized or clotted blood is used. formation of le-cells in vivo is rarely demonstrated in routinely stained bone marrow smears or in joint fluid from patients with polyarthritis (color plate a), but it is highly suggestive of sle when present. a laboratory experienced in performing and interpreting le cells is necessary. artifacts • le cells must be differentiated from "tart" cells, which are neutrophils that have phagocytosed intact nuclei. the le cell test is complement dependent, and low concentrations of complement, excessive heparin, or failure to use freshly drawn blood may cause false-negative results. • steroid therapy alters test results. the le cell test is more sensitive to effects of steroids than is an ana titer. • ideally a minimum of three to four le cells on a slide is necessary for a diagnosis of sle. the test should be performed at least three times before results are considered negative. the test is specific for sle but insensitive. negative results are common in sle patients that are ana positive. such patients may lack the particular autoantibodies to histone-dna involved in le cell formation but have other types of ana detectable by immunofluorescence. positive test results may rarely be obtained in other diseases (e.g., osteochondritis dissecans, nonimmunologic joint disease, neoplasia, disseminated intravascular coagulation). if a positive le cell preparation is obtained, an ana titer and tests to obtain other evidence of sle are indicated (as described earlier under antinuclear antibody). an ana titer is the preferred screening test for sle. see chapter . dogs and cats showing marked thrombocytopenia (< , /µl) may have imt. this is typically a diagnosis of exclusion because no widely available test allows a definitive diagnosis of imt. measurement of platelet-associated antibodies and assay for antimegakaryocyte antibodies have been performed, but as of this writing, neither has been proven to have the desired sensitivity or specificity in clinical practice. a recently reported technique seems promising (scott et al, ) . occasionally indicated • dogs, particularly small breeds, suspected of having rheumatoid arthritis (ra) because of lameness, heat, swelling, or pain of multiple joints, particularly peripheral joints. crepitation and joint laxity may be detected in chronic cases. nonspecific signs include anorexia, fever, depression, and reluctance to move and may precede clinically or radiographically detectable evidence of joint disease. disadvantages • insensitive (i.e., many false-negative results) and not highly specific for ra in dogs because of relatively low titers. analysis • serum is submitted refrigerated but unfrozen. the rose-waaler test is the recommended test for canine rf (autoantibody reacting against a patient's own igg). canine rfs are predominantly igg but may also be mixed complexes of igg, iga, and igm. factors are detected by incubating rabbit iggsensitized sheep red blood cells (rbcs) with serial dilutions of the patient's serum (the rabbit rose-waaler test). if rf is present, agglutination occurs. because canine sera often contain naturally occurring antibodies to sheep rbcs, a control must be used with unsensitized sheep rbcs. if agglutination to an equal or higher dilution appears in the control, natural antibodies must be absorbed from the sera before testing for rf. latex agglutination tests for canine rf are not recommended because results are poorly reproducible and lack specificity. latex agglutination titers may differ substantially from rose-waaler titers. both tests are available through human laboratories; proper test controls are necessary. • for the rose-waaler test in normal animals, the differential titer (difference between titers at which agglutination of unsensitized versus sensitized sheep rbcs occurs) should be less than eight (barta, ) . a titer against sensitized rbcs not corrected for the actual titer of natural antibodies to sheep rbcs can be misleading because some normal animals have higher titers of naturally occurring antibodies to sheep rbcs. some laboratories perform the rose-waaler test by preabsorbing all test sera with sheep rbcs. in this case a titer of less than is expected in normal dogs. artifacts • serum submitted for rf testing should not be frozen, because rf activity (especially igm) may be destroyed, causing a false-negative result. canine rf tends to self-associate, forming multimeric complexes that significantly lower the detectable titer. wide, sometimes negative, fluctuations in rf titer occur over time; these fluctuations do not appear to correlate with disease severity. false-positive results may occur in the rose-waaler test if a patient's serum has antibodies against sheep rbcs and appropriate controls or absorption of these antibodies is not performed. joints is the most reliable means of diagnosing canine ra. histopathologic examination of synovium allows an early diagnosis and therapy in patients lacking classic radiographic changes. an ana titer helps distinguish sle from ra; but it is occasionally positive for ra. finding both types of autoantibodies may represent the rare, combined occurrence of both sle and ra (a so-called overlap syndrome) or merely the appearance of multiple autoantibodies in a patient with ra or sle. in either case, clinical criteria are required for diagnosis. immunofluorescent testing of tissues uses a fluorescent dye conjugated with an antibody (i.e., fluorescein isothiocyanate [fitc] reagent) that detects antigen, immunoglobulin, or complement. several techniques are used for immunohistochemical staining involving enzyme-conjugated antibody in a chromogenic reaction system. the testing may be direct or indirect. in the direct test, tissues are assayed for deposits of antigen, immunoglobulins, or complement. occasionally indicated • suspected autoimmune skin disease or (rarely) diseases of internal organs (e.g., kidney) that may have an immunologic basis. in veterinary medicine, the test is used mainly on biopsy specimens of erosive or vesiculobullous cutaneous lesions. advantages • a definitive diagnosis can occasionally be made; formalin-fixed tissue can be used for some immunohistochemical procedures, allowing routine histopathology and immunostaining on sections from the same biopsy. disadvantages • extreme care must be taken in tissue selection and preservation. the test result is markedly influenced by corticosteroids; some immunofluorescence procedures require a special fixative and transport medium or fresh, snap-frozen tissue. sample preparation • requirements for handling and submitting biopsied tissues vary according to the procedure and reagents used, so the laboratory should be contacted. in cutaneous diseases it is imperative that early primary lesions (i.e., vesicles, bullae, pustules) and a margin of uninvolved skin be obtained. multiple specimens are recommended. obtaining primary lesions may necessitate checking a patient several times daily to identify a suitable, newly erupting lesion. ulcerated, crusted, or scarred lesions are worthless. ideally, biopsy specimens should not be obtained from the planum nasale or foot pads if other primary lesions are available because positive staining occurs at the basement membrane of these sites in many normal dogs. biopsy specimens for routine histopathology should be taken from the same, or at least a similar, lesion. larger samples can be bisected to provide comparable material for both tests. the biopsy specimen should not remain attached to the wall of the fixative container because this may cause inadequate preservation and false-negative results. analysis • tissue sections are prepared and tissue incubated with labeled antibodies to igg, igm, iga, or c and examined by fluorescent microscopy for immunofluorescent assays or routine microscopy for immunohistochemical assays. normal values • healthy epidermis has no detectable deposits of immunoglobulins in the intercellular spaces or at the basement membrane. nonspecific fluorescence of the stratum corneum should not be mistaken for deposits of immunoglobulins. appropriate controls are necessary to detect nonspecific background staining. artifacts • biopsy of inappropriate lesions produces false-negative results. cutaneous bacterial infections may cause immunoglobulin deposits in pustules, which should not be mistaken for autoimmune disease. • corticosteroids and immunosuppressive drugs (e.g., cyclophosphamide) may cause negative results. if an animal is receiving short-acting corticosteroids, the drug should be withdrawn for at least weeks before biopsy. a longer period ( to months) may be necessary if long-acting injectable corticosteroids have been used. immunostaining results must be interpreted in light of clinical and histopathologic findings. immunoglobulin deposits can occur in other skin disorders, including mycosis fungoides, pyodermas, and acariasis. in these disorders, staining is usually patchy, focal, and present in pustules rather than in the adjacent tissues. in the indirect test, serum is assayed for circulating autoantibodies to a specific tissue component, such as cutaneous basement membrane, intercellular cement substance, or renal glomerular basement membrane. the ana test is another example of iit discussed previously. • as an adjunct test for suspected pemphigus, bullous pemphigoid, or immune-mediated glomerulonephritis. advantages • noninvasive method to detect circulating autoantibodies to tissue, especially when biopsy of these organs is problematic or nondiagnostic. disadvantages • significantly less sensitive than direct immunostaining, because a relatively large amount of antibody must be present to be detected. this test so rarely gives positive results in confirmed cases of autoimmune skin disease or immune-mediated glomerulonephritis that it is not recommended. routinely available tests are used to screen suspected cases of immunodeficiency. these tests include serial cbc examinations (total lymphocyte and neutrophil numbers), serum immunoglobulins (see causes of hypoglobulinemia), and antibody titers to common viral vaccines such as distemper or parvovirus. sustained lymphopenias (< /µl) are noted in some cases of severe combined immunodeficiency, and marked neutrophilias (> , /µl) are often observed in neutrophil function or chemotactic disorders (see chapter ). routine histologic evaluation and immunophenotypic staining of lymph node tissue taken at biopsy are occasionally useful in pursuing a diagnosis of congenital or acquired immunodeficiency. possible abnormal findings include depletion or altered distribution of b-lymphocyte or t-lymphocyte populations within the nodal architecture. tests for cellular immunity include lymphocyte blastogenesis (i.e., transformation), assays for cell-mediated cytotoxicity, enumeration of t-lymphocyte and b-lymphocyte subpopulations, neutrophil function, and evaluation of leukocytic and erythrocytic histocompatibility antigens. if cellular immunity needs to be evaluated, the veterinarian should contact a college of veterinary medicine or large diagnostic laboratory to determine availability. clinically significant phagocytic function disorders tend to occur in purebreds (e.g., irish setters, weimaraners) or closely related crossbreds as a congenital or inherited defect. these animals show chronic or recurrent bacterial infections from a young age, along with markedly elevated neutrophil counts and general unthriftiness. tests include phagocytic assays, bactericidal assays, chemotactic response, and testing for cell surface markers such as leukocyte adhesion molecules lfa- and mo- . the veterinarian should contact a college of veterinary medicine to determine availability. occasional indications • poor response to vaccinations, chronic unresponsive infections, persistently elevated or decreased lymphocyte counts, distinguishing between neoplastic and reactive lymphoproliferation by evaluating clonality. analysis • studies are usually performed on peripheral blood lymphocytes but can also be performed on lymph node tissue obtained by biopsy. the clinician should consult individual laboratories for sample specification. • inherited defects of the immune system, lymphosarcoma, lymphocytic leukemia, and some viral infections (especially retroviruses such as felv, fiv, and other viruses infecting lymphoid cells) change the proportions of t and b cells. occasional indications • poor vaccination response or recurrent infections. the lymphocyte transformation test is the most commonly used test for assessing functional capability of lymphocytes. disadvantages • the test is not readily available and is only a simulation of an in vivo situation; therefore, the results should be interpreted as an approximation only. analysis • isolated lymphocytes are exposed to various substances that cause their activation and division. the proliferation response of stimulated cells is quantitated by their increased uptake of radionucleotide compared with control cells from healthy animals of the same species and similar age. these tests can detect intrinsic lymphocyte function defects and serum suppressive factors, which can be found in many acquired disease states. if evaluation of lymphocyte function testing in vitro is contemplated, the reader should contact the local or regional veterinary school immunology laboratory for additional information on availability of testing. rose-waaler test laboratory techniques of veterinary clinical immunology immune complexes and rheumatoid factors in canine arthritides canine albumin results detection of antinuclear antibodies by indirect immunofluorescence in dog sera: comparison of rat liver tissue and human epithelial- cells as antigenic substrate kinetics of serum antiplatelet antibodies in experimental acute canine ehrlichiosis dog immunoglobulins: immunochemical characterization of dog serum, saliva, colostrum, milk and small bowel fluid concentrations of total serum ige, iga, and igg in atopic and parasitized dogs serum proteins and the dysproteinemias concurrent hypoadrenocorticism and hypoalbuminemia in dogs: a retrospective study hematologic and serum biochemical effects of long-term administration of anti-inflammatory doses of prednisone in dogs methimazole treatment of cats with hyperthyroidism immunologic profiles of cats with persistent naturally acquired feline leukemia virus infection quantitation of canine immunoglobulins serum immunoglobulin levels in grey collies immunologic methods for the detection of humoral and cellular immunity immune-mediated dermatoses in domestic animals: ten years after. ii, comp cont ed development of a sensitive immunoradiometric assay for detection of platelet surfaceassociated immunoglobulins in thrombocytopenic dogs diagnosis of autoimmune skin disease in the dog: correlation between histopathologic, direct immunofluorescent and clinical findings factor titer • because rf is an antibody against fc fragments of immunoglobulin molecules that become exposed only after antibody binds to antigen, any disease with long-standing immune complexes can eventually induce rf formation. in the rose-waaler test, a differential titer of greater than or equal to : is positive for rf (barta, ) . between % and % of dogs with ra have a positive rf test result. hence, a negative result does not eliminate rf. the rf test is rarely positive in normal dogs and occasionally positive in some patients with sle, because rf may be a part of the sle complex. incidence of rf in other arthropathies and systemic diseases has not been adequately studied via the rose-waaler method, but other methods have shown rf (in titers comparable with those of patients with ra) in these arthropathies (carter et al, ) . therefore a positive rf test result should never be the sole criterion for a diagnosis of canine ra.ra is a progressive, erosive, immunemediated polyarthritis that must be differentiated from other types of joint diseases, preferably before joint destruction occurs. unfortunately no test for canine rf is highly reliable in making this distinction. other routine tests indicated in making the diagnosis include joint radiographs and synovial fluid analysis. septic polyarthritis often causes erosive lesions, especially involving larger joints, plus evidence of sepsis on routine blood and synovial fluid examinations (see chapter ), including culture. in contrast, ra typically causes erosive lesions of smaller peripheral joints before progressing to larger joints. radiographic lesions may be lacking or inconclusive early in the course of ra. furthermore, no distinguishing cytologic features can reliably differentiate among ra, sle, and other types of immune-mediated joint disease that have similar joint fluid cytology. histopathologic examination of synovium from affected key: cord- - ty mxa authors: reller, l. barth; weinstein, melvin p.; baron, ellen jo title: implications of new technology for infectious diseases practice date: - - journal: clin infect dis doi: . / sha: doc_id: cord_uid: ty mxa new assays for the diagnosis of infectious diseases—particularly those that use molecular technologies—will revolutionize infectious diseases practices, but the fulfillment of the promise is several years away. problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in “normal” hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. clinicians must appreciate the shortcomings of new technology to use it effectively and appropriately. however, we are realizing tangible progress in our ability to detect new etiological agents; the availability of rapid, accurate diagnostic tests for previously difficult infections; and advances into new, human response—based paradigms for diagnostic testing. the promise of a star trek-inspired hand-held infectious diseases diagnostic device that scans a patient's body and immediately provides the information needed for diagnosis and treatment is probably years away. until that time, when clinicians and microbiologists become unemployed, we can use the amazing technologies that are already available. this overview will discuss a selection of technologies and provide an opinion about their utility, their pitfalls (summarized in table ) , and their potential. although the day when all diagnostic microbiology laboratories will routinely use molecular tools has not yet come [ , ] , many clinicians believe that a plethora of such tests is readily available. laboratorians are regularly asked to perform a pcr test to detect an agent that only a few published research studies have reported, with those studies usually describing only preliminary results. physicians often seem surprised that the laboratory cannot provide this service. a survey by the american society for microbiology published in provides a snapshot of the current environment in the united states. of the laboratories (representing community, academic, and commercial laboratories) that responded to the survey, % performed bacteriology tests, but only % performed any molecular tests for infectious diseases [ ] . the bulk of the latter laboratories offered only molecular testing for chlamydia/neisseria gonorrhoeae (as determined on the basis of college of american pathologists surveys participant summaries). for the foreseeable future, because of staffing and financial issues, many nonconsolidated or nonacademic hospital laboratories will not perform new, high-technology, expensive, and skill-demanding assays. there is a national shortage of clinical laboratory scientists. the number of training programs has decreased over the past decade, and qualified students are now choosing careers in medicine or computer science. nurses are paid dramatically more than clinical laboratory scientists-a further disincentive for students to consider a laboratory career-although the same level of professionalism and dedication to patient care is required. the overall vacancy rate among microbiology technologists is %, and almost one-half of all vacancies require at least months to fill [ ] . the staffing shortage in the pipeline in the united states today becomes more worrisome when combined with the aging of the current experienced staff. thirty-four percent of microbiologists working today are years old [ ] ; most of these will retire in the next years. their competence in molecular methods is miniscule. however, these senior microbiologists can interpret a gram stain and deliver an educated guess as to the identification of a pathogen at an early stage. infectious diseases clinicians have relied on these expert workers, and reliable molecular diagnostic tests are not readily available for many infectious agents commercial tests should only be used for validated specimen types transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations unknown extent of microbial dna in "normal" host tissues lack of necessary resources (human and economic) reimbursement often not sufficient to cover costs today's infectious diseases trainees are still being trained in laboratories utilizing such resources. the new, younger laboratory workforce is not highly skilled in either the conventional or the high-tech environment, and microbiologists in general are in short supply. we are facing a knowledge and practice gap for the next - years, during which time molecular tools will gradually fulfill their promise. even in those laboratories that are staffed with skilled microbiologists during the daytime, many critical test results are needed on the evening and night shifts, when the laboratories are staffed by nonspecialized laboratorians. as a result, physicians will have less trust in test results and will need to make a greater number of empirical decisions and use a greater number of broad-spectrum antimicrobial agents. another aspect of the dearth of experienced technologists is that testing has become more instrument based than discipline based. this is apparent in the migration of hepatitis and hiv serological testing from microbiology or virology departments to the immunochemistry laboratory, where generalists or chemistry technologists perform these tests along with tests for other serum factors, such as toxins and proteins. the testers are, in general, not knowledgeable about the agents for which they are testing, which could lead to interpretation errors or failure to recognize inappropriate results. it is difficult, at best, to validate test results (assuring the clinical utility, reliability, and reproducibility of results) using new technologies. traditional culture-or antigen-based comparator methods often yield results that fail to correlate with the newer, more sensitive tests. finding clinical criteria or alternate molecular targets to verify which result is correct can be tedious, expensive, and occasionally impossible. obtaining adequate standards or positive patient samples to validate test results and to train performing technologists is also challenging. one example is pcr of csf specimens for herpes simplex virus meningoencephalitis; this is considered to be the best diagnostic assay available, because cultures are insensitive, and brain biopsy is too invasive [ ] . the difficulties in finding enough samples and in creating seeded samples with known viral loads for validation studies have prevented or delayed development of this and other tests in many laboratories [ , ] . in fact, identical problems have impeded submission and us food and drug administration (fda) approval of commercial assays for herpes simplex virus. some analyte-specific reagent test kits are available for both herpes simplex virus and enteroviruses, but they still require extensive in-house validation studies. the threat of an avian influenza pandemic may help spur the development of multiplex molecular assays for respiratory viruses [ ] . the use of laboratory tests for diagnosis of enteroviral cns disease was shown to be cost effective long ago [ ] , but the availability of rapid molecular tests for this purpose has been long coming. in many circumstances, tests that infectious diseases physicians have heard about (e.g., at national meetings, such as that of the infectious diseases society of america) will be available only as send-out tests to referral laboratories, accompanied by the attendant transportation problems and possible specimen degradation, delayed results, and costs. if an available molecular test is not performed in the local laboratory, one of the most important benefits-rapid results-is not realized, because the sample must be sent to a distant reference laboratory. even after the newest generation of real-time molecular test systems, such as the genexpert test for group b streptococci (cepheid), slated for fda clearance as moderately complex, becomes available [ ] , their initial cost may delay widespread implementation. there are, of course, some widely performed molecular methods, such as hiv load [ ] and nucleic acid amplification (naa) assays for chlamydia trachomatis and n. gonorrhoeae that use genital samples or urine specimens [ , ] . however, many physicians assume that one can just as easily test an eye swab as a cervical swab, without appreciating that the laboratory must perform an extensive validation of a sample not included in the original fda clearance of the device if a report is to be issued (and the test is to be paid for) [ , ] . many molecular tests are limited to reference laboratories or for research investigations only. of course, not all new technology is nucleic acid based, and i will also discuss other methods. a number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (advandx fish for staphylococcus aureus [advandx] and genprobe for group a streptococci [genprobe]), hybrid capture (digene for human papillomavirus; digene), pcr, branched-chain dna (bdna; bayer diagnostics), and transcription-mediated amplification (probe-tec for chlamydia and n. gonorrhoeae; becton dickinson). sample volume (which encompasses both original sample volume and number of nucleic acid sequences present in the final amplified sample portion), transport conditions, dilution factors, inhibitory factors, genome changes, instrument problems, and operator error all contribute to false-positive and false-negative test results [ , [ ] [ ] [ ] [ ] . even closed systems at the detection end do not prevent cross-contamination from positive sample processing at the front end. for example, current fda restrictions require that papanicolaou smears be first performed when a single suspension of cervical cells is received in preservative, with requests for both cytology and for detection of human papillomavirus, chlamydia species, and n. gonorrhoeae; this contributes to the common finding that insufficient sample size remains for the infectious diseases tests after the papanicolaou sample has been removed [ ] . unfortunately, unlike direct visual examinations in which sample quality can be assessed, a negative result of such an assay includes no comment on the quality of the specimen. although molecular tests that use whole blood samples for detection of the agents of sepsis are not yet available, several such assays are in development. volume will be a factor in the sensitivity of these tests. the amount of bacteria in blood obtained from a patient with bacteremia is often ! cfu/ml [ ] , yet the volume used in most naa reaction vials is ! ml. even if the sample is concentrated in some way, the chance that microbial genetic material will reach the reaction vial could be very small, resulting in false-negative results. in samples containing human neutrophils or erythrocytes-the very samples most likely to harbor the infectious agent-it is challenging to concentrate microbial dna without also adding overwhelming amounts of human somatic dna, and the available frontend methods (extraction and filtration columns, magnetic particle capture, and silica-based systems) still lack efficiency [ , ] . manufacturers are spending most of their energy on backend technology (detection and reporting). front-end processing is urgently needed, ideally resulting in the development of a creative new method for concentrating cell-rich specimens (such as purulent fluid, blood, and sputum) from humans to allow for sensitive detection of microbial nucleic acids. diagnosis of tuberculous meningitis is another example of the problems inherent in amplification technology using pcr [ ] . patients may have confounding signs and symptoms, the number of organisms in the csf sample may be very low, and conventional tests are insensitive and/or slow. direct acid-fast staining of csf specimens has a sensitivity of ∼ % [ ] . the volume of csf needed for adequate culture is at least ml (preferably ml), because mycobacterium tuberculosis is extremely buoyant in csf as a result of its waxy cell wall; thus, concentration by centrifugation is inefficient [ ] . smears for acid-fast bacilli made from the sediment must be layered and examined exhaustively-sometimes for min-in the hope of detecting the rare m. tuberculosis rod [ ] . naa would seem to be the answer. sadly, naa tests display an overall sensitivity of % (range, %- %) and a specificity of % (range, %- %), as determined by a meta-analysis of published studies, of which used home-brewed (individual laboratorydeveloped and -validated) methods [ ] . when results from the laboratories that used commercially available assays were evaluated separately, the overall sensitivity decreased to % (range, %- %). these are the assays that are likely to be available to most clinicians. the naa results were equal to those for the acid-fast bacilli smear. clinicians must realize that unwanted reliance on new technology may lead to diagnostic errors. another highly favored technology for laboratory diagnosis of infectious diseases, whether testing tissue directly or testing isolated colonies, is identification by nucleic acid sequencing. there are also pitfalls in this approach. for example, many organisms, although they may be antigenically or biochemically distinct, are virtually genetically identical. members of the bacteroides fragilis group, for example, are highly related and cannot be separated easily by standard sequencing methods [ ] . most clinicians realize that escherichia coli and shigella species are highly related [ ] , but they have not considered the difficulty that this relatedness would pose if we relied on sequencing to identify these genera directly in patient samples. the extent of shared genes and taxonomically (versus phenotypically) shared traits among most microbes is unknown. another issue that vexes clinicians is the taxonomic confusion caused by genetic investigations. rhinosporidium seeberi, for example, is an agent of mass lesions in the sinus and mucous membranes. this organism has often been observed in histopathologic sections, but it has never been grown in culture. it resembles the spherule of coccidioides immitis, however, so it has long been considered an "unculturable" fungus. recently, s rrna sequencing placed the organism into a group of protozoan fish parasites [ ] . we are constantly faced with new names for familiar organisms-and even with new organisms that may or may not be important in familiar syndromes. before more-extensive testing was performed, the newly discovered mycoplasma fermentans (originally called mycoplasma incognitus) had been implicated in both gulf war syndrome and hiv infection [ , ] . it was later found to be quite common in humans [ ] . after effective therapy, results of pcr of genital samples obtained from patients with c. trachomatis remain positive for weeks [ ] . nucleic acid is detectable but probably not viable. we do not know the extent of carriage of unculturable microbial or "normal" microbial dna in other healthy hosts. the cost of equipment, expensive reagents, and additional skilled personnel needed is not easy to justify. for example, the fda has cleared a real-time pcr test for group b streptococcal vaginal/rectal colonization during labor [ ] . widespread use of this test could negate the need to perform cultures for pregnant women during weeks - of gestation, and it would solve the problems associated with treating women who present in labor without screening test results [ ] . currently, % of women receive prophylactic penicillin during labor [ ] . this number would decrease if only women with pcr results positive for group b streptococci at labor were treated [ , ] . the problem, however, is that current recommendations [ ] have already reduced the incidence of early-onset neonatal group b streptococcal disease to less than the national health objective of . cases per live births, and additional improvement is not cost-effective [ ] . lucile packard childrens hospital johnson center, a stanford university medical center affiliate on the same campus, delivers ∼ babies annually. to perform the pcr assay immediately after each sample is received (a necessity to assure that prophylaxis is administered for at least h before delivery), we would have to staff technologist at all times. test performance takes ∼ min of hands-on time, and the test itself runs min, so a technologist must perform continuous sample management. twenty-four/seven staffing for days per year would require . clinical laboratory scientists, at a labor and overhead cost of $ , . the reagents-not counting the cost of the instrument itself-cost $ , annually, for a total yearly cost of $ , . stanford university medical center (stanford, ca) patients have a colonization rate of % among women in labor, resulting in babies at risk per year. to prevent potential group b streptococcal infections using this test, the cost per infection avoided would be $ , . this is a hard sell to hospital administrators who are focused on the bottom line. potential laboratory staff labor savings with the use of random-access, moderately complex molecular systems, such as genexpert (mentioned above), may help to bring down costs. costs for new technologies are often added onto existing testing, so overall diagnostic costs increase. centers for medicare and medicaid services reimbursement is lagging dramatically behind the use of new tests. in the northern california reimbursement area, our laboratory receives only $ . for a pcr test for bordetella pertussis and bordetella parapertussis, although it costs the laboratory more than $ to test each sample, because the tests are always performed one specimen at a time, which necessitates testing an additional controls simultaneously. the future is not all bleak, of course. new agents of important diseases are being discovered with the help of molecular technologies. among those to have been elucidated recently are tropheryma whipplei, bartonella henselae, ehrlichia chaffeensis, and mycoplasma genitalium [ ] . infectious disease-related challenges are ready for solutions with our new molecular tools. the etiology of % of cases of pharyngitis is unknown [ ] , and the etiology of %- % of cases of diarrhea is unknown [ ] , as is the etiology of %- % of cases of pneumonia [ ] . we cannot cultivate ∼ % of the organisms in the subgingival crevices of patients with periodontal disease [ ] . all of these mysteries regarding vexing syndromes will eventually yield to molecular technologies. proteomics (i.e., profiling the proteins generated by human cells in response to various stimuli, including components and products of infectious agents) is in its infancy, but exciting developments are enticing. the spots of dna or rna on "gene chips" can be designed to be homologous with nucleic acid sequences in the sample, representing nucleic acids found in both the normal situation and the activated state of transcription or representing various genetic sequences unique to a vast array of microbes for detection of infectious agents [ ] . samples are treated to break down their dna or rna into small discrete sequences, for which an identical sequence exists on the chip. if the sample nucleic acid finds its match, it binds and emits an electronic signal [ ] . such a human-response chip can be used to determine a patient's response to potentially toxic antimicrobial treatments in advance of delivery. if the patient lacks enzymes to break down toxins or cannot metabolize a drug effectively, alternative therapies can be used to avoid dangerous adverse effects [ ] . in another prospective microarray-based test, human leukocyte response to various infectious agents may be used to pinpoint the etiology before the agent itself can be detected [ ] . development of this sort of technology is on a fast track, to facilitate detection of bioterrorism agents before the symptomatic phase of disease renders widespread preventive measurements inadequate [ ] . proteomics is being used to fine-tune the development of new anti-infectives as well [ ] . one aspect of microarray technol-ogy yet to be standardized and codified is the monumental problem of data analysis [ ] . an entire new discipline of bioinformatics has developed for this purpose. this challenge of interpreting the vast volume of data points generated by microarray studies is acquired along with the technological advances, and its resolution will require a collective and extensive effort. in summary, the future potential utility of these incredible technologies-and of numerous others not mentioned herewill revolutionize infectious diseases diagnostics. however, the shortcomings of these technologies must be recognized. present dangers include failure to support the need for traditionally trained microbiologists, allowance of expertise to be moved to sites distant from patient care activities, inappropriate trust of new technology, and underestimation of the value of clinical diagnosis based on the acumen of experienced laboratorians and infectious diseases practitioners. dna probes for infectious diseases molecular and cellular microbiology: new tools of the trade survey of clinical microbiology laboratory workloads, productivity rates, andstaffing vacancies herpes simplex encephalitis: children and adolescents cumitech -verification and validation of procedures in the clinical microbiology laboratory verification of infectious disease molecular assays: a self-study module (cd-rom or web-based) a multiplex rt-pcr for detection of type a influenza virus and differentiation of avian h , h , and h hemagglutinin subtypes the clinical relevance of 'csf viral culture': a two-year experience with aseptic meningitis in a rapid and highly accurate assay for the detection of enterovirus infections in cerebrospinal fluid samples using the genexpert dx system impact of human immunodeficiency virus type (hiv- ) genetic diversity on performance of four commercial viral load assays: lcx hiv rna quantitative, am-plicor hiv- monitor v . , versant hiv- rna . , and nuclisens hiv- qt comparing first-void urine specimens, self-collected vaginal swabs, and endocervical specimens to detect chlamydia trachomatis and neisseria gonorrhoeae by a nucleic acid amplification test comparison of methods for detection of chlamydia trachomatis and neisseria gonorrhoeae using commercially available nucleic acid amplification tests and a liquid pap smear medium validation of molecular-diagnostic techniques in the parasitological laboratory diagnostic pcr: validation and sample preparation are two sides of the same coin failure of commercial ligase chain reaction to detect mycobacterium tuberculosis dna in sputum samples from a patient with smear-positive pulmonary tuberculosis due to a deletion of the target region reproducibility of positive test results in the bdprobetec et system for detection of chlamydia trachomatis and neisseria gonorrhoeae false-positive gen-probe direct mycobacterium tuberculosis amplification test results for patients with pulmonary m. kansasii and m. avium infections the current status and potential role of laboratory testing to prevent transfusion-transmitted malaria characteristics of apparently false-negative digene hybrid capture high-risk hpv dna testing occurrence and documentation of low-level bacteremia in a community hospital's patient population comparison of different pcr primers for the rapid detection of severe acute respiratory syndrome coronavirus using rna extraction methods comparison of six dna extraction methods for recovery of fungal dna as assessed by quantitative pcr rapid diagnosis of tuberculous meningitis: what is the optimal method? comparison of conventional bacteriology with nucleic acid amplification (amplified mycobacterium direct test) for diagnosis of tuberculous meningitis before and after inception of antituberculosis chemotherapy the bacteriological diagnosis of tuberculous meningitis diagnostic accuracy of nucleic acid amplification tests for tuberculous meningitis: a systematic review and meta-analysis rapid identification of the species of the bacteroides fragilis group by multiplex pcr assays using group-and species-specific primers sequence analysis of four shigella boydii o-antigen loci: implication for escherichia coli and shigella relationships rhinosporidium seeberi: a human pathogen from a novel group of aquatic protistan parasites lack of serological evidence for mycoplasma fermentans infection in army gulf war veterans: a large scale case-control study mycoplasma fermentans in individuals seropositive and seronegative for hiv- serological responses to mycoplasmas in hiv-infected and non-infected individuals monitoring of chlamydia trachomatis infections after antibiotic treatment using rna detection by nucleic acid sequence based amplification multicenter study of a rapid molecular-based assay for the diagnosis of group b streptococcus colonization in pregnant women comparison of rapid intrapartum screening methods for group b streptococcal vaginal colonization perinatal screening for group b streptococci: cost-benefit analysis of rapid polymerase chain reaction risk factors for early-onset group b streptococcal sepsis: estimation of odds ratios by critical literature review prevention of perinatal group b streptococcal disease: revised guidelines from cdc centers for disease control and prevention. diminishing racial disparities in early-onset neonatal group b streptococcal disease-united states discovering new pathogens: culture-resistant bacteria etiology of acute pharyngitis in children: is antibiotic therapy needed? the management of acute diarrhea in children: oral rehydration, maintenance, and nutritional therapy practice guidelines for the management of community-acquired pneumonia in adults. infectious diseases society of america dna microarray technology: devices, systems, and applications molecular signatures for diagnosis of infection: application of microarray technology use of dna microarrays to monitor host response to virus and virus-derived gene therapy vectors comparative dna microarray analysis of host cell transcriptional responses to infection by coxiella burnetii or chlamydia trachomatis applications and challenges of dna microarray technology in military medical research using microarray gene signatures to elucidate mechanisms of antibiotic action and resistance iterative group analysis (iga): a simple tool to enhance sensitivity and facilitate interpretation of microarray experiments potential conflicts of interest. e.j.b. has been on the speakers' bureau for becton dickinson and cepheid and has received research support materials from cepheid, roche molecular diagnostics, and advandx. key: cord- -yaxawqhj authors: bucknall, r.a. title: the continuing search for antiviral drugs date: - - journal: adv pharmacol doi: . /s - ( ) - sha: doc_id: cord_uid: yaxawqhj this chapter discusses the continuing search for antiviral drugs. many virus diseases, both of humans and animals, have been successfully controlled by vaccines. these successes have naturally led to improvements in the spectrum and duration of protection offered by vaccines until, at present it is difficult to see how antiviral drugs could compete with vaccines in the control of many virus diseases. one may cite smallpox, yellow fever, polio, and recently measles among human diseases, newcastle disease, marek's disease, and infectious bronchitis among poultry diseases—an area of veterinary disease control where vaccines have been particularly important. research into the treatment of virus diseases by drugs is at present directed toward three general areas: ( ) attempts to stimulate the defense mechanism of the host animal, ( ) large screening programs to find drugs which directly block some virus-specific process, and ( ) alleviation of the symptoms of the disease. the treatment of the symptoms, rather than the cause of a disease, has been the mainstay of medical practice from time immemorial, and this is still the case with most virus disease. the short incubation period of many virus diseases will inevitably restrict the therapeutic use of antiviral drugs and in cases where symptoms have already appeared. although research into the mechanisms of virus infection is carried out by many sections of the scientific community, the search for antiviral drugs is almost exclusively the province of pharmaceutical manufacturers. the reasons for this are partly historical, but chiefly it is because the facilities for running large-scale screening programs are expensive and can only be met by commercial and, occasionally, governmental resources. because of the need to protect their discoveries from unauthorized exploitation, a good deal of secrecy inevitably surrounds the work being carried out in commercial organizations. this secrecy is regrettable but necessary, since the survival of such organizations depends largely then on getting a fair financial return on the money invested by them in research. the security aspects of commercial research naturally restrict frank and constructive discussions between competitors as well as third parties, and this has been particularly true in antiviral research. perhaps it was a revolt against this enforced isolationism which led, at least in part, to the first conference on antiviral substance's held by the new york academy of sciences in , in which manufacturers disclosed many of the details of their antiviral research and had a chance to discuss their failures and comparative successes (whipple, ) . since then there have been a number of reviews of progress in the field of antiviral chemothrrapy, and in most of these there have appeared comments and recommendations ivhich indicate that a radical rethinking is taking place of the prospects for antiviral drugs (osdene, ; mcfadzean, ; goz and prusoff, ; swallow, ). it was natural in the early s to espect that antiviral drugs would be discoverrd which would be analogous to the antibacterial antibiotics, the darlings of the prrvious decade. the experience up to date has proved that this was not to br the case, and despite prodigious efforts by the drug houses, only three clinically useful antiviral agents, which are far from perfect, have emerged. i believe thcre are lessons to be learned from this disappointing record, and i hope that the following remarks may help to continue further the critical reappraisal of this field, so that future progress may be faster. before embarking on a search for antiviral drugs, a number of points must be considered in order to assess thr technical feasibility of treating or preventing a virus disrase u-ith a drug. too often in the past massive screens have bccn set up against many viruses in the hope that a drug would turn up, and it would then find a natural place in human or veterinary medicine. although it is true that random screening still offers the best chance of discovering new drugs, unless a realistic appraisal of the whole project is made a t the outset, the products of random screens could well be useless as potential medicines. somr of the more important considcrations are listed below. a. diseases of economic importance i n ordcr to he commercially viable a drug must sell in sufficient quantities to pay for its devclopmcnt and manufacture as well as for future research. because of this, and because antiviral chemicals tend to inhibit specific viruses. diseases of low incidence or loneconomic importance are ruled out as primary targets for drug devclopment. this may seem inhumane, particularly in the field of human virus diseases, but the fact remains that it is no easier to find a drug against rabies than against influenza, and the sales from a specific antirabies drug would never cover its own developmrnt costs. diseases of loiv incidence or low cconomic importance, no matter how serious the outcome may be for the infected individual, inevitably must remain the subjects of sponsored research. nevertheless, treatments for some of these diseases may emerge as drugs are developed against major diseases. b. immunological control many virus diseases, both of humans and animals, have been successfully controlled by vaccines. these successes have naturally led to improvements in the spectrum and duration of protection offered by vaccines until, today, it is difficult to see how antiviral drugs could compete with vaccines in the control of many virus diseases. as examples one may cite smallpox, yellow fever, polio, and, more recently, measles among human diseases, and newcastle disease, marek's disease, and infectious bronchitis among poultry diseases-an area of veterinary disease control where vaccines have been particularly important. despite these triumphs, vaccines are not, and probably never will be, the complete answer to the control of certain virus diseases. it is in these areas where drugs would be useful, and it is on these diseases that efforts should be concentrated. the two most important human diseases in this class are influenza and the common cold. when a novel strain of influenza appears among the human population, as happened in , , and , existing immunity to the previous current influenza strain is not effective, and widespread epidemics of disease occur. the disease spreads so rapidly after it first appears that it is not possible to develop, distribute, and administer a vaccine based on the new strain soon enough to protect useful numbers of the population. even after the initial overwhelming pandemic, successive epidemics will occur as the disease penetrates into pockets of the community that 'had escaped infection. the disease is then maintained partly by the continuing appearance of susceptible juveniles, partly by spontaneous antigenic modifications in the virus enabling it to overcome previous immunity, and partly by the general decline in immunity of other individuals with the passage of time. after the initial pandemic, it is theoretically possible to control the disease with widespread vaccination, but in practice this is not done. consequently the disease smoulders on in the community, appearing as isolated cases and occasional outbreaks and epidemics. these are the conditions under which the disease normally exists, and it is this situation, rather than the much publicized pandemics, which causes the greatest economic loss to industrialized countries. the overall loss in - in great britain due to the asian influenza pandemic was estimated at x million, but the continuing loss, from that time on has been at least x million each year. losses in europe, north america, japan, and similar industrialized communities must be romparablr, and if only a fraction of the disease could be prevented by a drug, the economic benefits would be enormous. losses due to the common cold are comparable. the careful study of lidwell and williams ( ) showed that approximately x lo working days arc lost cach year in great britain alone from the common cold. scvertheless, the prospects for a common cold vaccine are poor because of the large number of viruses which are known to cause the disease. there are known rhinoviruses (kapikian, ) , probably a comparable number of as yct unclassified rhinoviruses, a growing catalog of coronaviruses (kapikian, ) , and a selection of other viruses including myxoviruses, adenoviruses, and herpcsviruses (tyrrell, ) , all of which have been isolated from clinical colds. it is the serological diversity of these etiological agents which makes the prospects for a vaccine so poor, and the common cold must, therefore, be considered as a target, even though a difficult target, for antiviral drugs. besides the problems of antigenic variation, exemplified by influenza, and thc multiplicity of serotypes, exemplified by the common cold, there are two further problems associated with the control of respiratory diseases by parmterally administered vaccines. the first is that circulating antibodies appear in only small amounts in respiratory mucus, and, consequently, the degree of protection afforded to the respiratory tract is less and of shorter duration than might be expected. the second problem has been brought to light by the use of experimental vaccines against respiratory syncytial virus disease in infants. when infants who had been vaccinated parenterally against this disease contracted the natural disease, they were more ill than infants who had not received the vaccine. the reason seems to be that the circulating antibodies resulting from parenteral vaccinations not only offer little protection to the respiratory tract, but when a natural infection occurs, these antibodies combine with the virus antigens at the surface of the respiratory epithelial cclls causing an inflammatory response with a corresponding increase in the severity of clinical symptoms kim et al., ; kapikian et al., ) . chanock et a . ( ) have pointed out that if an immunopathological process involving serum antibodies occurs during respiratory syncytial virus infection, then stimulation of local, respiratory tract, secretory antibody by intranasal instillation of live or inactivated virus may give adequate protection without unwanted hyperreactivity. a similar allergic reaction between virus antigen and preexisting antibody is a factor, possibly a major factor, in the pathological processes initiated by herpesviruses (jones and patterson, ) and marks the herpes diseases as possible candidates for antiviral drug development. one factor that deserves more careful consideration than it usually receives is the way in which a potential antiviral drug would be administered to the animal or patient requiring protection. clearly a common cold treatment would be unacceptable if it had to be given intravenously times a day. but there are less obvious, but no less real, difficulties in dosing large herds of cattle or sheep so that effective protection is maintained. with freeranging animals the duration of protection from a single dose would need to be prolonged to offset the labor of administering the dose. also, it is easier to dose herds by injection than by mouth, so that certain veterinary antiviral drugs may not be required in an orally active formulation. conversely, oral dosing, preferably by an addition to food or drinking water, is the most convenient way of dosing poultry. the onset of symptoms in most virus diseases is acute and may be the first indication that the host has contracted an infection. because of this, it is usually assumed that antiviral drugs will only be of value in preventing and not in curing virus diseases. nevertheless, although the periods of virus growth in infected individuals may be short, they may well be long enough to allow useful therapy. for example, pate et al. ( ) have shown in volunteers infected intranasally with coxsackie a virus that maximum virus growth precedes the onset of symptoms by hours. but from their work it may be seen that a considerable amount of virus growth is concurrent with the period of overt symptoms, and application of antiviral drugs during this period of - days might well prevent the full development of the disease. the work of douglas et al. ( ) with volunteers shows that a similar period exists in acute rhinovirus infections, and dawkins et al. ( ) and wingfield et al. ( ) have shown that the course of influenza in humans can be modified, even after the onset of symptoms, by treatment with -aminoadamantane. it hardly seems necessary to point out that before undertaking a search for a drug against a particular disease, the etiological agent of the disease should be unequivocally identified. there are a number of important virus diseases for which the causative agent is either unknown or is in doubt, for example, bovine pneumonia and human epidemic viral gasteroenteritis. it would be a mistake to set up screens against agents that were only suspected of being implicated in these diseases in case subsequent work should demonstrate that these were not in fact the causative agents. although it is difficult to predict changes in governmental legislation toward public or animal health, nevertheless, the existing and prospective legal position in various countries should be considered since these may affect the prospects for potential drugs. for example, in great britain, foot and mouth disease is controlled by the policy of slaughter and compensation, but in other countries the disease is controlled by vaccination. in the lattrr countries, a drug may find a ready market, but if legislation should change, then that market would be lost. in summary, we may say that before embarking on a search for antiviral drugs, the target disease must be carefully selected by a consideration of all the relevant factors. the more important of thesc a r t : . there must be an adequate market for the drug. . there should be no effective immunological control, and no prospects . due regard should be given to the practicability and the timing of . the etiology of the disease should be clearly established. other relevant factors, e.g., medical or veterinary legislation, should be takcn into consideration. in table i , a number of virus diseases of economic importance are listed together with some comments to illustrate how many seemingly attractive drug-target diseases are in fact precluded by other factors. for such control. dosing the patients or animals at risk. it is easy to list the properties of the ideal antiviral drug-wide spectrum of activity, nontoxic, accessible to the target organ, etc. what is not so easy is to predict what sort of properties one might expect from antiviral leads detected by screening programs. all the same, it is only by intelligent attempts to do just this that screens may be designed to detect compounds that one day may lead to the development of useful medicines. the scientific literature abounds with reports of antiviral chemicals discovered by screening random compounds in tissue culture systems, but all too frequently these compounds turn out to be false positives or active only against some relatively unimportant virus. for the products of a tissue culture screen to be of potential value, the screen must meet the requirements outlined below. first, the screen should be able to process large numbers of chemical compounds, or fermentation products, since the more that are tested, the greater the chance of success in finding active leads. perhaps the time will come when new drugs can be designed and synthesized on entirely rational grounds, but at present most active leads are chance discoveries. buthala ( ) quotes % of all compounds tested in a tissue screen as showing some antiviral activity, but in my experience the rate varies from to o.ol$!&, the higher rate referring to influenza a viruses, and the lower rate to picornaviruses. bauer ( ) has suggested that the larger the virus, the more susceptible it is to inhibition, since, for any given intracellular concentration of drug, a large virus will encompass, both physically and in terms of synthetic requirements, more drug molecules than a small one. undoubtedly, this principle will contribute to our observed high rate of inhibition of influenza virus, but another important factor seems to be that the adsorption of influenza viruses to cellular receptors is particularly vulnerable to interference by extraneous substances. given that only a fraction of a percent of all compounds tested in tissue culture will show activity and that of these only a small proportion will show activity in animal models, a realistic screening rate would be not less than compounds a year. at rates less than this, the chances of finding useful compounds become so small as to make the whole project not worthwhile. in many of the published screening procedures, the virus with which the screens are run seem to have been chosen more for the ease with which they can be handled rather than for their relevance to any virus disease target. for example, ehrlich et al. ( ) describes a screen where the primary test viruses include parainfluenza type , measles, and poliovirus, and johnson ( ) describes a screen that includes pseudorabies, adenovirus , and mouse hepatitis virus. of course, if wide-spectrum leads appear, the choice of test virus may be irrelevant, but the antiviral compounds (as distinct from interferon inducers) known at present are characterized by their relatively limited spectrum of activity, e.g., methisazone is active only against poxviruses (bauer and sadler, ) and possibly adenoviruses (bauer and apostolov, ) ; l-aminoadamantane is active only against influenza a and as and not against other myxo-or paramyxoviruses (davies et al., ) ; guanidine and a-hydroxybenzyl benzimidazole are active only against picornaviruses and not against other small ribonucleic acid (rna) viruses (eggers and tamm, ) . thus, whenever possible, the viruses used in routine screens should be those that are responsible for the clinical large-scale screens use large numbers of tissue culture cells, and there has been an inevitable trend toward the use of continuous cell lines in screening procedures. such cells have many attractive features. they grow rapidly, they can easily be obtained in large quantities, they remain "the same" year after year, they can be madr to prrform useful technical tricks such as rapidly changing the ph of their medium and surviving for long periods under agar, and, perhaps most important, they will support the growth of a wide range of viruses. continuous cell lines seem to be the natural choice for running routine screens. xevertheless, it is worthwhile remembering that many of the desirable technical properties exhibited by these cells may be a direct result of their neoplastic nature, and to use a continuous rather than a primary or diploid cell in a tissue culture system is to take yet another step away from the natural disease. it is truc that antiviral agents, such as l-aminoadamantane and methisazone, which can be shown to protect humans against virus diseascs, also exert their antiviral action in neoplastic cells in tissue culture, for example hela and kb cells, but we have striking evidence that this may not always follow. we have recently discovered a family of chemical compounds that have high activity against rhinoviruses when grown in human diploid lung cells, but virtually no activity against the same viruscs growing in monkey kidney cells, hela cells, or kb cells (bucknall, unpublished results) . these compounds and any others that may exhibit this property would have been missed in tests carried out in continuous cell lines. in summary, a tissue culture screen should be able to proccss large numbers of tcst compounds, using viruses as relevant as possible to the diseases for which a drug is required, and should employ normal rather than neoplastic cells. unfortunately, in most of the published screening procedures the last two requirements have been sacrificed to technical considerations designed to increase the number of compounds tested, as the following descriptions will show. in its simplest form, a test for antiviral activity involves treating cultures of cells with a range of concentrations of a test compound. first the maximum concentration tolerated by the cclls is assessed; then, second, the growth of virus at lowcr concentrations of compound that are not cytotoxic is measured. several ingenious methods have been devised for measuring these two responses-cytotoxicity and virus growth-all designed to facilitate the screening of large numbers of compounds. for example, herrmann et al. ( ) devised a zone-inhibition test in which large flat dishes of chicken cells were infected with test virus, overlaid with agar containing a vital stain, and paper discs impregnated with test compounds placed on the surface of the agar. compounds with antiviral activity showed two concentric zones around the paper disc, the innermost being pale in color due to the destruction of host cells by cytotoxic concentrations of compound diffusing from the disc. outside this was a deeply staining zone where cells were exposed to nontoxic concentrations of compound which also protected them from the destructive effects of the virus with which they had been infected. beyond this, where the concentration of compound was too low to protect the cells, the cell sheet was destroyed by virus and stained poorly. thus, by visual inspection of the dishes after to days, active compounds could be quickly detected. rada et al. ( ) devised a similar agar diffusion test in which test compounds were applied to the virus-infected cell sheets in circular wells in the agar overlay. although agar diffusion tests are capable of processing large numbers of test compounds, they suffer from two drawbacks. first, they are of comparatively low .sensitivity in detecting both the cytotoxic and antiviral levels of compounds, and second, they are limited to viruses that produce plaques under agar. rightsel et al. ( ) devised a system based on the fact that if cells were damaged either by the toxic effects of a chemical compound or by virus growth, they would not swing the ph of their medium. thus, by incubating virus-infected cells in a series of concentrations of a compound and then looking for the cultures that had changed the color of the phenol red indicator in their medium from pink to yellow, active compounds could be detected. this technique has also been used to assay neutralizing antibody and interferon action (pauker, ). finter ( ) described a system whereby the cytotoxic effects of test compounds could be assayed by the reduction in the amount of neutral red taken up by treated cells, and, similarly, the cytopathic effects of virus growth could be quantitated by measuring the reduction in the uptake of neutral red by infected cells. the system can readily be adapted to the screening of test compounds for antiviral activity. if myxoviruses are used in this system, because their cytopathic effects may not be pronounced, their growth is best monitored, not by a reduction in neutral red uptake, but by a quantitative hemadsorption method which matches the neutral red uptake method in its accuracy and sensitivity (finter, ) . in contrast to the eone-inhibition and ph-swing tests, the neutral red uptake test is precise in operation and may be used to demonstrate fine differences in the relative toxicity and activity of test compounds; it is probably no more timeconsuming than the former tests. a system of testing for antiviral agents based on the inhibition of nucleic acid synthesis was dcscribcd by lliller et al. ( ) and has been used to screen compounds and mold metabolites for antiviral activity (miller et ul., ) . for the test, hela cells were suspended in a medium containing uridine- h. if a test compound has toxic effects on the hela cells, then the cellular r s a synthesis, as measured by u r i d i n~-~h fixation, will be reduced. similarly, if cells are infected with an r s a virus and treated with sctinomycin d. then r s a synthesis will be due to virus growth only. thus, if test compounds reduce this virus-directed rxa synthesis at concentrations that do not affect cellular r s a synthesis, then the compound is exerting a specific effect on virus growth. the test can also be used for deoxyribonucleic acid (dsa) viruses, the cellular and virus dxa synthesis being monitored by including th~midine-~h in the medium. virus dsa synthesis is distinguished from cellular dsa synthesis by disrupting the cells at the end of the test and treating them with dcoxyribonuclease when encapsulated virus dsa is resistant to digestion and the unprotected host cell dsa is not. thus, the selective effect of test compounds on the synthesis of virus dsa can be measured. the authors claim that the system operates satisfactorily ivith a range of viruses-some of them important disease organisms-and is simple, reliable, and rapid. the chief criticism of this method is that, because nucleic acid synthesis is used as the sole measure of virus growth, test compounds that might act on subsequent stages in the virus replicative cycle may not be detected. for example, any disturbances in the sequencing of virus nucleic acid, inhibition of structural protein synthesis, or failure of assembly or release of mature virions, would provide a sound basis for a useful drug, but these phenomena may not be detected in this type of test. also, since high infecting doses of virus are used to give satisfactory operation of this test (up to virus particles per cell), the test may be rather insensitive in detecting antiviral activity. all antiviral activity is, in the broadest sense, competitive, either a t the level of cellular membrane receptors or at an cnzymic or template level. thus, the more virus is used to initiate infection, the less effective an antiviral compound is likely to be. although this factor will not turn a highly active compound into an inactive one, it may well obscure low levels of activity which might be useful starting points for chemical exploitation. the real value of miller's test is the use of the important biochemical system of nucleic acid synthesis to monitor the toxic manifestations of test compounds. this subject is discussed furthrr in the following section. reference has already been made to four methods for measuring the toxicity of chemical compounds in tissue culture cells: direct cytopathic ef-fects, vital dye uptake, metabolic activity (ph-swing), and nucleic acid inhibition, and there is no shortage of other methods. nevertheless, the inadequate assessment of compound toxicity in antiviral testing probably gives rise to more false leads than any other single cause, before discussing how compound toxicity might be measured, it must first be defined. strictly, any interference with cellular metabolism by an extraneous compound is a toxic effect, and the most stringent tissue culture test of lack of toxicity is the continued normal division and growth of cells in the presence of an extraneous compound. however, this test is too cumbersome for use in rapid screening procedures, and simpler, but less critical, tests are invariably used in primary screens. undoubtedly, the simplest method of assessing compound toxicity is by direct microscopic examination of cells for cytopathic effects or more subtle morphological changes. it is necessary for the observer to be trained to detect such changes, and an arbitrary scale must be devised to record the observations, but if these simple requirements are met, the method is generally successful. it may be objected that this system would be unworkable where large numbers of compounds are being screened because of the correspondingly large numbers of microscopic examinations required; but given a good low-power microscope, an experienced reader, and the fact that most random compounds tested will show no antiviral activity and will, therefore, not require more than a cursory examination, the system is reliable, fast, and economical. in the author's laboratory a system of this kind has been in use for over years, and it is possible for one worker to screen a hundred compounds against three viruses each week. we have found that with this system, compounds appear to be toxic a t lower concentrations than with either the zone diffusion or the dye uptake method. we conclude, therefore, that our method is more sensitive than the others mentioned in detecting the toxic effects of compounds. the direct microscopic assessment of toxicity is not without its deficiencies, but if the method is seen only as a preliminary determination of toxicity, these deficiencies are not serious. chief among these (and this applies even more to indirect methods) is the occasional failure to detect certain types of toxicity. for example, from time to time we have had compounds which appeared to prevent virus growth and to show no toxicity to confluent sheets of tissue culture cells, these cultures looked normal for several days in the presence of the compound, but viruses would not grow in these cells. nevertheless, further studies (see below) have shown that the compounds were exerting an inhibitory effect on some aspect of the cellular metabolism and it was this which prevented virus growth. we have investigated this effect with (a) inhibitors of nucleic acid synthe-sis and ( b ) uncouplers of oxidative phosphorylation, two classes of compound that are particularly prone to giving misleading results. nucleic acid inhibitors are often slow to produce cytopathic effects in confluent monolayers of cultured cells. the d s a synthrsis of such cells is low, and sufficient r s a synthesis is often maintained in the presence of partially effective concentrations of an inhibitor, enabling the cellular structural integrity to be sustained. all the same, an invading virus is unable to replicate in a cell under these reduced circumstances, and this will lead to an apparent antiviral specificity. this is the mechanism by which the chlorinated ribofuranosylbenzimidazoles exert their antiviral effects (bucknall, ) . these compounds were extensively studied as antiviral agents before their "activity" was found not to be specific for the virus (tamm et al., ; tamm and srmes, ; tamm and overman, ) . uncouplers of oxidative phosphorylation also often appear to be antiviral agents becausc concentrations that greatly reduce the energy-generating systems of cells in confluent monolayers are often slow to produce morphological changes. in this half-poisoned state, the cultures appear normal, but do not support virus growth, and thus another false "lead compound" is generated. as mentioned earlier, these remarks apply to all tissue culture systems to a greater or lesser extent, and tissue culture tests for antiviral activity must always be regarded as strictly preliminary. active leads from such tests must always be subjected to the closest scrutiny to determine whether the activity is truly specific for a virus-coded process or simply results from a subtle toxic effect on the host cell. the margin betwen the maximum nontoxic concentration and the minimum antiviral concentration of a test compound is conveniently expressed as thrrapcutie ratio = max. nontoxic concentration/min. antiviral concentration and will vary according to how these two concentrations are determined. the simplest and most stringent test of the maximum nontoxic concentration of a compound in zdtro is to grow cells in the presence of the compound and determine the maximum concentration a t which division and growth will proceed normally. if this concentration, and lower ones, protect the cells from virus attack, then this is an unequivocal demonstration that the compound is exerting a specific effect on some aspect of virus replicat ion. like miller et al. ( ) , we have found the inhibition of cellular nucleic acid synthesis, particularly r s a synthesis, to be a useful system for detecting the toxic effects of test compounds. cells are treated with a range of concentrations of a compound, then the uptake of ~r i d i n e -~h into acidinsoluble material is measured and compared with that of normal cells (bucknall, ) . the test is simple to run, and since the nucleic acid metabolism is a cardinal area in the cellular metabolism, even if a compound has no direct effect on the nucleic acid synthesis, disturbances of other synthetic or homeostatic mechanisms are quickly reflected in changes in the synthesis of rna or dna or both. in fig. , the dose-response curves of one experimental compound are determined in human diploid lung cells by the three methods outlined above-direct cytopathic effect in confluent monolayers, inhibition of rna synthesis, and inhibition of cell growth in newly seeded cultures. although this compound is not a specific inhibitor of rna synthesis, the inhibition of rna synthesis and the production of cytopathic effects run close together. at concentrations that indirectly affect the nucleic acid synthesis, sufficient disturbance is caused in other areas of the cellular metabolism to lead to a general cytopathic effect. cell division is affected a t lower concentrations and in this particular case, inhibitory (and therefore toxic) effects can be detected with concentrations times lower than those that cause cell destruction, nevertheless, even with cell growth as a measure of toxicity, and effects on the cellular growth rate (&-a) are higher than those that suppress virus growth, indicating that ici , is exerting a specific effect on virus growth. ( % end points: cpe, pg/ml; rna synthesis, pglml; cell growth, . pg/ml; virus growth, . pg/ml.) there is a clear margin between the toxic and antiviral effects, as may be seen from the virus yield curve. fusidic acid, which has been reported to show specific antiviral activity in tissue culture (acornley et al., ) , was also tested in the same way (fig. ) . in this case, the concentration causing % cytopathic effect after hours was pg/ml, whereas virus yield was depressed to % by only pg/lml, giving an apparent therapeutic ratio of . but when the effects of fusidic acid on cellular synthesis were studied, it was clear that cellular rka synthesis was drastically reduced by pg,!ml. thus, fusidic acid probably reduces virus growth by inhibiting cellular, rather than virus, synthetic processes, and probably accounts for the fact that this compound showed no clinically useful effects in virus-infected volunteers, despite good levels of drug in blood and nasal secretions (acornley et al., ) . since the toxic effects of compounds in vitro usually increase with time, it is important when comparing toxicity and antiviral activity, to ensure that the compound has been in contact xvith cells for the same length of time in each case. in the above experiment, the cytopathic effect, rna synthesis, cell growth, and virus inhibition were all measured in cells that had been exposed to the compound for hours. when a virus disease is limited to a particular target organ, such as the respiratory tract, it is of great value to be able to culture a portion of the organ for in vitro studies. the culture of portibns of trachea has been extensively used to study the growth of respiratory viruses (hoorn and tyrell, , ; mcintosh et al., ; craighead and brennan, ; herbst-laier, ) , and recently organ cultures of human embryonic gut have been used to study the agents of human "virus" gastroenteritis ( d o h et al., ) . the technique could presumably be extended to the study of viruses, such as polio, rabies, smallpox, and herpes, which localize in specific organs of infected individuals. we have found the use of human embryo and animal tracheal pieces of value in studying the toxicity and the antiviral activity of leads produced by tissue culture screening programs. our technique is to excise a trachea and cut it transversely into rings - mm thick. these are placed in x in. tubes with ml of eagle's medium and rolled exactly as conventional tissue cultures. with a low-power microscope the ciliary activity of the respiratory epithelium is assessed on an arbitrary scale of to . in the presence of a test compound, the reduction of ciliary action is a highly sensitive measure of compound toxicity, and it is easy to determine the concentration at which full ciliary activity can be maintained (fig. ) . at lower concentrations the effects on virus growth may be measured by harvesting the culture fluid at intervals and titrating for infectious virus. by using this technique, we have found that almost % of the so-called active compounds produced by a tissue culture screen against influenza a appear negative when tested in ferret tracheal cultures. in almost all cases, compounds were toxic at lower concentrations in tracheal cultures than in conventional tissue culture monolayers, as judged by a cessation of ciliary activity. in a proportion of these compounds, some data concerning their biochemical action were available, and in most cases these drugs were uncouplers of oxidative phosphorylation, nucleic acid inhibitors, or general antimetabolites. the inhibition of ciliary action in tracheal cultures is, therefore; a much more sensitive index of toxic effects than morphological changes in monolayers. in fig. , the % cilia-inhibitory concentration of ici , is . pg/ ml. this effect is detected at a concentration times lower than is necessary to cause morphological changes in conventional tissue culture cells (fig. l) , presumably because the metabolic patterns of the ciliated cells are more complex than those of static cells in culture and are, therefore, more readily disturbed. in general, the concentrations of compounds that suppress ciliary activity arc comparable to those that prevent cell growth, except in the case of specific inhibitors of dsa synthesis for which cell division and growth are usually more sensitive than ciliary activity. any conventional technique may be used to measure virus growth in antiviral tests-cytopathic effect, plaque reduction, yield of infectious virus, and ht.madsorption, bring thc most common. because of thcir simplicity, cytopathic effect and hcmadsorption are widdy used, hut these techniques must be used with some precautions if certain types of antiviral activity are not to be missed. in order to speed up the rate of antiviral testing, the quantity of challenge virus is often increased to a theoretical maximum of virus particle per cell. the whole cell culture then behaves synchronously, and results are obtained in whatever time the virus takes to complete its replicative cycle-usually between and hours. with this procedure, however. a test compound that prevented the formation of infectious virus but was unable to protect the infected cell from destruction would not be detected. for example, in a relatively complex virus, such as influenza, it is not difficult to imagine that rna synthesis could be interrupted while hemagglutinin production continued, much as it does in the van magnus effect. the result would be a monolayer showing full hemadsorption and yet no transmissible virus would have been formed. test compounds that produce this effect would be of great interest as potential drugs but could be missed in tests where the dose of challenge virus is too high. wherever possible, tests should permit several cycles of virus growth to occur so that compounds that interrupt any part of the cycle may be detected. there is a school of thought that tissue culture testing is so artificial as to be of little value in detecting useful antiviral substances. it is argued that by testing for antiviral effects directly in animals, the activity that is detected is likely to be more valid and more useful than that detected in tissue culture. it is true that the majority of active compounds detected in tissue culture screens are not active in animals, even after full authentication of the antiviral activity by tests such as those discussed above. the reason for this is usually that the compounds do not reach the target organs in sufficient amounts to show activity rather than because of some intrinsic defects in the antiviral activity of the compounds. also, apart from interferon inducers, unless a compound manifests some activity in vitro, it is highly unlikely to do so in vivo. on the one hand, it is argued that a virus growing in a tissue culture cell is of little relevance to the processes by which that virus causes disease in the whole animal. on the other hand, it can be said that, since virus growth is the basis of the pathological processes, if virus growth can be halted, then the disease can be stopped. furthermore, the literature discloses that some highly irrelevant viruses are being used in animal test systems and that, even when human pathogens are used, e.g., influenza, they require extensive adaption to their animal host and the course of the disease is usually very different from that in humans. finally, there are no convenient animal models for studying the growth of human rhino-and coronaviruses and, unless tissue culture tests are used, there could be no screening for antiviral compounds against these important pathogens. there is, therefore, no convincing theoretical advantage in using animals for routine antiviral screens. this, together with the cumbersome nature of animal tests and the difficulties of "scaling-up" to test large numbers of compounds makes tissue culture testing a more attractive proposition for the initial screening program. the foregoing remarks apply, of course, only to the detection of compounds that have a direct effect on specific virus processes, e.g., absorption, penetration, and replication. in the field of interferon inducers, immune enhancers, and other stimulators of thr host defense mechanisms, obviously one has no choice but to use test animals; but here one is concerned to detect any overall rffcct on the course of a disease rathrr than accurately t o model a particular human or veterinary infection. accordingly, the choice of test system is less critical provided it fulfills certain requirements. for instancc, (a) thr virus and test compound should be administered a t separate sites to avoid any possible local destruction of the challenge virus by test compound; ( ) the test compound should be given parenterally to give the best chance of absorption, and (c) the dose of challenge virus should be sufficiently small to allow a useful incubation period before symptoms develop. the following system has been used successfully by us. groups of mice are dosed intraperitoneally with test compounds a t , . , and . mg/ kg on four successive days. twenty-four hours after the first dose, they are challenged intramuscularly with jild,, of semliki forest virus, and after the last dose they are observed for symptoms twice daily. the mcan rcciprocal day of death (mrdd) for each test group is calculated after days and comparcd with that of a similar undosed group as w l l as with that of a group givcn four daily injections of a protective agent such as polyinsinie-polyrytidilir acid (poly ic) . figure shows the typical response of mice treated nith poly ic and untreated controls. under these particular conditions, the t~ response curves overlap. by selecting an mrdd of . as the criterion of "active" or ' nactive," then theoretically % of all inactive compounds tested will appear as spurious actives and would require to be retested to establish their true status. some caution is needed in interpreting the converse overlap. given known active compounds, or a single active compound tested times, then tests in every would miss such a compound. but in practice, the vast majority of compounds passing through the test will be inactive, and the chance that the occasional true active compound will by chance fall into the " % missed" category is correspondingly reduced. even with an in vivo test reduced to such a minimum as this, it still requires a large effort in terms of manpower and facilities to test realistic numbers of compounds. although many human viruses will grow in animal hosts it is often difficult to assess the potential value of an antiviral compound for human use by using animal models. there are five main reasons for this. first, a relatively benign human virus infection will often follow a very different, and often severe course in an animal. for example, influenza virus, herpes simplex, and coxsackie viruses may cause much more serious diseases in laboratory animals than they do in man. second, human viruses often must be adapted by multiple passaging before they will grow satisfactorily in animal hosts, and, therefore, the challenge virus in the animal model may be a very different creature from the original human pathogen. third, the quantity of virus administered to an animal in order to produce some measurable effect, e.g., symptoms, virus isolation, and seroconversion, is usually vastly greater than would ordinarily be encountered by the natural host, and this can have a profound bearing on the efficacy of any curative agent. for example, finter ( ) has shown that the protection offered to mice by doses of interferon is greatly increased as the quantity of challenge virus is reduced. fourth, the fate of a drug when administered t o an animal may be very different from that seen in man. and last, a compound may show toxio effects in man which it did not show in animals. the last two points are probably the most important in determining how far the results obtained with animal models are relevant to man. in theory the above considerations should operate in both directions; that is, a compound that shows a positive result in an animal model may be positive or negative in man, and a compound that is negative in an animal may be negative or positive in man. but, since many animal models offer a greater challenge to the therapeutic potential of a drug than the natural disease in man, a positive result in an animal model always gives great hopes that a positive result might be achieved in man. this consideration often encourages the evaluation of potential antiviral drugs in man on the very slimmest of grounds. an example of the dilemma that an animal model may pose is afforded by the ork of boyle and his colleagues ( ) on the compound skf . this compound was shown to be active against a number of viruses, including a wide range of human rhinoviruses, in tissue culture. the problem arose of how to evaluate this compound in vivo. there are no smallanimal modrls of human rhinovirus infections, and the authors, therefore, decided to test the compound in chimpanzees, which are one of the few primates susceptible to human rhinoviruses. because of lack of knowledge on infectivity of human rhinoviruses for chimpanzees, the authors gave up to , ooo tcd,, of challenge virus to each animal to ensurc infcction. the animals were given the drug orally times a day, and the course of the disease was monitored by virus shedding from the nose. the rate of antibody rise was also measured. the numbers of animals in each experiment were necessarily small-usually or treated with drug and or controls. the final results were tantalizingly inconclusive: not clearly negative, nor convincingly positive that the drug had produced a curative effect. the investigators admit that this system is far from satisfactory but conclude from their results that the compound is n-orthwhile studying further in human subjects. the same conclusion, however, would probably have been reached if the compound had been clearly inactive in the chimpanzees, on the grounds that the excessive doses of challenge virus and unknown factors in the chimpanzee metabolism could have led to this result. animal models of human virus disease must at best be regarded as poor imitations of the natural condition, and results obtained with animal models, whether they are positive or negative, encouraging or discouraging, should be interprcted cautiously and never be used as the sole basis for predicting the outcome in man. research into the treatment of virus diseases by drugs is a t present directed toward three general areas: ( ) attempts to stimulate the defense mechanism of the host animal; ( ) large screening programs to find drugs that directly block some virus-specific process; and ( ) alleviation of the symptoms of the disease. the first approach is exemplified by the variety of interferon inducers which are a t present under intensive study. a disappointing feature of these is their uniformly low activity in man, despite highly promising results in laboratory animals, such as mice, rats, and rabbits. perhaps the interferon response in man and primates is less important in defense against virus disease than it is in other taxonomic groups. searches are being made for more general stimulants of host defense mechanisms, for example, stimulators of phagocytosis and the immune response, but very little progress has been reported so far. the search for drugs that will directly inhibit virus replication, by stopping a virus-coded synthetic process, or the absorption, penetration, uncoating, assembly, or release of virions, has been intensive and is still continuing. nevertheless, the products of this effort will find application only in a relatively small number of virus diseases for the reasons outlined above. only for those diseases of high economic importance, and for which no effective vaccines are available, will specific antiviral drugs ever be a commercial reality. the present paucity of such drugs is undoubtedly due largely to the intimate association of viruses at the molecular level with their host cells. for this reason, disease targets must be carefully defined, screening procedures made as meaningful as possible, and the limitations of animal models be clearly recognized. only by attention to these details can the maximum effort be brought to this difficult problem. again, the lack of clinically useful drugs allows no more than speculation on the possibilities of drug-resistant viruses emerging when antiviral drugs are eventually in widespread use. the phenomenon of drug resistance in viruses is well established in the laboratory (melnick et al., ; tamm and eggers, ; renis and buthala, ) , and, unless potential antiviral drugs are free of this serious defect, their commercial life will be embarrassingly short. the treatment of the symptoms, rather than the cause of a disease, has been the mainstay of medical practice from time immemorial, and this is still the case with most virus disease. the short incubation period of many virus diseases will inevitably restrict the therapeutic use of antiviral drugs, and in cases where symptoms have already appeared, the physician and layman alike will have recourse to the extensive armamentanurn of palliatives available for alleviating the symptoms of virus disease. all the same, this is clearly an unsatisfactory state of affairs, and the ultimate goal of antiviral research is the prevention of virus disease. as the understanding of viruses increases, so a more rational approach to the chemotherapy of virus diseases will become feasible. also, random discoveries of antiviral activity in novel chemical compounds will shed further light on those areas of virus metabolism that are susceptible to chemical attack. with increasing con-tributions from both these approaches, virus chemotherapy should soon emerge from a theoretical possibility to a practical reality, and antiviral drugs ivill make their long awaited contributions to clinical medicine. modern trends in medical virology zn "virus-induced immunopathology arch. gesanlfe virusforsch. zn "diagnostic procedures for virus and rickettsia infections amer zn "topics in medicinal chemistry ezperientia , virology , . tamm, j., and overman antiviral substances key: cord- - l scdqk authors: kiechle, frederick l.; arcenas, rodney c. title: utilization management in a large community hospital date: - - journal: utilization management in the clinical laboratory and other ancillary services doi: . / - - - - _ sha: doc_id: cord_uid: l scdqk the utilization management of laboratory tests in a large community hospital is similar to academic and smaller community hospitals. there are numerous factors that influence laboratory utilization. outside influences like hospitals buying physician practices, increasing numbers of hospitalists, and hospital consolidation will influence the number and complexity of the test menu that will need to be monitored for over and/or under utilization in the central laboratory and reference laboratory. clia’ outlines the four test categories including point-of-care testing (waived) and provider-performed microscopy that need laboratory test utilization management. incremental cost analysis is the most efficient method for evaluating utilization reduction cost savings. economies of scale define reduced unit cost per test as test volume increases. outreach programs in large community hospitals provide additional laboratory tests from non-patients in physician offices, nursing homes, and other hospitals. disruptive innovations are changing the present paradigms in clinical diagnostics, like wearable sensors, maldi-tof, multiplex infectious disease panels, cell-free dna, and others. obsolete tests need to be universally defined and accepted by manufacturers, physicians, laboratories, and hospitals, to eliminate access to their reagents and testing platforms. this chapter will review the numerous factors that infl uence laboratory test utilization in a large community hospital (table . ). assessment of laboratory test utilization usually relies on data compiled after a utilization review or analysis of the necessity, appropriateness, and effi ciency of laboratory tests on a concurrent and/or retrospective basis. most laboratory utilization studies have been reported from academic medical centers [ - ] , however, there are often common fi ndings in large community hospital settings [ - ] . the major difference between an academic center and community healthcare system is usually the number of hospital-employed physicians versus independent physicians with their own offi ce practices. some large community hospitals have only employed physicians on their medical staff like kaiser permanente, henry ford hospital, and others. generally, it will be easier to assemble a group of specialists to convene a laboratory utilization committee meeting, if the physicians are accustomed to leaving their practice responsibilities and going to a hospital-oriented committee meeting in the middle of the day. since the focus of this committee is to review the evidence-based evaluation of a new or old laboratory test to rule in or out a specifi c disease, attendance and the quality of participation will vary depending on the physician's commitment to the project. in a large community hospital, it may "save time" during these meetings if homework is assigned beforehand. "this includes what do people need to read, think about, bring with them, or come prepared to discuss so the meeting will be more productive" [ ] . one of the authors (flk) has worked for years directing the clinical laboratory and outreach laboratory at a large community hospital (william beaumont hospital) in royal oak, mi and for the past years at a six hospital county healthcare system (memorial healthcare system) in hollywood, fl with the co-author (rca). we will review several of the issues listed in table . . in preparation for the shift from fee-for-service to a valuebased payment system [ ] large community hospitals have been actively engaged in three enterprises which will impact laboratory test utilization: buying physician practices, increasing the use of hospitalists and consolidation of hospitals. in the early s during the initiation of health maintenance organizations (hmos) , hospitals purchased physician practices. in general, at that time, hospitals had a diffi cult time managing the physicians and their practices. during this second more recent phase of buying, contracts are designed to enhance physician productivity [ - ] . the "key motivation for hospital acquisition of physician practices is the ability to gain market share for inpatient admissions and outpatient services by capturing referrals from physicians employed by the owned practices" [ ] . carlin et al. [ ] documented a shift in inpatient admissions, outpatient ct scans and mri procedures from three large multispecialty clinic systems to a two hospital-owned integrated delivery system (ids) after the ids purchased them. this same shift of referral patterns to the new hospital owner will also be true for laboratory tests ordered by newly acquired physician practices. in the usa % of physicians were independent in compared to % in [ ] and % of male and % of female physicians in [ ] . in , % of physicians were employed by hospitals compared to % in [ ] . a downside of this trend is the fi nding that hospitals charge more when the doctors work for them attributing the cause to higher overall costs [ ] . this current trend should drive more laboratory testing from new hospitalbased physicians to the hospital central laboratory with the consequence of potential utilization issues. the hospitalist model of inpatient care is one of the most rapidly growing forms of medical practice in the usa since its introduction in the mid- s [ , ] . in , there were more than , hospitalists in the usa [ ] which has increased to , in [ ] . most hospitalists practice in hospitals with greater than beds [ , ] . their average starting salary was greater than that for internal medicine or family practice physicians in [ ] . hospitalists work strictly in the hospital and oversee the care of complex patients with the goal of reducing the need of transferring patients from one physician to another [ ] . most large community hospitals use a voluntary hospitalist system in which primary care physicians can choose to admit to a hospitalist service or attend to their own patients [ ] . large community hospitals are more likely to adopt a hospitalist model if their case mix complexity was greater than the national average for medicare's diagnosis rated group index, while high health maintenance organization market share resulted in lower interest in this model [ ] . the hypothesis that the hospitalist model will lead to a reduction in the patient's length of stay and total hospital costs has been demonstrated [ , - ] . hospitalists may order excessive diagnostic tests secondary to their lack of previous knowledge of the patient [ ] . the choosing wisely campaign sponsored by the american board of internal medicine foundation, consumer reports, and more than specialty societies have recommended reduction or elimination of inappropriate use of radiologic, laboratory, and therapeutic procedures [ , - ] . the fi rst societies provided fi ve selections each, of which % were related to laboratory tests or pathology [ ] . one of these lists from the society of hospital medicine recommended reducing the use of repetitive common laboratory testing when the patient is clinically stable [ ] . in a quality improvement project focused on hospitalists, an effort was made through education to reduce the repetitive use of complete blood counts and basic metabolic panels [ ] . these panels are often embedded in order sets established for specifi c diseases or for specifi c physicians to simplify computerized physician order entry [ ] . there was a -month baseline period before the intervention followed by a -month intervention period [ ] . the intervention resulted in a % reduction of these two panels ordered per patient day associated with decreased direct costs of $ . per patient and annualized savings of $ , [ ] . this study illustrates how a small segment of laboratory test ordering physicians can impact expenses through overutilization and by analogy underutilization of laboratory tests. like the fi rst round of hospitals buying physician practices started in the early s, so did the consolidation or mergers of hospitals [ ] . there has been a recent increase in both horizontal and vertical consolidation [ , ] . horizontal consolidation involves hospitals merging with other hospitals that supply similar services in geographic proximity [ , ] . these mergers are most likely to be investigated for antitrust violations [ ] . vertical consolidations involve hospitals consolidating with other health care provider entities [ , ] . from to , hospital mergers and acquisitions were announced involving hospitals [ ] . sixty percent of hospitals are now part of health systems. the downside to these mergers has been a - % increase in prices secondary to increased market share [ ] . strategies have been suggested for avoiding this market disequilibrium [ , ] . no us hospital markets were rated highly competitive [ ] while the german market is competitive and the number of hospital systems decreased by % from to [ ] . there are myths associated with the latest hospital merger activity. the fi rst myth is that consolidation is equivalent to integration [ ] . the second is that higher quality is associated with size rather than leadership and competition [ , ] . evidence supports the suggestion that hospitals in competitive markets tend to have better administrative management [ ] . the combination of hospital mergers and increased hospital-employed physicians [ ] will lead to increase in laboratory test volumes and the need for robust utilization management practices. the clinical laboratory improvement amendment of (clia' ) went into effect september , . the regulations categorize laboratory procedures based on test complexity using well-defi ned criteria: waived, moderately complex, and highly complex or provider-performed microscopy . these regulations defi ne the universe of tests that a large community hospital laboratory is directly or indirectly responsible for their utilization management. there are a variety of clia-tests that have been classifi ed as waived by the fda and a list of them from to present can be found at www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfclia/ testswaived.cfm . the implementation of point-of-care testing (poct) usually involves a desire to decrease the total turn-around time for an analytical test and improve patient outcome [ ] . however, decreased turn-around time does not always equal improved patient outcome [ , ] . two prospective studies analyzed the effect of the poct i-stat device (abbott, abbott park, il) on length of stay in the emergency department after a control period when the central laboratory was used. the i-stat cartridge that analyzed sodium, potassium, chloride, urea, glucose and calculated hemoglobin was used. neither study revealed any change in the length of stay or clinical outcome for emergency department patients, although both showed a decrease in time required to obtain laboratory results for the six tests on the cartridge when the istat was used. the blood test was not the rate-limiting step in the patient's length of stay [ ] . in a similar study using fi ve different testing cartridges for the istat (inr, lactate, brain natriuretic peptide, troponin t and chemistry with hemoglobin and hematocrit), singer et al. [ ] reported a reduced turn-around time for poct compared to the central laboratory which translated into a reduction in time to completion of iv contrast ct and the length of stay of those specifi c patients. it is not clear whether relocating poct tests to the patient's bedside increases [ , ] or decreases [ ] the test volume of that test in the central laboratory. it has been reported in both adult and newborn intensive-care units that patients with indwelling arterial lines have more blood drawn for laboratory studies than patients without arterial lines [ , ] . the blood loss may be great enough to require a transfusion [ ] . certainly, utilization management of poct programs will require investigations to determine the relationship between total laboratory turn-around time for results, patient outcome and hospital costs using cost effectiveness analyses [ ] . there are at least different sources of body fl uids in a human [ ] . some of these are laboratory specimens that are examined under the bright-fi eld or phase contrast microscope and are classifi ed as provider-performed microscopy (ppm) by clia' [ , ] . a separate cms license is available for sites performing these assays which include koh preparation, pinworm detection, fern test, microscope urinalysis, semen analysis for presence of sperm and motility, and eosinophils in nasal smears [ , ] . it is wise for the laboratory poct administrative committee to assist in the initiation of a ppm testing program in collaboration with the ppm license holder for that clinically defi ned program, like fern testing in the labor and delivery area under the direction of a staff ob/gyn physician. in this model, training and utilization management is not under the direction of the hospital poct administrative committee [ , ] . in order to audit laboratory test utilization year to year it is "essential to understand how test volumes are actually counted" [ ] . are test panels bundled and counted as one test or are the test panels unbundled and each test in the panel counted separately. in an evaluation of the total inpatient test volumes from to for the department of clinical pathology at william beaumont hospital, royal oak, mi, it was determined that the method for counting inpatient tests changed in and [ , there are two categories for cost reductions : "hard" cost savings and "soft" cost avoidance. tangible "hard" cost savings are often achieved by bringing reference laboratory tests inhouse to the clinical laboratory (or eliminating the reference laboratory test altogether) [ , ] . the more intangible "soft" cost avoidance includes such things as decreases costs associated with the introduction of a new laboratory test with the intent to decrease costs in the future. it also can occur when a cost is lower than the original expense that would have otherwise been required if the cost avoidance exercise had not been undertaken. since processes consume overhead and overheard costs money, any signifi cant process improvement could represent signifi cant cost avoidance for an organization. total cost includes direct and indirect costs [ ] . direct cost includes personnel time to prepare and perform the test, reagents, quality control, profi ciency testing, and equipment depreciation. indirect costs including reporting costs (computer) and hospital overhead. incremental or marginal costs include only variable direct costs and not the indirect costs [ - ] . therefore, incremental costs demonstrate what it would cost to perform one more laboratory test, assuming the equipment and facility are already available. neither total cost analysis nor incremental cost analysis includes an analysis of the defect rate or failure to achieve established goals, like turn-around time [ ] . they are defi ned as internal or external failure rates. internal failure costs are incurred by the testing center as a consequence of a defect in the testing system. the receiver of the test results incurs the external failure costs. over utilization of laboratory tests incurs both internal and external failure costs in the excess time spent in the laboratory to generate the result and then excess insurance charges to the patient and nursing/physician time to evaluate the results. to illustrate cost avoidance , consider the presentation of potential enterovirus meningitis in the emergency department. children and adults with detectable enterovirus in the cerebrospinal fl uid (csf) may exhibit symptoms of meningitis including photophobia, stiff neck, acousticophobia , severe headache with vomiting, confusion, diffi culty concentrating, seizure and sleepiness. a molecular test for enterovirus detection will alter the patient's length of stay in the emergency department. if the patient is positive for enterovirus in the csf specimen, the patient will be discharged for home care until the viral meningitis resolves (table . ). if the patient does not have enterovirus in the csf, they will need further hospitalization to rule out a bac-terial source for the meningitis with culture and sensitivity studies (table . ). romero [ ] has demonstrated the cost range for hospitalization related to enterovirus testing/care of infection to be $ - with an average length of stay of - days. we used $ for the calculation in table . , which illustrates a cost avoidance of $ , for patients with or without enteroviral detection by molecular methods. "cost per unit went down if you could make longer and longer runs of identical products. this gave rise to the theory of economies of scale " [ ] . the laboratory achieves economies of scale and lower unit costs per test by expanding the volume of laboratory tests it analyzes. in the early s, the number of inpatient laboratory tests at william beaumont hospital began to decrease. to fi ll the gap, after a -year preparation period, we initiated an outreach program (beaumont reference laboratory) expanding our laboratory testing services to non-patients from physician offi ces, nursing homes, and other hospitals [ , ] . several years later ( ) beaumont reference laboratory joined a regional laboratory network of other hospital-based laboratory outreach programs in michigan, joint venture hospital laboratories , to accommodate the wide geographic coverage required by third party payers [ , ] . the participating laboratories are independently owned and operated. a central network administrator coordinates negotiations for managed care contracts. the volume of brl specimens grew to half of the total volume of clinical pathology procedures of six million tests in . this increased volume permitted an expansion of the test menu in each laboratory section. in , we reviewed , , procedures ordered by physicians in nine subspecialty areas (family practice, pediatrics , internal medicine, cardiology, endocrinology, gastroenterology, nursing home, ob/gyn, and urology). the requisitions for physician, procedures per requisition and procedures/physician were calculated for each of the nine groups of physicians [ ] . family practice ( physicians) and internal medicine ( ) ordered the greatest number of total procedures as well as procedures/physician while urology ( ) ordered the least of these two categories [ ] . the tests ordered by each of the nine groups were counted in seven laboratory sections. all nine groups ordered more chemistry tests than any other category but the percent varied from . % for ob/gyn to . % for internal medicine. the most popular individual tests in fi ve laboratory sections (chemistry, hematology, immunology, microbiology, and molecular diagnostics) were calculated as an average number of a specifi c test ordered per physician per month. using this data, a laboratory section could prepare themselves for the increased utilization from a six-member internal medicine group that the beaumont reference laboratory sales force just signed up as a new client. this type of deep dive into specifi c physician specialty ordering patterns is an invaluable resource for managing a growing outreach business [ ] . the million requests for chemistry, hematology, and microbiology tests were included for all physicians in calgary, canada who ordered a test in fi scal year - [ ] . the physicians were divided into subspecialties and the average yearly cost per group and average yearly cost per physician in each of the groups was calculated. family practice and internal medicine had the greatest average yearly cost per group while hematology and nephrology had the highest average yearly cost per physician per group secondary to utilization of more expensive laboratory tests [ ] . this cost-based approach to utilization review requires the calculation of an average median cost for each test which in the usa would be much less than the price listed on the hospital's charge master. there was a synergistic relationship between the growth of beaumont reference laboratory and test mix complexity in each laboratory section. in the molecular diagnostics laboratory started in , chlamydia trachomatis (ct) nisseria gonorrhoeae (ng) were performed in urine using the ligase chain reaction in and pcr in [ , ] . more than % of the requests for these two assays are from brl clients (table . ). the increased volume of these two assays helped turn the molecular diagnostic section into a profi t center in years. annual utilization review revealed that the outreach program contributed , / , = % of the volume, hospital a ( / , = %) and hospital b ( / , = %). the multiplex assay using primarily urine specimens made a margin of $ . per assay billed (at that time) based on an average medicare reimbursement ($ . ) and cost/test of $ . . why was there an exceptionally low ng volume from hospital b? after an investigation it was learned that hospital b chose to do the less sensitive ng culture assay [ ] to retain laboratory test volume which was encouraged by their hospital administration. also, a myth existed at hospital b that ng would not survive the transport time ( - min) to hospital a. the ordering physicians at hospital b prevailed and the request for molecular detection of ng at hospital b was followed. this case illustrates just how complex problem solving in utilization management issues can be in a large community hospital. some new technologies are defi ned as disruptive innovations , when they offer new paradigms in diagnostics (table . ) [ , , ] . all seven of the technologies listed in table . share similar issues including clarifi cation of the best applications for routine clinical use, paucity of evidence-based outcome literature to review, education of practitioners and physician users of the clinical information generated and software to convert big databases the method generates into useful information. the references in table . will direct attention to these issues for the seven disruptive innovations [ - ] . as the paradigm shifts and these strategies become incorporated into daily clinical practice, the debate about appropriate utilization will diminish. this next section will devote time to describing the impact of current changes in microbiology ( mass spectrometry for bacterial identifi cation [ , , ] and multiplex molecular panels for infectious agent detection for respiratory viral panels and gastric pathogen panels) and future changes ( microscopy for antibacterial drug sensitivity). traditionally, the laboratory diagnosis of most infectious disease pathogens has relied on culturing and in vitro growth of the causative agent. once culture growth has been achieved, then automated and/or manual biochemical tests can be performed to identify the microbial organism(s). these methodologies are dependent on skilled medical technologists to perform the manual tasks required to determine the bacterial identifi cation (id). the approach to id and antimicrobial susceptibility testing (ast) has been dependent on testing a single pathogen at a time, regardless if the culture [ , ] growth yielded multiple, signifi cant pathogens. although automated id and ast systems can run multiple isolates to help streamline the workfl ow and maximize throughput, the basic testing is still individually performed for each isolate being analyzed. another limiting factor for culture based detection methods is that some bacteria do not grow well or at all in vitro adding to the potential of missing a signifi cant organism(s). viral cultures are time-consuming because cytopathic effects (cpe) must be observed before other methods can be used to determine the viral identifi cation [ - ] . the development of viral antigen based testing [direct fl uorescence antigen (dfa) and other rapid antigen testing devices] directly from the sample shortened the culture time to obtain a faster diagnosis. however, the reliable performance of the viral antigen based testing is highly dependent on the quality of the sample collected and is less sensitive than viral cultures [ ] . a suboptimal specimen could lead to a false negative antigen/dfa result. are viral cultures and antigen based testing truly needed in a clinical microbiology/virology laboratory since molecular methods are becoming the new gold standard? [ - ] . many routine clinical microbiology/ virology laboratories do not have the capabilities to perform viral cultures lacking the physical space and expertise to interpret the cpe [ ] . as technology advances, the traditionally " agrarian society " of the laboratory is becoming more industrialized with the implementation of automation, molecular based testing, and use of mass spectrometry ( maldi-tof -matrix-assisted laser desorption ionization-time of flight). many of these advances are revolutionizing how microbiology testing is performed and disrupting how traditional clinical microbiology workfl ows and processes are set up. however, all of these technological advances are shortening the time for a laboratory diagnosis and ultimately maximizing the impact to patient care and how physicians at a large community hospital will utilize the more rapid microbiology laboratory services. there is a trend in clinical microbiology to develop syndromic panels using molecular techniques. for example, positive blood culture panels have been developed to reduce time to start the most appropriate antibiotics in the patient. once a blood culture bottle is fl agged as positive, a gram stained smear is prepared to determine the presence of bacteria (and potentially yeast) in the patient's blood sample. if any organism(s) are seen, a call is made to the patient's healthcare provider so that broad-spectrum antimicrobial therapy can be initiated until the confi rmed microbiological id is resulted. a caveat for the clinician is that s/he must make their best educated guess for determining which antibiotic treatment to use. clinical microbiology laboratories typically publish an antibiogram so that clinicians and hospital pharmacists know the prevalence of susceptible and resistant phenotypes for their most common bacteria isolated. although this provides a good start and useful reference, there is a heavy emphasis on antimicrobial stewardship and tailoring therapy as soon as possible so that there is less pressure for the development of antimicrobial resistance . many institutions have developed or are in the process of developing formal antibiotic stewardship programs/committees in an effort to improve the utilization of antimicrobial treatments. molecular methods have been developed that will, within one test, identify a number of pathogens from a positive blood culture sample. these methods have decreased the amount of time to provide a more defi nitive id and an abbreviated antimicrobial resistance genetic profi le. advandx/ biomerieux, inc. utilizes pna-fish (peptide nucleic acidfl uorescent in situ hybridization) and detection of a positive fl uorescent signal directly from a positive blood culture . gram stained smear fi ndings typically are resulted as "gram positive cocci in clusters" or "gram negative rods" (table . ). this information is useful in deciding broadspectrum therapy, but a more focused therapy is the ultimate goal to ensure that the pathogen is adequately treated. the pna-fish assays offer four basic assays [ staphylococcus (gram positive), enterococcus (gram positive), gram negative, and candida ] that complements the gram stain result so that clinicians at least have a presumptive genus identifi cation. additional pna-fish probes do have the ability to separate s. aureus /coagulase-negative staphylococcus and a meca probe for the identifi cation of mrsa. use of these pna-fish assays requires a fl uorescent microscope to visualize the results. a number of studies have shown the clinical benefi ts of pna-fish implementation as part of the blood culture workup before the confi rmatory culture growth and potentially identifying methicillin resistance genotype, in the example of s. aureus , before the full antibiotic susceptibilities can be performed [ - ] . antibiotic therapy can, therefore, be tailored or deescalated as appropriate. similar to the pna-fish scenario, when utilizing cepheid's xpert mrsa/sa blood culture test the gram stained smear prepared from the positive blood culture smear will determine whether cepheid's assay should be run. cepheid's methodology is real-time pcr based and does not require any subjective interpretation of the results by the laboratory staff. the cartridge for the xpert mrsa/sa test houses all the reagents and is compartmentalized to accommodate the nucleic acid extraction, pcr amplifi cation, and detection in one device. the testing is automated once the sample is loaded into the test cartridge and the software analyzes the pcr amplifi cation curves to determine if a patient's blood sample is positive or negative for mrsa or mssa [ - ] . the cepheid and advandx tests must be added to the already existing workfl ow, and serves as another laboratory tool to more quickly determine the pathogen identifi cation and a preliminary ast profi le. nanosphere, inc. and biofire diagnostics, inc. approach testing from positive blood culture bottles by targeting the most common pathogens (bacteria or yeast) that can cause sepsis. this is a unique approach due to the overlap in patient symptoms for a specifi c syndrome or condition. when the symptoms overlap, clinicians have diffi culty defi ning the causative pathogen(s) infecting their patient solely from the clinical picture, and delaying specifi c pathogen-based therapy. use of these syndromic multiplex molecular panels streamlines the testing process to more of a "one-and-done" approach. nanosphere offers different panels: ( ) gram positive ( bc-gp panel ); ( ) gram negative ( bc-gn panel ); and ( ) yeast ( bc-y panel ) and the organism(s) observed from the gram stained smear will determine which panel(s) to run. additional testing with the gram positive and gram negative panels also includes testing for certain antibiotic resistance genes encoding for methicillin ( meca ) and vancomycin ( vana and vanb ) resistance (table . ). there are many studies showing overall good performance for the bc-gp panel [ - ] , gram negative species and candida spp. panels [ , ] . there are limitations with molecular testing as observed by buchan et al. [ ] . a positive meca target was not able to be assigned due to the presence of a mixed infection. in this case the full antibiotic sensitivity testing is still recommended because the traditional methods test each bacterial pathogen individually. beal et al. [ ] noted that when blood culture infections were caused by one pathogen, there was good performance of the multiplex molecular assays. when polymicrobial blood culture infections were noted, there was only % agreement with the routine cultures. mestas et al. [ ] also noticed a lower percentage agreement for polymicrobial infections when compared to monomicrobial infections. polymicrobial bacteremia is relatively rare, but can potentially be severe [ ] . again, cultures are still required to identify the full antibiotic susceptibility profi le, and to identify pathogens that are not included in the multiplex molecular panels. the filmarray blood culture identifi cation panel (bcid) is another comprehensive panel that covers gram positive, gram negative, and yeast pathogens (table . ) and a gram stain is not required. however, it is still good routine practice to perform the gram stain to correlate results with the molecular panel results and the eventual culture testing and antibiotic susceptibility testing. altum et al. [ ] observed that certain pathogens were detected in routine cultures that were not detected in the filmarray panel because those pathogens were not in the molecular panel. so although the comprehensive panel covers the most common pathogens, clinical intuition is still ultimately needed especially when clinical symptoms and other laboratory data point to a bacteremic process in the setting of a negative filmarray panel. overall, these assays show the potential for a decreased tat and a preliminary susceptibility profi le based on the antibiotic resistance genes tested [ , , , ] . the ability to have a more rapid answer that is technically more sensitive and specifi c will have positive downstream effects on patient care and antibiotic stewardship. the impact of these rapid pcr blood culture assays on the clinical end users (infection control, pharmacy, length of stay, and overall hospital costs) is not well defi ned. one study by bauer et al. [ ] demonstrated clinical benefi t after implementing the cepheid xpert mrsa/sa assay for positive blood cultures. a -month pre-pcr period was evaluated followed by a -month post-pcr period. there was an overall shorter length of stay ( . days shorter) and mean hospital costs were $ , less than what was observed in the pre-pcr period. infectious disease pharmacists were more effective in deescalating or changing to more specifi c antibiotic therapies compared to the pre-pcr period. benefi ts were gained by having a more rapid and sensitive test. when adopting newer molecular methods, the laboratory must work with their clinical counterparts to determine the clinical utility of a more rapid test. the cost and potential benefi ts of the newer tests may not be warranted if the clinical staff is not able to effectively utilize this information in their workfl ow. even though the downstream benefi ts have been documented and are almost inarguable from a clinical perspective, there are fi nancial and workfl ow impacts to the microbiology/molecular laboratories that implement these assays. as mentioned prior, the gram stain results from the positive blood cultures will help drive the culture workup. thus, there is the time required for a blood culture bottle to alarm as positive, and then the culture time waiting for growth on the culture plates. the use of these molecular methods must be introduced into the workfl ow and will add additional work because culture id and ast methods still must be performed. in the setting of having a continual decrease of incoming medical technologist graduates and an increasing number of laboratorians retiring, this puts the burden of additional testing on the existing staff. another example of a clinically benefi cial, but disruptive test within the laboratory is the development of respiratory pathogen panels. molecular multiplex panels have been developed to target the general syndrome of a respiratory illness. table . shows that there are a variety of fda-approved assays available with a varying number of pathogens offered within their respective multiplex assay. each assay also requires varying levels of hands-on-involvement and molecular expertise required by the medical technologist. prior to the implementation of a respiratory virus panel (rvp) in our institution, the only viral testing offered were the rapid antigen immunochromatographic devices for infl uenza a/b and respiratory syncytial virus (rsv). with the addition of offering rvp testing, we are now able to provide our clinicians with a more comprehensive answer of which virus(es) are occurring in their patient. this benefi ts transplant, immunocompromised, and oncology patients who have more frequent respiratory viral infections [ - ] . we had serendipitously brought in the rvp before the h n -infl uenza a outbreak which demonstrated the poor performance of the rapid antigen testing [ ] . because of this observation, many laboratories have discontinued their rapid antigen test offerings and now only offer molecular tests. in our laboratory, we have observed a decline in rapid infl uenza and rsa antigen testing (fig. . ) . the spike in volumes in - was related to the h n infl uenza a outbreak. we will eliminate these rapid antigen tests in favor of a rapid molecular test for infl uenza and rsv. an algorithm will refl ex a negative rapid molecular infl uenza a/b and rsv test to a more comprehensive viral and/or bacterial panel. when compared to the dfa and/or shell vial culture, a molecular multiplex respiratory virus panel saved time and lowered costs to the patient [ , ] . despite the clinical benefi ts observed, a limitation of molecular based methodologies is that they are batched and can take hours to perform in the laboratory. for example, in our laboratory the testing time is - h as compared to the -min it takes to run the rapid antigen testing. that trade off in time to result is offset by the increase in sensitivity, specifi city, and breadth of viral pathogens discovered. this can be a challenge for clinicians because many times they will want a fast answer for the purposes of triaging or taking action on a patient. however, the question that should be asked of them is whether they want a bad quality, rapid answer or a good quality, not-so-fast answer. biofire diagnostics, inc. has attempted to solve the testing time problem by offering a comprehensive respiratory pathogen panel that tests directly from the respiratory specimen. only one patient can be run on one instrument and the assay time is approximately h. there will be certain institutional settings where this technology will have benefi ts such as an urgent care clinic, smaller community hospital, or within a laboratory that has minimal molecular testing experience. however, for those institutions with a higher volume where batch testing is more optimal, the biofire may not be the best solution. there are other commercial panels that differ in the number of pathogens offered as well as various levels of medical technologist involvement (table . ). the decision to implement one of these panels is driven by a myriad of factors such as cost, workfl ow, physician demand, and the technical capabilities of the laboratory staff. whatever respiratory pathogen panel is introduced, remember that the sample testing volume is highly dependent on seasonal variations. figure . shows a graph of our volumes over two respiratory virus seasons (august through april ) with our peak volumes occurring over the winter months. this variability can have a signifi cant impact to how microbiology/molecular laboratories are staffed. physician demand, coupled with an increase in testing volumes, may be high enough to warrant increasing the number of runs per day as the staffi ng levels allow, potentially leading to an increase in employee overtime hours. interestingly during fig. . the decline in the rapid antigen infl uenza and rsv testing volumes in response to the introduction of rvp testing in conjunction with the h n /infl uenza a outbreak the respiratory virus season, amidst reports of the infl uenza vaccine having suboptimal effi cacy [ ] , we observed a large increase in rvp testing volumes compared to the prior season. thus, one factor that is virtually impossible to control is the antigenic drift/shift of the infl uenza a virus affecting the effectiveness of the current vaccine in use. assay performance may also be affected due to genetic mutations being introduced into the pcr targeted gene regions. with the limitations of culture and antigen based testing , co-infections were greatly under-appreciated for respiratory viral infections. one can expect an increased incidence of co-infections with multiplex molecular panels. figures . and . show our experiences with co-infections among pediatric and adult patients. the clinical signifi cance of these co-infections is not completely understood in relationship to modulation of disease severity [ - ] . research is needed to fully understand virus-virus and bacteria-virus co-infections and their interactions with the other pathogens present as well as the pathogen-host interactions . every respiratory virus season, our laboratory publishes a " virogram " that shows the prevalence of viruses currently circulating among the patient population (fig. . a, b ) . infectious gastrointestinal illness is another syndrome targeted by commercial vendors. as of this writing, there are a number of fda-approved assays from luminex, inc. , biofire diagnostics, inc. , becton dickinson diagnostics, inc. , nanosphere, inc. , and genprobe-prodesse (table . ) . clinicians are often unaware of what pathogens are actually included when they order a stool culture and ova & parasite (o&p) testing [ ] . similar to respiratory illness symptoms, the symptoms of an infectious gastrointestinal (gi) illness overlap also making it diffi cult to ascertain the true pathogen(s) causing the disease. the development of an infectious gi panel that targets bacterial , viral , and parasitic pathogens , provides a more effi cient approach to diagnosis compared to standard practices. the appeal to the clinical microbiology laboratory is the consolidation of culture, antigen, biochemical, and single-molecular analyte testing into one comprehensive panel. the implications to the state and public health laboratories that rely on culture isolates for epidemiological typing and characterization may not be immediately recognized when considering these molecular stool panel tests. because of the improved ability to detect a pathogen(s) with molecular methods as compared to culture, there will be scenarios when the molecular test is positive and the culture growth is negative. it is imperative that clinical laboratories communicate with their state/public health laboratory counterparts to come up with an amenable solution given that there will be discordant molecular and culture results if an isolate is required to be sent to the state/public health laboratory. similar to respiratory co-infections , gi co-infections are also an under-appreciated aspect of disease and pathogenicity. what potentially makes gi co-infections more confusing and would require some additional clinical scrutiny is that some bacteria can be colonizers (i.e., c. diffi cile ) and so the burden of determining clinical signifi cance is left to the clinician. maldi-tof is another technology that shortens the time to result for determining the microbial identifi cation of clinically signifi cant pathogens. the reader is referred to a number of reference review articles on the technology itself [ - ] . recently, maldi-tof systems have been made commercially available for use in the clinical microbiology laboratory. how this technology compares with the currently available testing (culture/biochemical and dna sequencing) is outside the scope of this chapter [ - ] . maldi-tof does outperform the conventional methods in overall accuracy and time to result. our laboratory has implemented maldi-tof as an identifi cation tool. results are available in approximately day earlier when compared to our traditional culture based testing. branda et al. [ ] found that maldi-tof reduced turn-around time by . days compared with their traditional testing. a side effect that we have observed is an increased number of calls from clinicians asking for the antimicrobial susceptibility results. these results are available the next day from our automated ast system. in addition laboratories will need to adapt their workfl ow processes when maldi-tof testing is implemented. the upfront cost of instrumentation is high (approximately $ , ), resulting in delayed implementation in some clinical microbiology laboratories. the fi nancial savings are realized in the cost per isolate of running the maldi-tof compared to the cost per isolate for a traditional work-up [ , , ] . there can be reductions in the reagent and laboratory costs when compared to culture/ biochemical methodologies [ , ] . despite the initial capital expenditure to obtain the instrumentation, there are cost-savings after maldi-tof is implemented. if the organism is not in the maldi-tof database, it will need to be confi rmed by traditional methods and/or dna sequencing . another potential limitation is that the defi nitive speciation by maldi-tof can confuse clinician end users when they see a new bacterial genus/species name that they do not readily recognize and may pose challenges in deciding what antibiotics to prescribe. this new defi nitive identifi cation is a result of technological advancements that have a greater ability to further speciate bacteria when only a genus answer may have been given with traditional techniques (i.e., coagulase-negative staphylococcus or enterobacter cloacae complexes). from the laboratory perspective, changes in nomenclature must be updated in the laboratory information system as appropriate when microorganisms undergo taxonomic reclassifi cations. future advancements with maldi-tof technology also will affect the clinical microbiology laboratory workfl ow. studies have preliminarily shown the ability to detect the pathogen directly from a patient sample (i.e., positive blood cultures [ , , ] and urines [ - ] ), bypassing the current requirement for testing on a culture isolate. however, it should be stressed that direct sample testing is in the very early stages of development. antibiotic susceptibility testing has also been examined and hrabak et al. [ ] provide an in-depth review of using maldi-tof for these purposes. interestingly, this technology has also been described in identifying the species of ticks potentially minimizing the ectoparasite experience normally required [ ] . technological advancements are focused on shortening the time of pathogen detection so that clinical action can be taken much more quickly. two relatively new companies have been working on methodologies that will further disrupt clinical microbiology practices. t biosystems, inc. has recently received fda approval for the detection of fi ve candida species ( c. albicans , c. tropicalis , c. parapsilosis , c. krusei , and c. glaboratoryrata ) direct from the patient's blood sample without prior incubation within a blood culture bottle. the t biosystems assay claims to detect these candida species within h. this technology shortens start time for appropriate candidemia treatment. patient mortality is decreased, the earlier treatment is started [ ] . having the ability to identify the particular candida species is critical since c. glaboratoryrata and c. krusei have signifi cant rates of azole resistance [ , ] . similar to the other blood culture tests mentioned above, this technology will not eliminate the need for culture/pcr and antimicrobial susceptibility testing after a blood culture bottle becomes positive. the technology allows for processing of the whole blood sample, since a thermostable mutated dna polymerase that is not affected by inhibitors in whole blood detection is used to amplify dna. detection of any pcr product is done via t magnetic resonance technology. ( www.t biosystems.com ). clinical trials data show an overall sensitivity of . % with a mean time of . h for detection and species identifi cation [ ] . the limit of other studies have demonstrated earlier detection and its effect on antimicrobial stewardship [ , ] . because this is a relatively new technology, hospitals and other healthcare institutions are currently determining the most optimal and cost effective way to utilize this technology. this test is not intended as a screening tool, but should be used in a more targeted patient population where candidemia is more signifi cant and more likely to occur. accelerate diagnostics, inc. has developed a methodology for both rapid pathogen identifi cation and antimicrobial susceptibility testing that can purportedly be performed within h ( www.accerlatediagnostics.com ). the company is conducting clinical trials on blood culture pathogen panel at the time of this writing. the technology utilizes fish dna probes to identify the panel pathogens that may be present. the antimicrobial susceptibility testing results are determined by single-cell microbiological analysis via time-lapse computerized images of the pathogen's growth characteristics in the presence of a particular antibiotic. the blood culture pathogen panel assay is intended to be the company's fi rst fda-approved assay with other sample type panels in their assay pipeline. automation in the microbiology laboratory has been a slow to make an impact unlike the other laboratory sections (i.e., chemistry, urinalysis, etc.) attributable to the inherent manual process of specimen preparation required. vendors are developing automated plate streakers for more consistent yields with culture plating. also, companies are developing automated specimen processors that can be programmed to inoculate a battery of plates. one can imagine the advantages to be gained with high volume sections of the laboratory such as urine cultures [ - ] . the implementation of microbiology automation is in its infancy and there is debate on the utility of automation and its widespread adoption. the potential is there for a large impact on the manual workfl ow and disruption of how clinical microbiology laboratories function. obviously, there is a fi nancial aspect to the implementation of automation and the estimated total cost of a total automated microbiology solution can be in the millions of dollars [ ] . it is not out of the realm of possibilities for further advancements for a total microbiology laboratory automated technological solution where clinical microbiologists may be able to function from a "virtual" bench able to work up cultures and set-ups for other downstream tests from a computer touchscreen/tablet eliminating the potential hazard of being exposed to pathogenic and/or bioterrorism organisms. the arrival of new equipment in a large community hospital laboratory, chemistry automation [ ] for example, creates a lot of stress on the staff to complete the performance verifi cation of the new quantitative analytical systems [ , ] . the practicing physician and healthcare system depend on this equipment to perform well. the assays will require verifi cation of calibration , linearity , analytic measurement ranges, accuracy, precision, appropriateness of the reference range and quality control requirements [ - ] . a variety of poct and main chemistry laboratory methods for hba c have been evaluated to see if that meets the total allowable error goal set by the cap proficiency testing program and the national glycohemoglobin standardization program (ngsp) [ - ] . "clearly, many methods, including a few poc methods, do perform well in laboratories, as seen by data from the cap proficiency surveys" [ ] , our new system was not one of those good performers. we replaced immunoassays for hba c (roche diagnostics method, siemens medical solutions diagnostics-potential new method) with a capillary electrophoresis method (sebia) [ - ] . during the evaluation of these three hba c methods, the roche immunoassay reported hba c values ( . - . %) for four patients with no hba but had hbsc. during the screening of random patients, % had homozygous or heterozygous variants [ ] . hb n-baltimore comigrates with hba c on capillary electrophoresis while hb silver spring and other hb variants did not [ ] . in this case, a method for hba c had to be quickly evaluated to replace the immunoassay originally planned for implementation to prevent repeated profi ciency testing failures and potential discontinuation of the hba c assay. an obsolete test is a test that is no longer in use or no longer useful (table . ) [ , - ] . an effective way to evaluate whether a test has become obsolete is to review it at the laboratory utilization committee that is responsible for the laboratory formulary [ ] . the formulary concept comes from the play book of the pharmacy and therapeutics committee that approve medication for use by medical providers and under what circumstances. when a newer more effective drug is fda approved it may replace an older less effective drug in the formulary. in the laboratory, the perfect obsolete test cannot be ordered by a medical provider because the reagents are no longer provided by the in vitro diagnostics industry. for example, protein bound iodine (pbi) [ ] is no longer available at any reference laboratory because the test reagents are no longer manufactured. however, t uptake is just as obsolete and useless; however, its reagents are still manufactured by many vendors and still offered by reference laboratories [ ] . in a utilization review of our hospital's send out test volume, it was asked by the reference laboratory why physicians ordered so many t uptake assays from them. i said it is not on our formulary just like ck mb [ - ] , but both of these obsolete tests and others are still ordered and performed by your reference laboratory. the response was "we offer the test because physicians order the test," however, if the reagents were not available from the manufacturer, it is unlikely the reference laboratory would develop a laboratory developed test to support obsolescence. the workaround for removal of the obsolete tests from the hospital laboratory formulary usually involves the use of an emr that has reference laboratory test ordering built for the convenience of the medical providers. if this feature is not inactivated for inpatients the hospital laboratory formulary develops a leak from which a fl ood of abuse can originate. until locally defi ned obsolete tests are universally accepted and eliminated from the test lists of hospitals, manufacturers, and reference laboratories, the discovery of ingenious work-arounds will occupy the time of the medical providers who by habit are accustomed to having the obsolete test results by their side. the utilization management of laboratory tests in a large community hospital is similar to academic and smaller community hospitals. there are numerous factors that infl uence laboratory utilization (table . ). outside infl uences like hospitals buying physician practices, increase in the placement of hospitalists and hospital consolidation will infl uence the number and complexity of test menu that will need to be monitored for over and under utilization in the central laboratory and reference laboratory. the laboratory utilization committee and laboratory formulary stewardship are key to a successful beginning. there are numerous excellent suggestions and reports of the successful implementation of remedies that have been reviewed and arranged in generic toolkits or tool boxes [ , , ] or with solutions for specifi c laboratory sections like microbiology [ , ] , toxicology [ ] , chemistry [ ] , transfusion medicine [ ] , and molecular diagnostics [ - ] . this useful approach provides a resource for the exploration of laboratory test utilization management issues and their potential resolution using a method that is successful in your local geographical environment. 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emerging and future uses for maldi-tof mass spectrometry in the clinical microbiology laboratory disposable platform provides visual and color-based point-of-care anemia self testing a smartphone dongle for diagnosis of infectious disease at the point of care new quick and cheap bedside test for cortisol uses smartphone can hospital rounds with pocket ultrasound by cardiologists reduce standard echocardiology? point-of-care ultrasound in medical education-stop listening and look defi ning digital medicine tattoo-bases non-invasive glucose monitoring: a proof-ofconcept study all-organic optoelectronic sensor for pulse oximetry bioinformatics for beginners. genes, genomes, molecular evolution, databases and analytical tools. london: academic computational solutions for omics data confi rming variants in next-generation sequencing panel testing by sanger sequencing digital imaging in pathology guideline from the college of american pathologists pathology and laboratory quality center why 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desorption ionization-time of fl ight mass spectrometry for identifi cation of clinically signifi cant bacteria that are diffi cult to identify in clinical laboratories performance and cost analysis of matrix-assisted laser desorption ionization-time of fl ight mass spectrometry for routine identifi cation of yeasts for the diagnosis of infectious diseases direct identifi cation of bacteria in positive blood cultures: comparison of two rapid methods, filmarray and mass spectrometry evaluation of three rapid diagnostic methods for direct identifi cation of microorganisms in positive blood cultures direct identifi cation of bacteria causing urinary tract infections by combining matrix-assisted laser desorption ionization-time of fl ight mass spectrometry with uf- i urine fl ow cytometry procedure for microbial identifi cation based on matrix-assisted laser desorption ionization-time of fl ight mass spectrometry from screening-positive urine samples direct identifi cation of urinary tract 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microbiology laboratory: fact of fantasy? automation in the clinical microbiology laboratory emerging technologies for the clinical microbiology laboratory laboratory automation in clinical microbiology: a quiet revolution automation in clinical bacteriology: what system to choose? the future of diagnostic bacteriology the william beaumont hospital experience with total laboratory automation verifi cation of method performance for clinical laboratories verifying performance characteristics of quantitative analytical systems satisfying regulatory and accreditation requirements for quality control three of hemoglobin a c point-of-care instruments do not meet generally accepted analytical performance criteria utilization of assay performance characteristics to estimate hemoglobin a c result reliability performance of hemoglobin a c assay methods: good enough? evaluation of the sebia capillarys fl ex piercing for the measurement of hb a c on venous and capillary blood samples effects of rare hb variants on hb a c measurements in eight methods hemoglobin a c: evaluation of methods antiquated tests within the clinical pathology laboratory requiem for a heavyweight: the demise of creatine kinase-mb creatine kinase-mg. the journey to obsolescence should the qualitative serum pregnancy test be considered obsolete? aetna clinical policy bulletin: obsolete and unreliable tests and procedures the interpretation of the serum protein-bound iodine: a review cerebrospinal fl uid myelin basic protein is frequently ordered but has little value. a test utilization study acg clinical guidelines: diagnosis and management of celiac disease laboratory formularies the laboratory test utilization management toolbox reducing unnecessary laboratory testing using health informatics applications. a case study in a tertiary care hospital effect of population-based interventions on laboratory utilization. a time series analysis utilization management in the blood transfusion service clinical requests for molecular tests. the -step evidence check improving molecular genetic test utilization through order restriction, test review, and guidance genetic counselor review of genetic test orders in a reference laboratory reduces unnecessary testing differences in brca counseling and testing practices based on ordering provider type key: cord- -yvek vjz authors: althaus, t.; thaipadungpanit, j.; greer, r.c; swe, m.m.m; dittrich, s.; peerawaranun, p.; smit, p.w; wangrangsimakul, t.; blacksell, s.; winchell, j.m.; diaz, m.h.; day, n.p.j; smithuis, f.; turner, p.; lubell, y. title: causes of fever in primary care in southeast asia and the performance of c-reactive protein in discriminating bacterial from viral pathogens date: - - journal: int j infect dis doi: . /j.ijid. . . sha: doc_id: cord_uid: yvek vjz objectives: we investigated causes of fever in the primary levels of care in southeast asia, and evaluated whether c-reactive protein (crp) could distinguish bacterial from viral pathogens. methods: blood and nasopharyngeal swab specimens were taken from children and adults with fever (> . ˚c) or history of fever (< days) in thailand and myanmar. results: of patients with at least one blood or nasopharyngeal swab specimen collected, ( . %) had a target organism detected. influenza virus type a was detected in / cases ( . %), followed by dengue virus ( cases, . %), respiratory syncytial virus ( cases, . %) and leptospira spp. ( cases, . %). clinical outcome was similar between patients with a bacterial or a viral organism, regardless of antibiotic prescription. crp was higher among patients with a bacterial organism compared to those with a viral organism (median mg/l, interquartile range [ - ] versus mg/l [≤ - ], p-value . ), with an area under the curve of . , % confidence interval ( . - . ). conclusions: serious bacterial infections requiring antibiotics are exceptions rather than the rule in the first lines of care. crp-testing could assist in ruling out such cases in settings where diagnostic uncertainty is high and routine antibiotic prescription is common. the original crp randomised-controlled trial (rct) was registered with clinicaltrials.gov, number nct . fever is a common reason for seeking healthcare in southeast asia and as malaria incidence declines, bacteria and viruses now represent the main contributors to acute febrile illness [ ] [ ] [ ] [ ] [ ] . identifying these pathogens is challenging, even in well-resourced laboratories with specialised staff, and most aetiological data for febrile illness originate in tertiary hospitals [ ] . hospitalised patients, however, are by definition more severely ill, often with important comorbidities, implying that findings may not be applicable to febrile patients attending primary levels of care. primary care in low-middle income countries (lmics) is typically characterised by a shortage in human resources, diagnostics and evidence-based guidelines [ ] . studies investigating causes of fever in this environment are few and frequently of poor quality: enrolment is often limited to a single clinical presentation and specific age category, and microbiological investigations rarely use goldstandard methods [ ] [ ] [ ] . additionally, most primary care patients attend early after symptom onset with non-severe presentations, lowering the chances of detecting a pathogen [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . empiric treatment guidelines are therefore based on limited epidemiological evidence and are often implemented by insufficient and poorly trained staff, contributing to irrational antibiotic prescription practices [ ] [ ] [ ] . high prescription levels are partly driven by frequent clinical overlap between bacterial and viral infections, challenging the identification of patients who might benefit from antibiotics [ , , ] . given these limitations in clinical judgment and laboratory structures, point-of-care testing (poct) to guide fever management could be beneficial in primary care settings [ ] . pathogen-specific tests represent one such option but several barriers undermine their potential use: these only exist for a small number of pathogens, with inconsistent performance, and most are antibody detection-based that might preclude the distinction between active infection and past-exposure [ , ] . a few antigen detection-based pocts exist but their integration in low-level care is unrealistic: a salmonella typhi rapid test requires laboratory infrastructure with poor detection in blood even at high concentrations and results are not available before - hours [ , ] ; test sensitivities for influenza virus a, respiratory syncytial virus (rsv) and group a streptococcus antigen-based pocts are inconsistent j o u r n a l p r e -p r o o f [ ] [ ] [ ] [ ] ; and accurate dengue antigen-based rdts have not been found to be cost-effective in resource-poor settings [ , ] . non-specific host biomarkers measure the host-response to stimuli, and have been evaluated in the context of fever to discriminate between bacterial and viral pathogens [ ] . c-reactive protein (crp) is one of the most studied host-response biomarkers of bacterial infection, consistently showing high sensitivity and moderate specificity, and crp pocts have been shown to be cost-effective in resource-poor environments [ , ] . however, % studies evaluating crp performance originate from high income countries [ ] . in southeast asia, these evaluations are mainly hospital-based [ ] [ ] [ ] other than a single community-based study [ ] . good diagnostic performance of crp in identifying bacterial infections was observed but generalisability was limited due to demographic, clinical and diagnostic heterogeneity of these studies. in this study, we aim to identify key organisms among acutely febrile children and adults attending primary health care in southeast asia, and to evaluate the performance of crp for discriminating between bacteria and viruses. chiang rai province is the northernmost province in thailand bordering myanmar and lao people's democratic republic. the majority of the population are thai, with approximately % ethnic minorities and hill-tribes. the six participating primary care sites were located within a -kilometre radius of chiang rai city centre, covering rural and peri-urban as well as mountainous and plateau areas. hlaing tha yar, lower myanmar, is a peri-urban township on the west side of yangon. the township has the highest rates of diseases related to hygiene and environmental conditions (e.g. diarrhoea, dysentery, and tuberculosis) in yangon [ ] . four sites were included: three primary care clinics and one outpatient department from a public governmental hospital. both chiang rai and hlaing tha yar are defined by a tropical climate. specimens were collected from febrile patients recruited into a previously described multi-centre randomised-controlled trial evaluating the impact of c-reactive protein (crp) testing on antibiotic prescription in primary care [ ] . febrile children and adults (defined as ≥ years of age) were recruited between june and august . inclusion criteria were age ≥ year with a documented fever (defined as a tympanic temperature > . ˚c) or a chief complaint of acute fever (< days), regardless of previous antibiotic intake and co-morbidities other than malignancies. exclusion criteria were symptoms requiring hospital referral defined as either impaired consciousness; inability to take oral medication or convulsions; a positive malaria test; the main complaint being trauma and/or injury; suspicion of either tuberculosis, urinary tract infection, local skin infection or dental abscess; any symptom present for more than days; any bleeding; and inability to comply with the follow-up visit at day . on the day of enrolment, all patients had demographic information collected and underwent a routine clinical examination including vital signs (blood pressure, pulse, respiratory rate, temperature). patients were followed-up after their enrolment both at day and day . of the , febrile children and adults recruited, were randomly allocated to the control group with blood specimens collected for off-site crp testing (as compared with the intervention groups that had crp tests performed on-site). details are illustrated in figure . antibiotics were prescribed to this group according to routine clinical practice, clinicians were not informed of the crp results or any aetiological findings. in case of co-detection in blood and np swabs, target organisms detected in blood were assumed to be the primary cause of illness. bacterial and viral aetiological groups included all cases where any bacteria or viruses were detected in blood, respectively, and only target viruses and bacteria detected in np swabs. we described organism distribution among children and adults (defined as ≥ years of age) separately. descriptive analysis for continuous variables with normal distribution used means and standard deviations (sd) and medians with inter-quartile ranges (iqr) for non-normally distributed continuous variables. comparison between groups used t-tests for normally distributed variables, the mann-whitney test for non-normally distributed variables, and chi-squared test for categorical variables. crp values were compared across aetiological groups and clinical syndrome using the mann-whitney u test for two-group comparisons and the kruskal-wallis test for multi-group comparisons. non-parametric receiver operating characteristic (roc) curves were plotted and the wald test was used to compare areas under the curve. covariates included the following factors: patient age and prior use of antibiotics. diagnostic accuracy was assessed by calculating the areas under the roc j o u r n a l p r e -p r o o f curves (auc). an auc of > . was considered excellent; . - . , very good; . - . , good; . - . , average; < . , poor [ , ] . sensitivity, specificity, and percentage of correctly classified cases were also assessed for the two crp cut-off points used in the original trial: mg/l and mg/l and these were compared with the accuracy of routine prescribing practice [ ] . data analyses were performed with stata version (college station, texas, usa). the protocol, informed consent form and case record forms were reviewed and approved by the of the patients prospectively enrolled and randomised into the trial control group, ( . %) had at least one blood or np swab specimen collected, including ( . %) children and adults ( . %). out of these patients, had only a np swab and no blood collected, while had only a blood specimen collected without a np swab. among these patients, had a blood specimen obtained on a dried blood spot (dbs). as shown in table , children presented significantly earlier after symptom onset than adults, with fewer comorbidities and less self-reported medication (p < . ). antibiotic intake declaration was similar in children and adults (p = . ). page of j o u r n a l p r e -p r o o f clinically, respiratory syndrome was the most prevalent presentation both in children and adults. within patients with a respiratory syndrome, the most frequent symptoms were localised in the upper respiratory tract including common cold, diagnosed in . % ( / ) of children and . % ( / ) of adults (p = . ). gastrointestinal syndrome was the second most prevalent presentation, and there were no differences between children and adults. blood specimens tested for bacterial screening, using taqman array card (n= ) and bacterial singleplex polymerase chain reaction (n= ) ** blood specimens tested for leptospira screening, using the taqman array card (n= ), the bacterial singleplex polymerase chain reaction (n= ) and the microagglutination test (n= ) *** blood specimens tested for orientia tsutsugamushi and rickettsia spp. screening, using taqman array card (n= ), the bacterial singleplex polymerase chain reaction (n= ), and the indirect immmunofluoresence assay (n= ) **** blood specimens tested using the taqman array card only (n= ) ***** blood specimens tested for dengue, chikungunya and zika virus screening, using taqman array card (n= ), the viral singleplex polymerase chain reaction on fresh blood (n= ) and dried blood spot (n= ) no evidence for a difference in antibiotic prescription was observed between the bacterial and viral groups at day , and clinical outcomes were also not significantly different between the two groups (table ). outcome characteristics by aetiological group in chiang rai, northern thailand and hlaing tha yar, lower myanmar, - . the prescription of antibiotics at the facility was considered between the enrolment at day until day of the follow-up severity was ranked from - with severity= as the less severe presentation crp: c-reactive protein elevated crp defined as ≥ mg/l in children and ≥ mg/l in adults sae: serious adverse event, defined as admission to hospital or death within days of enrolment broad-spectrum antibiotics include ceftriaxone, cefixime, ciprofloxacin, levofloxacin, azithromycin, and amoxicillin with clavulanic acid. among patients with a bacterial organism, two-thirds did not receive any antibiotic ( occurrence of sae, n (%) ( ) ( ) . unscheduled visits, n (%) ( ) ( . ) . antibiotic. no evidence for a difference in clinical outcomes was observed after days of follow-up, regardless of whether an antibiotic was prescribed. of we investigated the spectrum of organisms among febrile children and adults in the community and evaluated the performance of crp in distinguishing bacteria from viruses including its potential impact on antibiotic prescription compared with current practice. patients were recruited prospectively across ten sites in thailand and myanmar including urban, semi-urban and rural areas spanning over a full calendar year. in our study, leptospira spp., influenza virus and dengue virus were the leading organisms identified, which is consistent with previous reports in the region [ , ] . the broad inclusion criteria, allowing for enrolment of all patients over year old regardless of previous antibiotic intake, comorbidities, or clinical presentation, make our findings more generalisable than previous studies. investigating non-malarial acute febrile illness remains challenging in resource-poor areas [ ] , and despite screening for multiple organisms on blood and respiratory specimens, we were only able to identify a probable cause of fever in ( . %) of patients. this low detection may be explained by the inclusion of only non-severe outpatients [ , , ] , while other studies in southeast asia recruiting more severe and hospitalised patients identified an organism in around % of cases [ ] [ ] [ ] ] . only . % ( / ) of organisms detected were bacteria, which may be explained by the lower risk of bacterial infections in non-severely ill patients, and where present, characterised by lower bacterial loads [ ] . most bacteria were identified using a singleplex pcr and not the tac assay, while viruses were equally detected by these two molecular methods. this lower sensitivity in the tac assay for the detection of bacteria has been described in previous studies using multi-pathogen molecular detection platforms [ , ] . the trade-off between advantages for screening multiple organisms at the same time with a simplified molecular platform should be weighed against potentially lower sensitivity, especially for bacteria such as o. tsutsugamushi or leptospira spp., which are considered important drivers of acute febrile illness in southeast asia [ , ] . the tac assay to identify infections among neonates in south asia, but detected the presence of certain organisms among both controls and cases [ ] . a multi-country study into causes of severe pneumonia also excluded molecular assay results positive for k. pneumoniae because of poor assay specificity [ ] . furthermore, most of our patients presented with low crp regardless of whether a bacterial or viral organism was detected, and recovered regardless of whether an antibiotic was prescribed. it is likely that invasive bacterial infections requiring an antibiotic are exceptions while most primary care patients present with a self-limiting infection [ ] . other primary care-based studies have recently supported restriction of antibiotic prescription to a small minority of patients: in tanzania, a clinical trial using a mg/l threshold lowered antibiotic reduction to . % without affecting outcomes, while a u.s. study concluded that % of outpatients attending a general practice for a respiratory presentation should not even require a medical consultation, let alone an antibiotic prescription [ , ] . strategies whereby testing for crp as a predictor of clinical outcome rather than determining aetiology have been evaluated in primary care: a cluster-randomised controlled trial in belgium showed crp to rule-out serious infection using a mg/l threshold, while a systematic review found crp-testing to be useful in identifying serious infections among febrile children [ , ] . in our study, crp performance in distinguishing bacteria from viruses was average (auc . ) and lower than another study from the region which found (auc . among , patients with a microbiologically-confirmed diagnosis from thailand, cambodia and lao pdr [ ] our study has several limitations, mostly relating to the limited scope and accuracy of the reference diagnostic tests, and the impact of even slightly less than perfect "gold-standard" reference tests on the evaluation of new diagnostic and biomarker tests can be profound [ , ] . as mentioned above, the sensitivity and specificity of the multiplex tac assay was not optimal for bacteria detection, and the absence of convalescence specimens impeded our ability to diagnose patients based on serology, particularly with respect to bacterial zoonoses. even genuine detection of bacterial and viral dna in normally sterile sites cannot be used to conclusively determine causality, as this has been reported among healthy individuals, and in patients even weeks after recovery from infections, challenging the interpretation of molecular assays [ , ] . blood culture was not available and this further limited our aetiological investigation. we did not recruit a concomitant control group, which precludes robust attribution of causality in the organisms we detected, particularly in np swabs. in a paediatric study in asia and africa, the inclusion of controls matched with pneumonia cases weakened the evidence of causality for almost all organisms detected [ ] , and only rsv, hmpv, influenza virus a and b, parainfluenza virus type and b. pertussis were considered pathogenic, consistent with other lmicbased studies [ , ] . these organisms, however, are sometimes present in healthy individuals, with a prevalence of influenza virus among healthy children between - %, rsv at - % and hmpv between - % [ ] . on the other hand, we did not regard other organisms detected in np swabs such as rhinovirus, parainfluenza virus or s. pneumoniae as pathogenic, because these are commonly detected among healthy individuals [ , , ] . all these limitations in reference diagnostic tests might explain the average performance of crp in our analysis. we presented the key organisms detected among febrile children and adults attending primary healthcare in southeast asia. the performance of crp in distinguishing between bacterial and viral organisms was limited, although the current findings suggest that crp-guided treatment would increase the appropriate use of antibiotics with respect to aetiology. this is supported by the overall reduction in prescribing compared with current practice demonstrated in the original trial. our findings also support conclusions from previous studies that even in the presence of bacterial organisms, very few ambulatory patients are likely to benefit from the extensive and 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global epidemiology of scrub typhus. plos neglected tropical diseases the importance of leptospirosis in southeast asia. the american journal of tropical medicine and hygiene causes and incidence of community-acquired serious infections among young children in south asia (anisa): an observational cohort study causes of severe pneumonia requiring hospital admission in children without hiv infection from africa and asia: the perch multi-country case-control study. the lancet. . . van den bruel a safety and efficacy of c-reactive protein-guided antibiotic use to treat acute respiratory infections in tanzanian children: a planned subgroup analysis of a randomized controlled noninferiority trial evaluating a novel electronic clinical decision algorithm (epoct) necessity of office visits for acute respiratory infections in primary care diagnostic value of laboratory tests in identifying serious infections in febrile children: systematic review point-of-care c-reactive protein testing to reduce inappropriate use of antibiotics for non-severe acute respiratory infections in vietnamese primary health care: a randomised controlled trial the effect of uncertainty in patient classification on diagnostic performance estimations imperfect gold standards for biomarker evaluation van der pol b. duration of polymerase chain reaction-detectable dna after treatment of chlamydia trachomatis, neisseria gonorrhoeae, and trichomonas vaginalis infections in women. sexually transmitted diseases detection of the latent form of epstein-barr virus dna in the peripheral blood of healthy individuals microorganisms associated with pneumonia in children< years of age in developing and emerging countries: the gabriel pneumonia multicenter, prospective, case-control study the role of influenza, rsv and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high hiv sero-prevalence viral and bacterial interactions in the upper respiratory tract frequent detection of respiratory viruses without symptoms: toward defining clinically relevant cutoff values asymptomatic shedding of respiratory virus among an ambulatory population across seasons. msphere we thank all primary care patients and health workers from chiang rai primary care centres and hlaing tha yar public hospital and mam clinics for taking part in the study. we are very grateful to the study staff and to the clinical trial support group at mahidol-oxford tropical medicineresearch unit for ensuring the successful completion of the study. we thank heiman wertheim, arjen dondorp, direk limmathurotsakul, christopher parry, and paul newton for guidance on the study design; clare ling, toni whistler, ampai tanganuchitcharncha, areerat thaiprakhong, nattapon pinthong, prapaporn srilohasin and kyaw soe for laboratory support, as well as duangjai suwancharoen from the national institute for animal health (niah) for carrying out the leptospira mat. finally, we thank elizabeth ashley, jeroen bok, joshua cohen, ni ni tun, and khin yupar soe for their assistance in study site coordination. key: cord- -ybfxtc x authors: van doorne, hans; roesti, david; staerk, alexandra title: microbiology date: - - journal: practical pharmaceutics doi: . / - - - - _ sha: doc_id: cord_uid: ybfxtc x microbial contamination of pharmaceutical preparations may cause health hazard to the patient (e.g. infection, pyrogenic or allergic reaction), altered therapeutic activity of the product, or other decrease in quality (turbidity, loss of consistency, altered ph). this chapter provides a general introduction on pharmaceutical microbiology by focusing on the essential properties of micro-organisms. first of all the basic characteristics of life and the types of biological contaminants and potentially infectious agents of pharmaceutical products will be discussed: viz. prions, viruses, mollicutes, bacteria, fungi, and endotoxins. in the next section factors affecting survival and growth of micro-organisms are discussed. in addition to well-known factors such as time, temperature, and chemical and physical characteristics of the environment, attention will be paid to biofilm formation. primary microbiological contamination is prevented by implementing an adequate microbiological quality control and quality assurance program and by following cgmps during production. microbiological quality control of pharmaceutical preparations and monitoring of production areas depend on the detection and quantification of micro-organisms. the classical, growth based, methods and some of the commercially available alternative methods are discussed. understanding essential microbiological concepts is necessary in designing both microbiologically stable pharmaceutical products and ensuring an effective quality control and monitoring program within the manufacturing or preparation facility. although there is no universal definition of life, scientists generally agree that living systems share all or at least the characteristics: organisation, interaction with the environment, adaptation, metabolism, growth, motility and communication. organisms are composed of one or more cells, which are the basic units of life. each cell must be highly organised because growth and multiplication can only occur when the individual biochemical processes are synchronised. in higher organisms, organisation within the organs, and communication with other organs are essential for the normal functioning of the body. cells respond to chemical and physical input from the environment. a response is often expressed by motion. chemotaxis, the movement of a cell in response to a concentration gradient of a substance, is an example of such an interaction. adaptation is the accommodation of a living organism to its environment. it is fundamental to the process of evolution, by which cells change their characteristics and transmit these new properties to their offspring. metabolism involves the uptake of nutrients from the environment, their conversion to energy (adenosine triphosphate: atp) and cellular components, and the deposition of waste products (e.g. carbon dioxide: co ) or metabolites (e.g. toxins or antibiotics) into the environment. living things require energy to maintain internal organisation (homeostasis) and to produce the other phenomena associated with life. growth is the increase in biomass. a growing individual increases up to a point in size in all of its parts. reproduction is the result of a series of biochemical events that result in the production of a new individual (asexually, from a single parent organism, or sexually, from at least two differing parent organisms). in microbiology growth is often used as a synonym for reproduction. dormancy is a state of decreased metabolic activity in which there is no growth, i.e. no increase in biomass. it may be a dynamic state in which the number of newly formed cells balances the number of dying cells. the duration of this period is relatively short (hours, days). dormancy of bacterial spores may continue for considerably longer periods of time. many cells and organisms can move under their own power. movement to a new location may offer the cell new resources. motility however is not a characteristic of all living organisms. animals are typically motile, whereas plants are non-motile. in micro-organisms motility is dependent on the type of organism and sometimes even on the stage of the life cycle the cells have reached. throughout evolution humans and animals have developed a multitude of ways for communication. micro-organisms (bacteria, yeasts and moulds) can communicate through a process called quorum sensing. quorum sensing is the regulation of gene expression in response to fluctuations in cellpopulation density. quorum sensing exemplifies interactive social behaviour innate to the microbial world that controls features such as virulence, biofilm formation, antibiotic resistance, swarming motility, and sporulation [ , ] . in gram-negative bacteria, small molecules (e.g. acyl homoserine lactone (alh) [ ] ) serve as signals to recognise microbial cell population size. when a signal exceeds some threshold concentration the expression of specific genes is changed [ ] . if a microbial cell is introduced into a pharmaceutical preparation or onto a surface it will sense whether suitable conditions (nutrients, moisture, etc.) for growth are available (interaction with the environment). if possible the cell will adapt to its new habitat, and start to metabolise the available nutrients. eventually growth will take place. motility of individual cells will facilitate colonisation of other sites. production of toxins (in case of a pathogen) is a demanding biochemical process and will occur only when quorum sensing indicates that a sufficiently large population has developed. thus the interplay between all these characteristics determine whether a cell will be able to grow in a specific product, or on a surface. survival and growth of micro-organisms in pharmaceutical preparations is governed by extrinsic factors (particularly temperature) and intrinsic factors (product composition and physico-chemical characteristics). the combination of intrinsic and extrinsic factors will determine the types and number of micro-organisms that will develop in a product or on a surface. temperature has a strong influence on whether an organism can survive or thrive. temperature exerts its influence indirectly through water (which has to be in the liquid state), and directly through its influence on the organic molecules composing the living cells. mesophilic organisms are widespread in nature. they have the potential to grow in a temperature range of roughly - c. at temperatures above c some contaminants of water and air including different types of bacteria and moulds will fail to grow or grow more slowly. the optimum growth temperature for pathogenic bacteria is around c with an upper range from c to c. legionella pneumophila (l. pneumophila) is an exception; it will grow at temperatures up to c. geobacillus stearothermophilus is a thermophile and grows at temperatures between c and c. it is used as a test organism (biological indicator) to verify the efficacy of moist heat sterilisation processes. for reasons of chemical stability some preparations must be stored frozen. under these conditions (no liquid water) microbial growth is not possible. however, the majority of the preparations are either stored refrigerated ( - c) or at room temperature ( - c) , which will allow growth of most mesophilic micro-organisms. according to european good manufacturing practice (eu-gmp) regulations water for injection (wfi) should be produced, stored and distributed in a manner which prevents microbial growth, for example by constant circulation at a temperature above c (see also sect. . . ). the presence of water is essential to every form of life including micro-organisms. in the late s, it was recognised that water activity (or a w ), as opposed to water content, was the more significant factor in studying the relationship of water to microbial growth. the a w value is defined as the proportion between the water vapour pressure of the product and the vapour pressure of pure water at a common temperature. lowering the water content has historically been a convenient method to protect foods from microbial spoilage. examples where the available moisture is reduced are dried fruits, syrups, and pickled meats and vegetables. low water activity will also prevent microbial growth within pharmaceutical preparations, see also sect. . . . water activity values supporting microbial growth of a number of representative micro-organisms are provided in the usp [ ] . that chapter also suggests a strategy for microbial limit testing based on water activity. pharmaceutical cleaning operations usually involve a final rinse with water of suitable pharmaceutical quality. to prevent microbial growth, it is essential to dry the object as soon as possible after rinsing. although water is essential for microbial growth, a low a w value does not necessarily lead to cell death. for instance, some dry raw materials, especially those of natural origin, may be heavily contaminated with both endospores and vegetative cells. freeze drying in a suitable medium, for instance, is an excellent way to preserve pure cultures of viable micro-organisms. a water activity below . does not enable micro-organisms to grow. solid oral dosage forms such as tablets have in general an a w value lower than . which means that these products remain stable from a microbiological point of view over long periods of time if the product is stored in a waterproof blister that remains integral. micro-organisms require for their growth suitable nutrient sources of elements (e.g. c, h, o, p, s, n), minerals (e.g. na + , ca + , mg + ) and trace elements (e.g. cu + , mn + , co + ). even in a relatively nutritionally poor medium such as distilled water, the number of micro-organisms may be as high as - colony forming units (cfu)/ml, indicating that nutrients are present in sufficient quantity to allow proliferation of water-borne bacteria such as the pseudomonads. the presence of readily assimilated substances such as sugars or polyalcohols in dosage forms such as creams or syrups can lead to an increased probability of microbial adulteration of those products. a ph range of - does not exert any discernible selective influence on growth of pharmaceutically relevant types of organisms. below ph , growth of many bacteria will start to be inhibited. pathogenic and toxinogenic bacteria generally will not grow at ph values below . , but they may survive long times of immersion in weakly acidic solutions. yeasts and moulds unlike bacteria, generally tolerate acidic media quite well. optimum ph of most fungi is about ph . at more alkaline conditions, pseudomonads will predominate. for example, ps. aeruginosa is known to grow at a ph range of - . microbes are classified as aerobes or anaerobes. this is now defined in terms of oxidation-reduction potential (e h ). generally, the range at which different micro-organisms can grow are as follows: aerobes + to + mv; facultative anaerobes + to À mv; and anaerobes + to less than À mv. the redox potential of a normal aerobic nutrient medium is about + mv. thioglycolate medium, which is used for growth of anaerobic bacteria has an e h of about À mv. for reasons of chemical stability, the redox potential of some pharmaceutical preparations is kept at a low level by means of reducing agents such as sulfite, tocopherol or ascorbic acid. the effect of a reduced redox potential on the microbial flora of such preparations has never been studied. the number and types of micro-organisms that may develop in various pharmaceutical dosage forms is greatly influenced by the presence of substances with antimicrobial properties. antimicrobial active substances can be divided into three groups, as follows: • the first group consists of substances used for therapeutic or preventive antimicrobial purposes, for example: antibiotics, chemotherapeutics, and disinfectants. • the second group consists of preservatives (see sect. . ), used to guarantee the microbiological quality of the product throughout its shelf life. for example: esters of hydroxybenzoic acid, quaternary ammonium substances and sorbic acid are widely used in pharmaceutical and cosmetic preparations. other preservatives that are used include phenol, chlorhexidine, benzoic acid and benzyl alcohol. • the third group consists of excipients with 'collateral' antimicrobial activity that are principally added to dosage forms for reasons unrelated to their (sometimes weak) antimicrobial activity. for example, sodium lauryl sulfate is known to inactivate some gram-positive bacteria. similarly, edetate has weak antimicrobial activity, and it confers synergistic antimicrobial properties when combined with quaternary ammonium substances. in the term 'prion diseases' refers to a group of neurodegenerative disorders. these include scrapie (in sheep and goat), kuru (prion disease endemic amongst cannibalistic tribes in papua new guinea), bovine spongiform encephalopathy (in cattle) and creutzfeldt-jakob disease (cjd) (in humans) [ ] . prion diseases are characterised by long incubation periods ranging from months to years and are invariably fatal once clinical symptoms have appeared. in all prion diseases the infectious prions are generated in the brain of the afflicted animal. in the rare cases of interspecies transmission, such as from cattle to humans a 'template assisted replication' takes place. this means that the prions that replicate in the human brain have the amino acid sequence encoded by the dna of the host (human being) and not the sequence of the donor animal [ ] . of pharmaceutical preparations bse was first diagnosed in the united kingdom in and a large number of cattle and individual herds have been affected. interspecies tse transmission is restricted by a number of natural barriers, transmissibility being affected by the species of origin, the prion strain, dose, and route of exposure. transmission of scrapie to sheep and goats occurred following use of a formol-inactivated vaccine against contagious agalactia, prepared with brain and mammary gland homogenates of sheep infected with mycoplasma agalactiae [ ] . iatrogenic transmission of human prion disease can occur through medical or surgical procedures. an example is the injection of hormones such as gonadotropins extracted from cadaver pituitaries. current evidence indicates that, with respect to the risk of tse infection, urinary-derived gonadotrophins appear to be safe [ ] . the risks of urinederived fertility products could now outweigh their benefits, particularly considering the availability of recombinant products [ ] . cases of cjd have also been attributed to the use of contaminated instruments in brain surgery and with the transplantation of human dura mater and cornea [ ] . suppliers of materials may minimise the risks of contamination of tse by ensuring [ ] : • the source animals and their geographical origin • nature of animal material used in manufacture and any procedures in place to avoid cross-contamination with higher risk materials • production process(es) including the quality control and quality assurance system in place to ensure product consistency and traceability manufacturers of pharmaceutical preparations select their raw materials so they are tse free (see also sect. . . ). this can be ensured either by purchasing materials from non-animal origin or from non-tse relevant animal species (e.g. porcine instead of bovine). if material from tse-relevant animal species is purchased, it should be delivered with a certificate that confirms it free of tse. regular audits verifying this assumption should be performed by the manufacturer at the material's supplier manufacturing site. prions, unlike the normal prp c proteins, are very resistant to inactivation. the only methods that appear to be completely effective under worst-case conditions are strong sodium hypochlorite solutions or hot solutions of sodium hydroxide [ , ] . some cross contamination can be avoided by the use of disposable instruments, e.g. in tonsillectomy [ ] . a virus is a non-cellular genetic element, which is dependent on a suitable host cell for its multiplication. their size generally ranges from to nm. it has been argued extensively whether viruses are living organisms. the majority of virologists consider them as non-living as they lack many of the characteristics of life, such as independent metabolism. viruses exist in various states throughout their life cycle. in the extracellular state a virus particle is called a virion. virions are composed of a core of genetic material, which can either be in the form of dna or ribonucleic acid (rna), and a protein coat or capsid. in some viruses (enveloped viruses) the capsid is surrounded by a lipid bilayer membrane. attached to these membranes are specific proteins, which may play a role in the attachment of the virion to the host cell, or release from the host. thus, haemagglutinin and neuraminidase are two important enzymes present in the envelope of the influenza virus. the virions are metabolically inactive because they are devoid of a self-generating energy system, transfer rna, ribosomes, and so forth. many viruses do contain enzymes that become essential in rendering these agents infectious to susceptible hosts. viruses are obligate intracellular parasites. replication occurs only inside the cell of a suitable host. replication usually leads to destruction of the host cell. sometimes the viral dna is incorporated into the genetic material of the host. this principle is successfully used in genetic engineering, where viruses are used as vectors to incorporate a new gene in a cell. viruses are causative agents of many human, animal, and plant diseases. aids, sars, and avian flu are viral diseases, which are nearly daily covered by the headlines in papers and by the news items on radio and television. in - a 'spanish flu' pandemic killed over million people. the virus involved was most probably a mutation of some avian virus. the avian flu pandemic (caused by the h n variant) was, by comparison very small, as it has caused 'only' about fatalities. the great concern for virologists and epidemiologists is the extremely high mortality rate (over %) of infections with this virus. in the form of vaccines, viruses are inactivated or attenuated so as to prevent diseases in susceptible populations. the baltimore classification is the preferred way of classifying viruses. viruses are grouped into families depending on their type of genome (dna, rna, singlestranded (ss), double-stranded (ds) etc.) and their method of replication. a series of important medicines is derived from animal or human sources and may potentially be contaminated with undesired virus particles. such medicines include: • coagulation factors, immunoglobulins and albumin from human blood plasma • vaccines and monoclonal antibodies from cell cultures • proteins from cells altered by genetic engineering • homoeopathic preparations of animal origin vaccination is one of the most important public health accomplishments. however, since vaccine preparation involves the use of materials of biological origin, such as chinese hamster ovary cells, vaccines are susceptible to contamination by micro-organisms, including viruses [ ] [ ] [ ] . several cases of viral vaccine contamination have been reported. for example, human vaccines against poliomyelitis were found to be contaminated with sv virus from the use of monkey primary renal cells. several veterinary vaccines have been contaminated by pestiviruses from foetal calf serum [ ] . in the detection of fragments of a porcine circovirus was the reason for a temporary withdrawal of some commercial vaccines from the spanish market [ ] . several methods are being used or in development to reduce infectivity of blood products, including solventdetergent processing of plasma and nucleic acid crosslinking via photochemical reactions with methylene blue, riboflavin, psoralen and alkylating agents. several opportunities exist to further improve blood safety through advances in infectious disease screening and pathogen inactivation methods [ , ] . one potential way to increase the safety of therapeutic biological products is the use of a virusretentive filter [ ] . plasma pools may be submitted to serological tests and/or genome amplification assays before they are released for further fractionation [ ] . multidose containers and the environment were found to be the source of a number of nosocomial viral infections [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . presence of viruses in pharmaceutical preparations may be verified by performing either in vivo tests by inoculating the product directly in animals (e.g. rabbits, mice) or in-vitro tests such as polymerase chain reaction (pcr) or cell culture safety tests. along with the archea, bacteria belong to the prokaryotic organisms, i.e. cells that do not possess a real nucleus and that reproduce asexually. they are unicellular microorganisms with a size in general ranging from . to μm. their extraordinary diversity in terms of biochemical processes and metabolic characteristics enable bacteria to adapt themselves to a large variety of environments. indeed, some species have the capacity to grow in anaerobic (absence of free oxygen in the air) environments by using other electron acceptors than oxygen, such as sulphates or nitrates or by fermentation. other species may use energy and carbon sources for growth from not only organic substances but also from carbon dioxide and light energy. for this reason, bacteria have colonised most habitats on earth (soil, water, animals, plants) and even the most extreme environments such as deep-sea fumaroles or geysers. another fascinating (but critical in terms of product safety) characteristic of bacteria is their capacity to grow extremely fast if the environmental conditions in terms of nutrient availability, moisture and temperature become favourable. during growth, an individual cells first increases in size and then the cell is divided in two parts (binary fission). in nutrient media, bacteria follow four growth phases (see fig. . ). the first is the lag phase, during which the bacteria adapt to their new environment by repairing damaged structures and synthesising enzymes to catabolise nutrients in the medium. the second phase, the most spectacular, is the exponential phase during which nutrients in the medium are metabolised rapidly leading to a rapid doubling of the population of bacterial cells. the population of escherichia coli cells under optimal growth conditions can multiply each min. this would mean that after h the population would reach one million cells and after h, the volume of cells produced would be equivalent to the volume of planet earth! once nutrients start to deplete, the exponential growth is slowed down and the amounts of cells in the overall population remains stable; this is the third phase called the stationary phase. in this phase, secondary metabolites such as antibiotics are produced in higher quantities. the last phase is when no more nutrients are available and the amount of bacterial cells starts to drop. in the human microflora, there are at least times more bacterial cells than human cells and most of them are harmless. human bacterial infections are mainly caused by strict pathogenic species (less than % of bacterial species) or by opportunistic pathogens when the immune system of the person is depleted. bacteria may cause a large variety of infections, the most common being food poisoning, pneumonia, skin infection, urinary tract infection, throat and mouth infection, meningitis, eye infection. depending on the infectious agent, the minimum amount of microorganisms provoking an infectious dose varies greatly. for instance in some cases, only cells of shigella dysentriae need to be ingested to provoke dysentry but at least a , cells of vibrio cholera to provoke cholera [ ] . mollicutes, also known under the trivial name mycoplasmas, are the smallest free-living prokaryotic organisms and for years were thought to be viruses because they passed through the usual bacterial filters. they resemble protoplasts, because they lack a cell wall, but they are relatively resistant to osmotic lysis due to the presence of sterols in the cell membrane. in this respect the mycoplasmas form an exceptional group, because sterols are absent in other prokaryotic cells. mycoplasmas are widespread in nature and many are animal, plant or human pathogens. most mycoplasmas that infect humans are extracellular parasites. examples of human pathogenic mycoplasmas are mycoplasma pneumonia (infections of upper respiratory tract), and mycoplasma genitalium (nongonococcal urethritis) [ ] . mycoplasma contamination is a major concern for vaccine and biotechnological industries since the organisms may cause disease and may interfere with cell culture [ ] . peptones, and animal sera used as components of cell culture media may be sources of this contamination [ , ] . mycoplasmas can be cultured in liquid or on solid media. however, in contrast with other bacteria, their growth is slow, and a microbiological assay as described in the ph. eur. is time-consuming (at least days). alternative, rapid methods, based on nucleic acid technologies such as pcr, have been developed [ , ] . under certain conditions these methods may be used as an alternative method instead of the official, growth based method [ ] . bacteria may be composed of the following structural elements (see fig. bacteria become motile by means of flagella [ ] . bacterial flagella are protein threads which originate in a defined region of the cytoplasmic membrane and protrude through the peptidoglycan layer and the outer membrane. the number of flagella per cell and their position depends on the species. pseudomonas aeruginosa (ps. aeruginosa) has only one (polar) flagellum at the tip of the cell, whereas escherichia coli (e. coli) has numerous flagella spread over the entire cell surface (peritrichous). flagella may play an important role in pathogenicity [ , ] . the surface of cells of some bacterial species is covered with many ( to several thousands), thin ( - nm), and long (up to μm) threads called pili, or fimbriae. they play a role in the initial adhesion of bacteria to host tissues and inanimate surfaces [ , ] . attachment to a surface is the first step in biofilm formation. upon attachment on tissue cells they may trigger a number of biochemical signals from the host, which ultimately leads to the bacterial disease [ ] . capsules and slime layers -collectively called glycocalixconsist of source polysaccharide material secreted by the cell. a capsule is a rigid structure, whereas a slime layer, or loose extracellular slime, is more flexible, with diffuse boundaries. the glycocalix has several functions. it is involved in cell attachment and it may protect cells from being digested, a phenomenon known as phagocytosis. whilst encapsulated strains of streptococcus pneumoniae are highly pathogenic, non-encapsulated mutants are completely avirulent [ , ] . dextran, a slime layer product of leuconostoc mesenteroides of relatively low molecular weight can be used as a therapeutic agent in restoring blood volume [ ] . the outer surface of the bacterial cell plays an important role in the adhesion of the cell to various surfaces. in addition to the factors that have been discussed, adhesion may also be mediated by so-called surface-associated adherence factors, usually designated as adhesins. adhesion, which is the first step in a series of events leading to colonisation, biofilm formation and ultimately infection, is a specific process in which the adhesin "recognises" a receptor on the host surface. this specificity explains why micro-organisms such as influenza or mycobacterium tuberculosis can cause targeted infection of the respiratory tract but otherwise are relatively harmless when contacting other host tissues. the cell wall gives the cell its shape and strength. the cell wall must resist the internal osmotic pressure of the cell that is estimated to be about bar. the composition of cell walls of gram-positive bacteria is very different from those that stain gram-negative. peptidoglycan is the common cell wall component of bacteria (excluding mollicutes) and gives the wall its shape and strength. it is a polymer consisting of a backbone of alternating n-acetylglucosamine and n-acetylmuramic acid residues, cross-linked with small peptide bridges. peptidoglycan accounts for about - % of the wall of grampositive bacteria and for about % of the gram-negative cell wall. the gram-negative cell wall contains only a shallow peptidoglycan layer. on the outer side of this layer is the outer membrane, a complex structure consisting of four major components: phospholipids, lipopolysaccharide, proteins (e.g., porins), and lipoprotein. lipolysaccharide (endotoxin) is responsible for the pyrogenicity of the gram-negative bacteria. the cytoplasmic membrane, or plasma membrane is a phospholipid bilayer into which proteins/enzymes are embedded. the function of the cytoplasmic membrane is to act as a selective permeability barrier between the cytoplasm and the exterior environment. a mesosome is an organelle of bacteria that appears as an invagination of the plasma membrane and functions either in dna replication and cell division, energy production, or excretion of exoenzymes. flagella (if present) originate in a special structure in the cytoplasmic membrane (see the section on flagella under structure of the bacterial cell). the cytoplasm is a viscous liquid, which contains all other essential elements for the living cell. the genetic material is mainly organised in the genome, a circular string of dna. there is no discrete bacterial nucleus. the genetic code is translated into messenger rna and then transported to the ribosomes, where the protein synthesis occurs. the building blocks of the proteins (amino acids) are transported to the ribosomes by means of transfer rna. some genetic information such as antibiotic resistance may be encoded in plasmids -dna molecules that are independent of the genome and that can replicate themselves. some plasmids contain a set of genes (in the tra region) that enable the transfer of the plasmid by cell to cell contact (conjugation). the plasmid is replicated during this process and its genetic information (e.g. antibiotic resistance) is thus transferred to the recipient cell. there are both intra-species and inter-species plasmid transfer phenomena. the cytoplasm may also contain reserve material such as polyhydroxybutyric acid, and other substances of uncertain function (e.g. polyphosphate, volutin). some gram-positive rods such as the genera bacillus, geobacillus and clostridium are capable of forming endospores that enable these genera to survive harsher conditions, such as exposure to heat, radiation, or chemicals. bacterial spores are resistant forms of life. some experts have suggested that they may remain viable (capable of life) for millions of years. the bacterial spore has a complex structure, consisting of various layers, including coat and cortex, all of which play a role in long-term survival (see fig. . endospore formation is a non-reproductive process: one cell produces only one spore which, after germination, produces one vegetative cell. bacterial sporulation occurs when growth decreases due to exhaustion of an essential nutrient. it is a complicated process requiring the participation of more than enzymes. conversion to a vegetative cell involves three steps: activation, germination and outgrowth. activation can be accomplished by heating the spores to a non-lethal temperature. germination can be induced by a variety of events, including exposure to nutrients (amino acids, sugars, or purine nucleosides), non-nutrient germinants (dodecylamine, lysozyme) and heating [ ] . the spore loses its characteristic constituents, and heat resistance decreases dramatically. in the last stage water is taken up, and metabolism (synthesis of atp, destruction of bacterial spores is the ultimate goal of sterilisation processes. bacterial spores are typically used in biological indicators for validation and monitoring of sterilisation processes. pyrogens are substances that cause a febrile reaction. two groups of pyrogens can be distinguished: exogenous and endogenous pyrogens. the exogenous pyrogens form a heterogeneous group of substances; the most important one is lipopolysaccharide (lps) from the cell wall of gramnegative bacteria. lps, also known as endotoxin, has antigenic properties (o antigen) and causes fever when injected intravenously. lipoteichoic acid, muramyldipeptide, porins, glycans and nucleic acids, are examples of non-endotoxin pyrogens originating from bacteria (gram-positive and gram-negative), yeast and moulds. the pyrogenic activity of lps is much higher than that of most other pyrogenic substances. this is the reason why an in-vitro limit test for lps (the limulus amoebocyte lysate, or lal test) generally suffices for quality control purposes of parenteral medicines and raw materials, including water for injection. the european pharmacopoeia requires the rabbit pyrogen test for a number of vaccines, some antibiotics, and specific excipients including glucose, if intended for the preparation of large volume parenterals (see sect. . ). these products may be contaminated with pyrogens other than lps, or are known to inhibit the lal test. a third test, the monocyte activation test (mat) is based on the in-vitro activation of human blood cells by pyrogens. this leads to the release of pro-inflammatory cytokines tumour necrosis factor alfa (tnf-alfa), interleukin- beta (il- beta) and interleukin- (il- ) that are determined by enzyme-linked immuno sorbent assay (elisa). consequently, the mat will detect the presence of both exogenous and endogenous pyrogens in the test sample. the mat is suitable, after a product-specific validation, as a replacement for the rabbit pyrogen test [ ] . the reagent for the lal is isolated from the blood of the horseshoe crab (limulus polyphemus). the blood is collected from wild animals. many animals do not survive (mortality rates of up to - % have been reported), and this living fossil is threatened with extinction. it is to be expected that in the near future the mat test or other alternatives for the lal test and the rabbit test will be more generally introduced. the development of such new methods will significantly reduce animal testing. the commercially most successful alternative method, which replaces the rabbit pyrogen test for bacterial impurities in medicines with a test using human cells, could save the life of , rabbits a year. biofilms are multicellular, microbial communities held together by a self-produced extracellular matrix that adhere to biological or non-biological surfaces [ ] . a biofilm has a defined architecture, and it provides an optimal environment for the exchange of genetic material between cells, e.g. spread of antibiotic resistance. cells within a biofilm may communicate via quorum sensing (see sect. . . ), which may in turn affect biofilm processes such as detachment of cells. the ability to form biofilms is a universal attribute of bacteria and many other micro-organisms. elimination of bacteria in this mode of growth is challenging due to the resistance of biofilm structures to both antimicrobials and host defences. biofilms have great importance for public health because of their role in certain infectious diseases and their role in a variety of device-related infections. biofilm infections on indwelling devices or implants are difficult to eradicate because of their much better protection against macrophages and antibiotics, compared to free living cells, leading to severe clinical complications often with lethal outcome. fungi are widespread in nature and have considerable economic and medical importance, because: • they may contaminate and cause spoilage and deterioration of pharmaceutical preparations. mould and yeasts are the second cause of fda recalls in non-sterile pharmaceuticals [ ] . • this group of organisms is used by producers of active substances, including antibiotics, such as penicillins by penicillium species, or alkaloids, such as ergotamine by claviceps purpurea. • some fungi are pathogenic to humans. they may cause infections (e.g., trychophyton sp. or candida sp.), or produce toxic substances (e.g., aflatoxin by aspergillus flavus). two groups of fungi are relevant in the context of pharmaceutical products or processes: the moulds and the yeasts. their physical differentiation is not always clear, because some fungal species (e.g., candida, histoplasma and cryptococcus) show dimorphism, a phenomenon in which a filamentous and a yeast-like stage both exist. moulds are obligate aerobic micro-organisms; they grow on the surface or in the uppermost layers of the substrate. characteristic of moulds is the filamentous body, the mycelium. vegetative growth of moulds occurs at the tip of the individual filaments (hyphae). depending on the species, hyphae may be divided into compartments by means of septa (eumycetes). each septum contains a pore, which allows flow of cytoplasmic constituents from one compartment to another. the lower fungi (phycomycetes) have aseptate (coenocytic) hyphae; the mycelium is a multinucleated cell. asexual reproduction of moulds normally occurs by means of spore formation. from the mycelium special branches reach up into the air. at the tip of these conidiophores the spores (conidiospores) are formed on a genus specific structure. the colour of mould colonies on solid substrates (e.g., different shades of green for penicillium species, or black for aspergillus niger) is entirely due to the massive production of these conidiospores. mould spores may cause significant issues in the production of pharmaceutical preparations since they survive desiccation and may be transported via air, personnel or material flow into products. the spores are readily dispersed into the environment and may form a new mycelium. because of mechanical forces, such as those exerted during vortexing, hyphae may break up into smaller fragments, which may also form new mycelia. clumps of conidiospores may also break up into smaller units. such fragmentation caused by vigorous mixing in the course of microbiological examination of pharmaceutical samples may lead to considerable uncertainty in fungal counts. yeasts are typically unicellular organisms. yeast cells are spherical or oval. growth (asexual reproduction) takes place by a process called budding. a new cell is formed as an outgrowth of the mother cell, the daughter cell enlarges and finally the two cells separate. pathogenic dimorphic fungi usually form yeast-like cells in the human body and a mycelium at room temperature (e.g. histoplasma). candida sp. is an exception because it forms hyphae in the host tissue. sexual reproduction is associated with many yeasts and moulds. a stage in which spores are formed is always involved in the sexual process. depending on the type of sexual spore formation four groups of moulds can be distinguished: ascomycetes, basidiomycetes, zygomycetes, and oomycetes. the spores are called ascospores, basidiospores, zygospores, and oospores, respectively. fungi for which no sexual reproduction has been demonstrated are classified as fungi imperfecti (deuteromycetes). the majority of fungi thus far classified fall into this category. penicillium and some aspergillus species are well-known representatives of this group. the cell wall of fungi consists of - % polysaccharides. chitin is a common constituent of fungal cell walls, but is replaced by other substances such as mannan, galactosan or chitosan in some species. peptidoglycan, the common constituent of bacterial cell walls is never present. this phenomenon explains why fungi are insensitive to antibiotics that inhibit murein synthesis, such as the penicillins and the cephalosporins. sterols are essential structural components of the fungal cytoplasmic membrane. this characteristic makes fungi sensitive to antibiotics that interact with sterols, such as nystatin and amphotericin. in the previous sections the characteristics of potential contaminants of pharmaceutical preparations and their requirements for survival and growth have been discussed. there appears to be a complicated interplay between the type and characteristics of the micro-organisms (e.g. spore formation), their ability to form biofilms, the composition of the environment, and external factors, particularly the temperature. the fate of a micro-organism in a pharmaceutical preparation depends on this interplay. four different curves may be observed when numbers of colony forming units (cfu) are plotted against time (fig. . ) . microbial growth follows the well-known sigmoid growth curve, with lag phase, log phase and maximum stationary phase. microbial destruction under influences of heat, radiation or chemicals is frequently a first order kinetic process. when microbial destruction is plotted on a semi-logarithmic scale, a straight line is observed. a 'shoulder' is sometimes observed at the beginning of the curve. this lower death rate is attributed to the genetic repair mechanisms of the cells, e.g. when exposed to low doses of uv radiation. bacterial spores must be 'activated' before they can germinate and grow out to become prototypical vegetative cells. this phenomenon may also cause a 'shoulder' in survival curves. at the end of the survival curve, a 'tail' may be observed, indicating the presence of resistant cells or clumps of cells. true dormancy is found only in bacterial endospores. nevertheless, even vegetative organisms can produce an effective state of dormancy because of either a relatively slow death rate or growth and kill rates that offset each other. in pharmaceutical preparations another type of curve is sometimes observed. an initial decrease in the number of colony forming units may occur, followed by an increase. this phenomenon can be observed when analysing data from preservative efficacy testing of inadequately preserved dosage forms. it is the reason why in pharmacopoeial preservative efficacy tests the number of viable cells must be followed for a period of days (see sect. . ). microbial contamination of pharmaceutical products may result in deterioration of the product or direct hazard to the patient. whether a contaminated pharmaceutical product will trigger infection or disease in the patient depends on various factors such as: • number of micro-organisms (cfu per g or ml) • ability of the contaminant to grow and metabolise components of the product • properties of the particular strain • immunocompetence of the patient, due to disease (aids) or use of immunosuppressiva • route of administration deterioration or spoilage of the product because of microbial growth may result in several effects including: • loss of texture because of metabolism of oil/fat phase • loss of organoleptic quality because of production of olfactory products • loss of preservative efficacy because of metabolism of the preservative • loss of package integrity because of excessive gas production • loss of therapeutic activity because of metabolism of the active substance(s) • release of toxigenic substances, including toxins (e.g. aflatoxin) and pyrogens the contamination can be primary or secondary. primary contamination occurs at the premises or during preparation: • personnel. personnel account for the majority of contaminations in the clean room environments. this can be explained by the high number of micro-organisms located on or in the human body. the organisms may be introduced into the environment due to inadequate gowning or hygiene, infrequent or ineffective hand washing and disinfection procedures, unqualified behaviour (non-clean room adequate) of personnel, etc. in the aseptic production of sterile pharmaceutical preparations living micro-organisms should not enter the aseptic filling area and the product should not contain any viable microorganism. in those situations, low-level microbial contaminations of products occur mostly at critical interventions near to the product during processing. microbial contamination of non-sterile pharmaceutical preparations may not originate primarily from the human body, but raw materials, equipment, air and packaging material may also play an important role • raw materials. raw materials from natural origin may be highly contaminated with micro-organisms especially spore-forming bacteria and moulds and in some cases with more critical enterobacteriaceae. soon after a publication on salmonellosis in more than persons caused by the contamination of thyroid tablets with two types of salmonella originating from the raw material [ ] , proposals for the examination of non-sterile pharmaceutical preparations and acceptance criteria were published [ ] . • water. water may be used to clean equipment and clean rooms as well as a product component. water contains water-borne micro-organisms that may grow under low nutrient conditions. in a recent review of fda product recalls, almost half ( %) of them were due to contamination by water-borne micro-organisms such as burkholderia cepacia, pseudomonas species, or ralstonia pickettii [ ] . • air. micro-organisms may be carried over from dust or soil particles and may be transported into manufacturing areas by personnel, material or airflow. mould spores for instance were carried over from a highly contaminated source into the production room [ ] . • equipment. equipment may be contaminated if inappropriate cleaning, disinfection or sterilisation procedures have been performed. • primary packaging. the microbiological quality of primary packaging material is critical for sterile preparations. vials, ampoules and stoppers shall be sterile and free of pyrogens before filling. for non-sterile preparations the microbiological quality of the packaging material is less critical. because of the production process, bottles, tubes etc. will have only low levels of contamination, provided they have been packed, stored and handled under appropriate conditions. secondary contamination may occur during storage, transport, and administration of the product. the root cause for contamination during storage and transport is mainly insufficient closure integrity (see sect. . ). contamination during administration can be avoided by suitable design of the primary package (see sect. . ) and appropriate instruction of the medical staff or patient (see sect. . ). tubes are less prone to contamination than jars. in hospitals eye drops should only be used for one specific patient and preferably for one specific eye. microbiological quality assurance and microbiological quality control should be part of the pharmaceutical quality system of any production site. its main aim is to prevent microbial contamination in case of products required to be sterile (e.g. parenteral medicines), or to reduce the microbial counts and avoid objectionable micro-organisms in case of non-sterile products (e.g. tablets). the elements of a pharmaceutical quality system (pqs) that are crucial for microbiological quality regard adequate design of premises, procedures and controls. they are discussed in this section. the principles are included in current good manufacturing practices (cgmp) guidelines (see sect. . . ), which are legally binding for pharmaceutical manufacturers. microbiological quality assurance (qa) refers to the procedures in the quality system that ensures that microbiological requirements of the product are fulfilled. microbiological quality control (qc) refers to the tests performed to verify that the product meets the required specifications. the following procedures and measures concerning facilities should mitigate the risk of microbiological contamination: • qualified personnel. only trained and qualified personnel should enter areas where products are manufactured or prepared. personnel should wear dedicated gowning which provides a physical barrier between the body and the working environment. the more critical the activity or product microbiological requirements, the stricter the gowning. gowning may consist for instance of overalls, face masks, gloves (which are disinfected with ethanol) or even goggles in case of aseptic processing. for basic hygiene at the preparation of non-sterile medicines the main points are given here. contact between the product and the operator is to be prevented. thus: • equipment and production processes shall be designed so that direct contact between operator and product is minimised. • under no condition shall the product be touched with bare hands. if manipulation is unavoidable use utensils, such as forceps, or wear gloves. gloves shall be changed when appropriate, particularly at every preparation and after obvious contamination such as sneezing and wiping the nose. • refrain from talking above the product. coughing and particularly sneezing are difficult to suppress. wearing a facial mask and changing it at least every h will considerably reduce the risk of contamination by this route. the operator shall inform his or her superior in case of a disease such as a cold. (continued) • facial hair shall be appropriately covered; this may require the wearing of a head cover and a facial mask to cover moustaches and beards. this is also necessary from a safety point of view when operating with rotating equipment such as an ointment mill. from a pure microbiological viewpoint wearing an overall doesn't make sense other than the promotion of an attitude of working cleanly and neatly. already after - h the overall bears as much contamination as the personal clothing. directions for clothing are however also necessary to promote occupational safety and health (see sect. . . ) . the overall has to remain in the preparation area (thus taken off at lunch and coffee breaks) and has to be cleaned according fixed schemes, such as daily and when visibly contaminated. the overall shall have long sleeves and cover completely personal clothing. washing hands must always occur: • at the start of preparation • if hands are visibly dirty • after using the toilets • after sneezing and wiping the nose • between two different preparation processes, because of cross contamination nails have to be kept short and proper hand washing procedures include removal of watches, voluminous rings and bracelets (remaining off during the preparation process). washing hands technique requires preferably lukewarm water, soap from a dispenser, proper attention to thumbs, sufficient duration and proper drying with a towel because that will carry off micro-organisms too. • controlled environments. clean rooms in which pharmaceutical preparations are prepared processed, and packed are controlled for room pressure, humidity and temperature. they are segregated from other operating areas and may be entered via separate air locks for personnel and material. the incoming air of the clean rooms is filtered using hepa (high efficiency particulate air) filters that may retain more than . % of . μm air particles (see table . ). the higher the microbiological quality of the product or the critical the process step, the higher the clean room quality criteria. for instance in aseptic processing of sterile products for critical areas where the product is exposed to the surrounding environment, the air should not contain more than , particles of . μm size per cubic metre and should be devoid of viable micro-organisms (see air classifications in tables . and . ). clean room design should ensure that air, personnel and material flow is optimal to prevent microbial contamination from a less clean area to a cleaner area. isolators have been introduced as an alternative to conventional clean rooms for aseptic production. these may be large installations, in which complex operations such as large-scale aseptic filling of syringes can be performed. controlled environments also regard to aseptic handling in pharmacies, where they are achieved using laminar flow cabinets, biological safety cabinets or isolators (see sect. . ). • cleaning and disinfection. the procedures for cleaning and disinfection (destruction of micro-organisms -but not necessarily spores -by chemical agents, see sect. . . ) of equipment parts that are in contact with the product have to be validated. in addition, for the more critical products that are required to be sterile, the equipment parts that are in contact with the product need to be sterilised. sterilisation (destruction of micro-organisms including spores by heat) process of the manufacturing lines has also to be validated. for products, which are required to be sterile, the aseptic status of the production line is regularly evaluated by performing media fill simulations that consist of replacing the product with a microbial culture medium and evaluating if filled-media containers remain sterile. • reducing bioburden. the preparation processes may reduce or even eliminate living micro-organisms. for instance on the preparation of tablets, the tableting of a granulate into a tablet may kill non-spore forming microorganisms by the shearing forces of the interparticulate movement. products required to be sterile are either sterile filtered (filter . μm pore diameter, see sect. . ) or terminally sterilised directly in their container or package (e.g. steam sterilisation (sect. . . ), radiation (sect. . . ), ethylene oxide gas ( . . ) ). • water distribution system. the distribution and storage systems for water that is used for cleaning, sterilisation and preparation should be devoid of biofilms. a distribution system may be controlled by continuously circulating heated water (> c) in loops, avoiding one-way systems and dead ends, and application of disinfection steps such as adding ozone to the re-circulating water (see sect. microbiological testing is performed to monitor the microbiological bioburden and to ensure that the final product complies with the regulatory microbiological specifications. it comprises: • an environmental monitoring program in order to monitor the microbiological levels of classified rooms. air, product-contacting surfaces, working surfaces, floors and personnel are sampled. frequency and sampling locations are defined based on a risk assessment. maximum microbiological count levels should be defined either based on historical data or on regulatory guidelines. if they are exceeded, this may signal a deviation from normal conditions that would require an investigation and an evaluation on the impact on the respective product produced. trending of environmental results may also be performed in order to evaluate shifts in the overall hygienic conditions over an extended period of time to define appropriate corrective actions. see also sect. . . . • testing of primary packaging materials, raw materials (excipients, active substances, water) and products according to internal or official methods and specifications. microbial limits of pharmaceutical preparations are given in relevant monographs of the european pharmacopoeia. section . provides a deeper insight on the european test methods of pharmaceutical preparations and acceptance criteria. • monitoring water distribution and storage system. • root cause investigation (see sect. . . ) . when a test does not fulfil a microbiological acceptance criterion, this is considered as a deviation or out of specification result. this requires an investigation to determine the root cause of contamination, e.g. whether it occurred during laboratory testing, sampling or manufacturing. if a source of contamination has been found, corrective and preventive actions are put in place to eliminate and prevent re-occurrence of the contamination. failure to meet measures to prevent microbiological contamination of pharmaceutical preparations may have dramatic consequences. a major health issue related to microbiologically contaminated pharmaceutical preparations was the new england (continued) compounding center (necc) meningitis outbreak in the usa [ ] . on october , , the cdc (us centers for disease control) and the fda (us food and drug administration) issued a recall alert for pharmaceutical preparations produced by the necc, following a multistate outbreak of fungal meningitis and other infections among patients who received contaminated preservative-free methylprednisolone acetate epidural injections. most patients suffered infection by the fungus exserohilum rostratum and in august , cdc reported cases and deaths. after performing microbiological testing of the unopened incriminated product lots, cdc confirmed presence of exserohilum rostratum, along with other fungi (e.g. cladosporium cladosporioide, aspergillus fumigatus) and spore-forming bacteria (e.g. bacillus subtilis) [ ]. after inspecting the necc preparation area, the fda mentions in its report [ ] that moulds and bacteria were found in large numbers in many air and surface samples where the products were prepared. a number of physical and chemical techniques to eliminate or to destroy micro-organisms may be employed in order to assure that the microbiological quality of the product complies with pharmacopoeial requirements, immediately after production and throughout its shelf life. since these techniques are discussed in detail in other chapters, they are mentioned only briefly. physical removal of micro-organisms (filtration, see sect. . ) is applied for gases and liquids. high efficiency particulate air (hepa) filters are used to remove viable and non-viable particles from the air introduced in classified working areas (see sect. . . ). hydrophobic membrane filters are used as vent filters on tanks and to filter production gases. membrane filtration of liquids is applied to reduce the bioburden of raw materials and of final products (see sect. . ). in an aseptic process, membrane filtration is the final step before filling. during the production of a terminally sterilised product membrane filtration is applied to reduce the bioburden. micro-organisms may be physically destroyed by means of dry heat (see sect. . . ), moist heat (see sect. . . ) and ionising radiation (see sect. . . ) . dry heat sterilisation is primarily applied for glassware and some heat stable raw materials. the standard temperature is between c and c. ointments and some powders may be treated at lower temperatures because they are not stable enough. higher temperatures ( c and above) are used for the depyrogenation and sterilisation of glass vials. moist heat sterilisation at c for min is the method of choice for terminal sterilisation of finished products. sterilisation by means of ionising radiation of pharmaceutical preparations is not allowed in a number of countries. many active substances and raw materials are decomposed by the doses required for sterilisation. some polymers become brittle and glass may become discoloured. for these reasons there is only limited application for this sterilisation method for pharmaceutical preparations. radiation sterilisation is however widely used in the medical device industry. disinfection, sanitisation, decontamination, chemical sterilisation, are only a few terms for these processes. disinfection, defined as removal, destruction or de-activation of micro-organisms on objects or surfaces, is the term of preference in this book. disinfection of surfaces (gloves, equipment, floors and walls) is done with a range of products, including isopropyl alcohol, ethanol, quaternary ammonium compounds, biguanides and amphoteric agents. if a sporicidal activity is required (as alcohols are not sporicidal), oxidising agents such as chlorine/hypochlorite, peracetic acid, or hydrogen peroxide may be used. for medical devices a number of processes are available such as ethylene oxide and low-temperature hydrogen peroxide gas plasma sterilisation. the objective of preservation is to assure the microbiological quality throughout storage and the period of use. a number of substances, including parabens, chlorhexidine, and sorbic acid are used (see sect. . ). sterility tests appeared in the british pharmacopoeia for the first time in and in the united states pharmacopeia in [ ] . currently sterility testing is a legally binding release test for industrially manufactured sterile products. only under specific conditions, including an excellent track record and a high level gmp, national authorities may grant a product and site-specific approval for parametric release (release without performing a sterility test) (see sect. . ). for many products prepared in hospital pharmacies or in institutions such as blood banks, the batch size is too small (one or only a few units) or the shelf life is too short (< days) to perform a complete sterility test as described in pharmacopoeias. in such instances, such as with radiopharmaceuticals (see sect. . . ), the pharmacist has to rely on the aseptic precautions during preparation (see sect. . ). the use of rapid microbiological methods (rmms) may also be an alternative to test products with such short shelf lives. the objective of the sterility test is obviously to demonstrate that a batch is sterile, i.e. does not contain any viable micro-organism. there is an on-going debate on the rationale of the sterility test. the test is a destructive one and relatively small samples are taken from the batch. the results cannot be extrapolated to items that have not been examined. for terminally sterilised products a limit (sterility assurance level, sal of ) has been imposed for which there is no appropriate test methodology of sufficient sensitivity. the test will only detect those micro-organisms capable of growing to detectable levels under the defined incubation conditions (media, temperatures and time). the sterility test is however the last possibility to detect any gross error in the production process. this means that applying an appropriate quality system with stable and well-controlled preparation and sterilisation processes (and not just performing a sterility test on the final product) is the key to ensure that a product that purports to be sterile remains free of microbial contamination. regulatory initiatives strengthen the view that quality cannot be assured by final product testing, but should rather be assured by appropriate design of the manufacturing process (see sect. . ) . consequently, these initiatives emphasise process understanding and monitoring over final product testing. for the way in which the process is monitored to ensure sterility during aseptic handling, see sect. . . . after several years of negotiation the sterility tests of the european pharmacopoeia, the united states pharmacopeia and the japanese pharmacopoeia are harmonised [ ] . in the next sections the five steps of this harmonised test, as described in ph. eur. . . will be discussed: sampling, sample preparation, inoculation, incubation, and interpretation. prior to the routine application of the test, a suitability test with a range of specified test organisms shall demonstrate that growth of these organisms is not inhibited due to residual antimicrobial activity of the product. the monograph specifies the minimum number of items that shall be examined in relationship to the batch size, and the minimum volume/amount that shall be taken from each container. the samples used should be representative for the whole batch. furthermore immediately after an intervention in an aseptic filling operation (e.g. re-adjustment of a filling needle) the probability of contamination may be increased, and specific sampling for sterility testing may be justified. this has to be specified in relevant procedures. sample preparation includes all operations necessary before the actual examination can be performed, including opening of the primary packaging, withdrawal of the required amount and, if necessary, dilution or dissolution of the sample in a suitable liquid. the technique of membrane filtration is used whenever the nature of the product permits. the membrane is transferred to the growth medium, or the medium is transferred onto the membrane. alternatively, the prepared sample is inoculated directly into the appropriate media. this method is only used when the product (e.g. some vaccines) cannot be dissolved or diluted in a nontoxic diluent. the media used are fluid thioglycolate medium (ftm) for aerobic, micro-aerophilic and anaerobic bacteria, and soybean casein digest broth (scdb) for aerobic bacteria and fungi. ftm and scdb are incubated at - c and - c respectively, both for a period of not less than days. this relatively long incubation period seems to be justified, because an unacceptable proportion of contaminants would be missed by limiting incubation to days [ ]. the media are examined at intervals and at the end of the incubation period. if no growth is visually observed the sample passes the test. normally the sample shall be rejected if growth is observed in at least one of the media. however under certain conditions the test may be invalidated and in that case be repeated. ) and requirements regarding specific micro-organisms. limits depend on the route of administration, the nature of raw materials, the type of micro-organism, and on the fact whether an antimicrobial treatment can be given to the product (cf. the more stringent criteria for the aqueous preparations than for non-aqueous oral preparations reflect the greater potential for microbial growth of the former. e. coli must be absent from most of the preparations because this is an indicator organism for poor hygiene during production, or poor microbiological quality of the raw materials. products intended for inhalation must be free of staphylococcus aureus, because it may cause pulmonary infections. this organism also indicates poor hygiene during production. pseudomonas aeruginosa should be absent as well, because this organism may cause serious lung infections. because of the aqueous nature of these products the presence of this organism and other bile tolerant gram-negative bacteria is a serious potential risk. bile tolerant gram-negative bacteria form a complex group of micro-organisms comprising of the enterobacteriaceae and many other strains (formerly pseudomonads), including burkholderia cepacia [ ] and ralstonia pickettii [ ] . burkholderia cepacia is a waterborne organism and causes great problems to the pharmaceutical industry and hospitals. it may be resistant to many commonly used disinfectants and preservatives, such as chlorhexidine, and it may cause serious lung infections, particularly in compromised hosts, such as cystic fibrosis patients. salmonella must be absent from g of herbal preparations. this reflects the low infectious dose of this organism and the severity of infections. test methods for the microbiological examination are described in ph. eur. sections . . [ ] and . . [ ] respectively. section . . describes qualitative methods for the determination of the total aerobic microbial count and the total yeast and mould count. section . . describes tests for specified organisms. the total aerobic microbial count (tamc) is defined as the number of colonies observed on casein soya bean digest agar. the total combined yeast and mould count (tymc) is defined as the number of colonies observed on sabourauddextrose agar. the assessment consists of four steps: sampling, sample preparation/testing, incubation, and interpretation. in general the sample size shall be g or ml. an exception is made for those active substances for which the amount per dosage unit or per g or ml (for preparations not presented in dose units) is less than mg or ml. in these cases the amount to be tested shall be not less than the amount in dosage units or in g or ml of the product. any sample shall be representative for the whole batch. however batch sizes may range from extremely small (e.g. for some biotechnological products) to very large (e.g. a batch of tablets). the ph. eur. does not describe how the samples shall be taken and this must be put down in local procedures. if necessary the sample is dissolved and diluted in a suitable non-toxic diluent. buffered sodium chloride-peptone solution to which an emulsifier and/or a neutraliser for antimicrobial agents may be added is widely used. three methods may be used for the enumeration: membrane filtration, plate count, and most probable number (mpn) method. the advantages of the membrane filter method are its low limit of detection (lod) of < cfu/g or ml and the efficient separation of the micro-organisms from components of the product, particularly antimicrobial agents. for the pour-plate method, the sample is generally : dissolved in the diluent, and ml of the dilution is mixed with the agar. this corresponds to a lod of cfu/g or ml. the lod is sometimes higher (e.g. cfu/g or ml) if the product needs to be further diluted due to microbial inhibition, or lower in case of products with low microbial acceptance criteria. if the spread plate count technique is used the lod is a factor of ten higher (> cfu/g or ml), because only . ml of the absence of bile-tolerant gramnegative bacteria ( g or ml) special ph. eur. provision for oral dosage forms containing raw materials of natural (animal, vegetal or mineral) origin for which antimicrobial pretreatment is not feasible and for which the competent authority accepts tamc of the raw material exceeding cfu/g or cfu/ml not more than cfu of bile-tolerant gram-negative bacteria ( g or ml) absence of salmonella ( g or ml) absence of escherichia coli ( g or ml) absence of staphylococcus aureus ( g or ml) a colony forming unit (cfu): one or more micro-organisms that produce a visible, discrete growth entity on a semisolid, agar-based microbiological medium dilution can be spread over the surface of the agar plate. the precision and accuracy of the mpn method is less than that of the membrane filtration and the plate count methods. unreliable results are particularly obtained for moulds. for these reasons the mpn method is reserved for the enumeration of tamc in situations where no other method is available. casein soya bean digest agar is incubated for - days at - c. sabouraud dextrose agar is incubated for - days at - c. duplicate plates are prepared for each dilution and each medium. if the mpn method is used the tubes are incubated for - days at - c. at the end of the incubation period the colonies on the plates are enumerated. the number of cfu per gram or per ml of product is calculated for each medium from the arithmetic means of the plates. because of the relatively poor accuracy and precision of microbiological enumerations, according to the ph. eur. an acceptance criterion may be interpreted as follows: cfu: maximum acceptable count is cfu: maximum acceptable count is ; etc. the group of specified micro-organisms is a limited group of organisms which may be either pathogenic, or are indicator organisms for lack of hygiene during production. this group includes a number of organisms that have been discussed in a previous section, viz. escherichia coli, staphylococcus aureus, pseudomonas aeruginosa, and bile tolerant gramnegative bacteria. the group also includes: salmonella, clostridium, and candida albicans. tests for the detection of these organisms are described in the pharmacopoeias (e.g. ph. eur. . . [ ] ). salmonella belongs to the family of the enterobacteriaceae. over , species are known. salmonellae are differentiated by means of biochemical reactions and by serotyping. salmonellae are pathogenic bacteria causing food poisoning. the bacterium is present in many free-living and domesticated animals. pharmaceutical raw materials that have been contaminated include carmine, pancreatic powder and thyroid powder. bacteria from the genus clostridium are anaerobic, sporeforming gram-positive rods. the spores are heatresistant and can survive in foods that are incorrectly or minimally processed. the genus contains a number of dangerous pathogens, including clostridium botulinum, clostridium difficile, and clostridium tetani. candida albicans is a fungus that grows both as yeast and filamentous cells and is a causal agent of oral and genital infections in humans. systemic fungal infections including those by candida albicans have emerged as important causes of morbidity and mortality in immunocompromised patients (e.g., patients with aids, cancer chemotherapy, and transplantations). candida albicans biofilms may form on the surface of implantable medical devices. in addition, hospital-acquired infections by candida albicans have become a cause of major health concerns. in addition to these well-known organisms it has however been demonstrated that other organisms (e.g. burkholderia cepacia, or ralstonia pickettii) can cause infection when present in pharmaceutical preparations. for this reason the concept of 'objectionable organisms' was originally introduced in the usa. objectionable micro-organisms are defined as contaminants that, depending on the microbiological species, would adversely affect product safety and product quality. so the assessment of microbial safety of a medicine has to include the examination of absence of objectionable micro-organisms as well. one approach to determine whether an organism is objectionable is to perform a risk analysis [ ] , see also chap. . such an analysis should address at least four issues: • potential level of microbial contamination (total aerobic microbial count, total yeast and mould count) • identity and characteristics of possible micro-organisms present (pathogenicity, ability to metabolise product components, ability to survive or even grow in the conditions of the product) • product characteristics (presence of antimicrobials, water activity, route of administration, container and closure design) • potential impact on patients (for instance: is the preparation meant for immunocompromised patients or for neonates) the examination of pharmaceutical preparations for specified micro-organisms involves generally the following steps: sampling, sample preparation, resuscitation and enrichment, incubation on diagnostic or selective media, and evaluation. sampling and sample preparation is basically the same as for tamc and tymc determination and will not be further discussed. as a result of mild heat treatment, drying, or chemical antimicrobial treatment, cells may be sublethally injured. a cell is, by definition, sublethally injured if it is unable to grow on a selective medium that is typically suitable for normal healthy cells of that type. sublethally injured cells may recover when transferred to a suitable non-selective medium and thus regain all their normal characteristics, including resistance to selective antimicrobial agents and pathogenicity. this recovery process is called resuscitation. the examination of non-sterile pharmaceutical products for the presence of specified micro-organisms involves one or more steps with selective media. to increase the likelihood of detecting sublethally injured micro-organisms, the product is initially incubated in a non-selective (enrichment) medium. this non-selective culture thus may serve a twofold purpose: to first resuscitate sub-lethally injured cells and, secondarily, to facilitate their growth for purposes of further isolation and identification. for some organisms a second enrichment step in a selective medium is include in the method. table . gives an overview of the purposes of the media used for each (group of) specified micro-organisms. if there is no growth in the selective medium, the corresponding specified micro-organism is absent and the product complies with the requirement. if there is typical growth in the diagnostic medium a confirmation of the presence of the specified micro-organism should be performed using either biochemical tests or other identification methods (e.g. s rdna sequencing). in the previous sections only the conventional microbiological methods, developed in the late ninetieth and first half of the twentieth century, have been discussed. all these methods are growth-based methods that have their own limitations (long incubation periods, only viable micro-organisms that also grow on the media can be recovered, variability in nutrient media quality, etc.). in the past decades many new technologies have been developed with the first aim to reduce the time to obtain results of microbiological testing. the use of such rapid microbiological methods (rmm) is beneficial in terms of reduction of throughput time for release (especially of parenterals), early identification of product contaminations, allows for causal investigations to be carried out earlier, making it easier to find and eliminate contamination causes [ ] . for short shelf life products (< days), rapid microbiological methods are essential for assessing microbiological safety. in addition, automation by alternative methods enables to reduce hands-on time, human error and paperless data recording. before microbiological testing can be performed with an alternative method, the user must demonstrate that the alternative method is suitable for its intended purpose. this validation is based on demonstrating at least equivalent performance of the rmm compared to the traditional method and is performed according to ph. eur. . . ., usp < , > or pda tr- [ ] [ ] [ ] . it is beyond the scope of this chapter to discuss all available technologies, just one example of each of three detection principles will be mentioned here, viz., a growth based method, a non-growth based method and a nucleic acid determination method. for an encyclopaedic overview the reader is referred to the literature [ ] . bioluminescence atp is a metabolite present in all organisms (excluding viruses). the amount of atp per cell is species-dependent and also is dependent on the metabolic state of the cell. atp can be measured semi-quantitatively with the luciferin/luciferase system. this system (naturally occurring in the firefly) emits light in the presence of atp. the sample is mixed with a special reagent, which causes lysis of the cells, liberating the atp, followed by addition of the luciferin and luciferase reagents. the amount of emitted light is measured by means of a photomultiplier system and used as an indicator of the number of cells present. this principle can be applied for numerous purposes, such as the detection of micro-organisms in products or monitoring of cleaning and disinfection procedures. its use has been suggested for microbiological examination of sterile and non-sterile pharmaceutical preparations [ , ] . laser scanning cytometry a sample is filtered over a membrane filter and treated with a fluorogenic reagent. living cells actively take up the reagent and convert it to a fluorescent substance. the filter is scanned with a laser beam and the fluorescence is measured. the system records the position of the fluorescent item, so that it can be verified microscopically that the signal was not due to an artefact. the method is able to detect a single cell within about h post sample processing and testing. it is used to monitor large water systems in pharmaceutical plants [ ] . . . . nucleic acid based identification: ribotyping ribotyping measures the pattern that is generated when dna from an organism is treated with a restriction enzyme. dna is isolated from a pure culture. the genes encoding for s rrna are amplified with pcr, treated with one or more restriction enzymes, separated by means of electrophoresis and finally probed. the obtained genetic fingerprint is a stable marker that provides definitive species discrimination or even characterisation below species level. microbial chemical signaling: a current perspective bacterial quorum sensing: functional features and potential applications in biotechnology quorum sensing in gram-negative bacteria: small-molecule modulation of ahl and ai- quorum sensing pathways biosynthesis of peptide signals in gram-positive bacteria the united states pharmacopeial usp /the national formulary nf ( ) < >, application of water activity determination to non-sterile pharmaceutical products. the united states pharmacopeial convention human prion diseases prions. in: block ss (ed) disinfection, sterilization and preservation a relevant long-term impact of the circulation of a potentially contaminated vaccine on the distribution of scrapie in italy. results from a retrospective cohort study consensus statement on the bio-safety of urinary-derived gonadotrophins with respect to creuzfeldt-jakob disease detection of prion protein in urine-derived injectable fertility products by a targeted proteomic approach how is creutzfeldt-jakob disease acquired? minimising the risk of transmitting animal spongiform encephalopathy agents via human and veterinary medicinal products. european pharmacopoeia, th edn inactivation of transmissible degenerative encephalopathy agents: a review acid inactivation of prions: efficient at elevated temperature or high acid concentration use of pcr-based assays for the detection of the adventitious agent porcine circovirus type (pcv ) in vaccines, and for confirming the identity of cell substrates and viruses used in vaccine production root cause investigation of a viral contamination incident occurred during master cell bank (mcb) testing and characterization-a case study swine torque teno virus detection in pig commercial vaccines, enzymes for laboratory use and human drugs containing components of porcine origin human and animal vaccine contaminations circovirus and impact of temporary withdrawal of rotavirus vaccines in spain approaches to minimize infection risk in blood banking and transfusion practice effect of viral nucleic acid testing on contamination frequency of manufacturing plasma pools improvement of virus safety of an antihemophilc factor ix by virus filtration process pathogen safety of plasma-derived products -haemate p/humate-p nosocomial outbreak of epidemic keratoconjunctivitis accompanying environmental contamination with adenoviruses the survival of adenovirus in multidose bottles of topical fluorescein hepatitis c virus infections from a contaminated radiopharmaceutical used in myocardial perfusion studies hepatitis c transmission due to contamination of multidose medication vials: summary of an outbreak and a call to action transmission of hepatitis c virus during myocardial perfusion imaging in an outpatient clinic patient-to-patient transmission of hepatitis c virus through the use of multidose vials during general anesthesia nosocomial transmission of hepatitis c virus associated with the use of multidose saline vials the survival of herpes simplex virus in multidose office ophthalmic solutions nosocomial transmission of hepatitis b virus infection through multiple-dose vials the microbiology of safe food highlights of mycoplasma research-an historical perspective the scope of mycoplasma contamination within the biopharmaceutical industry the growth and long term survival of acholeplasma laidlawii in media products used in biopharmaceutical manufacturing effect of storage conditions on detection of mycoplasma in biopharmaceutical products mycoplasma testing of cell substrates and biologics: review of alternative non-microbiological techniques mycoplasmas. european pharmacopoeia, th edn functions of bacterial flagella bacterial flagellar diversity and significance in pathogenesis bacterial adhesion and entry into host cells pili in gram-positive pathogens bacterial pili: molecular mechanisms of pathogenesis genetic bases and medical relevance of capsular polysaccharide biosynthesis in pathogenic streptococci conjugate vaccines-a breakthrough in vaccine development leuconostoc dextransucrase and dextran: production, properties and applications spore germination monocyte-activation test. european pharmacopoeia, th edn microbial diversity in pharmaceutical product recalls and environments microbiological contamination of medical preparations microbiological quality of pharmaceutical preparations. guidelines and methods objectionable micro-organisms in non-sterile pharmaceutical drug products: risk assessment and origins of contamination fungal infections associated with contaminated methylprednisolone injections fda report on new england compounding pharmacy. www.fda. gov search on ucm the sterility testing of pharmaceuticals the incubation period in sterility testing microbiological quality of pharmaceutical preparations. european pharmacopoeia, th edn microbiological quality of herbal medicinal products for oral use. european pharmacopoeia, th edn burkholderia cepacia: this decision is overdue a multistate nosocomial outbreak of ralstonia pickettii colonization associated with an intrinsically contaminated respiratory care solution microbiological examination of non-sterile products: microbial enumeration tests. european pharmacopoeia, th edn microbiological examination of non-sterile products: test for specified micro-organisms. european pharmacopoeia, th edn overview of rapid microbiological methods evaluated, validated and implemented for microbiological quality control alternative methods for control of microbiological quality. european pharmacopoeia, th edn the united states pharmacopeial usp /the national formulary nf ( ) < >, validation of alternative microbiological methods. the united states pharmacopeial convention evaluation, validation and implementation of new microbiological testing methods pda. bethesda encyclopedia of rapid microbiological methods growth promoting properties of different solid nutrient media evaluated with stressed and unstressed micro-organisms: prestudy for the validation of a rapid sterility test identification of micro-organisms after milliflex rapid detection-a possibility to identify nonsterile findings in the milliflex rapid sterility test evaluation of the chemscan system for rapid microbiological analysis of pharmaceutical water key: cord- -pjtyv pv authors: kalokairinou, louiza; zettler, patricia j; nagappan, ashwini; kyweluk, moira a; wexler, anna title: the promise of direct-to-consumer covid- testing: ethical and regulatory issues date: - - journal: j law biosci doi: . /jlb/lsaa sha: doc_id: cord_uid: pjtyv pv widespread diagnostic and serological (antibody) testing is one key to mitigating the covid- pandemic. while at first, the majority of covid- diagnostic testing in the usa took place in healthcare settings, quickly a direct-to-consumer (dtc) testing market also emerged. in these dtc provision models, the test is initiated by a consumer and the sample collection occurs at home or in a commercial laboratory. although the provision of dtc tests has potential benefits—such as expanding access to testing and reducing the risk of exposure for consumers and medical personnel—it also raises significant ethical and regulatory concerns. this article reviews these challenges and shows how they parallel and also diverge from prior concerns raised in the dtc health testing arena. the first part of this paper provides an overview of the landscape of diagnostic and serological tests for covid- , anticipating how provision models are likely to evolve in the future. the second part discusses five primary issues for dtc covid- tests: test accuracy; potential misinterpretation of results; misleading claims and other misinformation; privacy concerns; and fair allocation of scarce resources. we conclude with recommendations for regulators and companies that aim to ensure ethically marketed dtc covid- tests. in the wake of the covid- pandemic, widespread diagnostic and serological (immunity) testing is considered key in containing the spread of the disease, as well as in easing stay-at-home measures and informing policies for restarting the economy. most tests, whether diagnostic or serological, are currently offered by healthcare providers who interface with the healthcare system. however, a number of companies have begun to offer covid- testing on a direct-to-consumer (dtc) basis : that is, the test is initiated by a consumer-not a healthcare professional-typically via the company's website. while a healthcare professional may be involved at some stage of the process that involvement may be as minimal as a brief review of a questionnaire that the consumer has completed as part of the purchasing process. as such, the consumer may have no direct contact with a healthcare professional (although some companies offer the option of post-test consultations in the case of positive results). in addition, the results of dtc tests do not necessarily become part of patients' health records, as the companies offering such tests operate independently of the healthcare system. the acquisition of the sample in dtc tests may occur in one of two ways: via at-home collection or in-laboratory collection. in the former, individuals order and receive an at-home collection kit, where they acquire the sample and mail it back to the company (or a lab that processes the results on behalf of the company). for inlaboratory collection, individuals make an appointment to visit a commercial laboratory where their sample is collected. both models of dtc covid- tests-at-home or in-laboratory collection-are distinguishable from those offered by hospitals and the term dtc testing has been used in the literature to describe different provision models of health products. for the purposes of this article, our key criteria for considering a test to be dtc are (a) that it is promoted directly to consumers; (b) the testing process is initiated by consumers, who order the test online or by phone and/or book an appointment to a commercial lab in order to have their sample taken; (c) it requires little to no involvement of a healthcare provider, and whatever involvement does occur is usually not in person. see health clinics, as it is the consumer who initiates the order and completes the testing process with little to no interaction with a healthcare professional. even though the covid- pandemic has changed the way much healthcare is delivered by increasing the use of telemedicine to minimize in-person visits, the doctor-patient relationship remains central. in this regard, the dtc testing model is distinct. although healthcare professionals employed by dtc companies may authorize the ordering of laboratory tests, they have little, and usually no direct contact with the consumer. indeed, from the perspective of the consumer, the process of ordering a dtc covid- test may feel similar to purchasing other goods or services. for example, to order the labcorp covid- diagnostic test, an individual must click through a brief questionnaire, after which they can input their credit card information, click 'order,' and thereafter receive shipping updates via email. the dtc provision of covid- tests by private companies may expand access to testing and contribute to the mitigation of the present public health crisis. in particular, there are potential benefits to at-home testing, which eliminates the risks of exposure that individuals and medical personnel collecting samples may incur. in addition, at-home testing reduces the demand for personal protective equipment required by sample collectors and decreases the testing burden for the healthcare system as a whole. however, dtc tests also raise significant ethical concerns and pose regulatory challenges. although the regulatory environment for covid- tests is not identical to that for other types of dtc health tests (such as currently marketed genetic or hormone tests), many of the concerns raised by dtc covid- tests parallel those wrought by other types of dtc health tests. at the same time, there are important contextual differences that make concerns over dtc covid- tests particularly urgent, such as the global population affected, the infectious nature of sars-cov- , and the historic challenges to the healthcare system and economy during the pandemic. as widening the provision of diagnostic and serological covid- tests may be crucial to containing the pandemic, it is important to critically consider the key issues that might lie ahead for dtc covid- testing. in this article, we examine the main ethical and regulatory challenges of dtc diagnostic and serological tests, focusing on the us context. the first part of this article provides an overview of the landscape of diagnostic and serological tests for covid- , anticipating how their provision models could evolve in the future. the second part identifies five primary ethical and regulatory issues for dtc covid- tests: uncertainty over the accuracy of test results; potential misinterpretation of test results by users; misleading product promotion and misinformation; privacy concerns; and fair allocation of scarce resources. each of these issues parallels prior concerns raised in the dtc health testing arena, but also diverges from them in important ways. we conclude with recommendations for regulators, companies, and other relevant stakeholders that can help ensure high-quality, accurate, and equitably distributed covid- tests, and inform the ethical provision of dtc health tests during public health crises. covid- diagnostic tests aim to determine whether a person is currently infected with sars-cov- , the virus that causes covid- . the most commonly used diagnostic tests during the covid- pandemic are polymerase chain reaction (pcr) tests. for the purposes of testing, a swab is taken from the patient and tested in a lab for the genetic material of the virus. although the typical sample used in these tests is obtained by a nasopharyngeal swab that reaches deep into the nose, the fda recently issued emergency use authorizations (euas) for diagnostic pcr tests using samples collected from shallow nasal swabs and saliva. while pcr is considered to be the 'gold standard' of molecular testing due to its high reliability, this high accuracy may not be applicable to certain rapid point-of-care pcr tests, which according to a recent preprint study, may miss up to % of infections. at present, the only non-pcr diagnostic test that has received an eua is an antigen test used on shallow nasal swabs can rapidly detect fragments of the virus. however, these antigen tests have a higher probability of producing false-negative results than pcr tests, as they cannot detect all active infections. although at first, the majority of covid- diagnostic testing in the usa took place in healthcare settings, a dtc testing market quickly emerged: first with companies marketing at-home tests without fda authorization, and more recently, with such tests authorized by the fda. specifically, in march , companies such as nurx, everlywell and carbon health began marketing at-home collection kits directly to consumers. the provision of tests by these companies involved healthcare professionals to various degrees (i.e. to review an eligibility questionnaire), although typically only after the consumer had initiated or completed the purchase of the test. the marketing of such tests largely coincided with the release of an fda guidance explaining that the agency would permit laboratories and commercial manufacturers to develop and offer covid- diagnostic tests as long as they notified fda that their assays had been validated and submitted an eua. this policy, however, did not apply to at-home sample collection, which instead required that fda issue an eua before marketing. after fda clarified this policy in an update to its guidance document, some companies pulled their at-home collection kits from the market. at least one other did so only after facing enforcement action from local authorities. dtc at-home collection kits, however, are rapidly reemerging with fda authorization. in april , pixel by labcorp received an eua for the first covid- diagnostic test with at-home collection (via a shallow nasal swab kit). currently, consumers can purchase this kit for $ after completing a brief online survey that assesses symptom level (severe, mild or none); potential exposure to coronavirus; and whether an individual is low-or high-risk. one month later, a second diagnostic athome kit that utilizes saliva samples was issued an eua. at present (august ), there are approximately a dozen companies, including everlywell, letsgetchecked, phosphorus, hims, vault health, and health.io, offering authorized at-home covid- diagnostic tests that involve nasal swab or saliva collection. notably, some of these companies have previously faced criticisms outside the covid- context. more specifically, commentators have raised ethical concerns about companies such as hims, whose business model permits consumers to order prescription drugs without interfacing directly with a healthcare professional. concerns about everywell's dtc tests measuring the immune response to food in order to determine food sensitivity. while diagnostic tests aim to detect an active infection, serological tests aim to detect antibodies in the blood, indicating that a person had been infected and recovered from covid- . the presence of such antibodies could potentially indicate that the individual has developed some level of immunity against the virus. the blood sample for these tests is usually obtained through a finger prick. the sample can be collected by an individual and sent to be analyzed in a lab, or be analyzed with laboratory equipment available at a point-of-care location (e.g. in a pharmacy or physician's office) that can deliver results within a few minutes. although the accuracy of these tests for covid- antibodies is not well established, they are at present widely available through numerous laboratories with or without a referral, often in a dtc context that requires consumers to initiate the testing process outside the healthcare system. the widespread availability of serological testing was made possible from a regulatory perspective because, until recently, fda exercised its discretion not to enforce requirements for laboratories and commercial manufacturers operating without an eua, as long as they provided a disclaimer that the tests had not been reviewed by fda and that results should not be used as the sole basis for confirming that someone has the disease. following concerns about the quality of many tests on the market, in may fda changed its approach, aligning its policy for serological tests with that for diagnostic tests. this means that like with covid- diagnostic tests, companies distributing at-home serological tests must obtain an eua before marketing their products. in addition, later the same month, fda published a list of serological tests that could no longer be marketed or distributed. this was because while the manufacturers of these tests had notified fda that they intended to seek an eua, eventually they either voluntarily withdrew their tests from the notification list or failed to apply for an eua. currently, at least two companies offer dtc covid- serological tests. as opposed to at-home collection kits, in this context, consumers initiate the test by making an appointment and having their sample collected in a lab. for example, the quest diagnostics serological test can be purchased online for $ after individuals complete a brief questionnaire that assesses whether an individual is currently symptomatic for covid- . other companies offer tests specifically to employers interested in testing their employees for covid- antibodies. although to-date there are no strictly at-home serological tests, these may be on the horizon: for example, scanwell together with lemonaid health are reportedly developing an at-home antibody test that will require consumers to extract a blood sample and share a picture of the blood testing stick with a healthcare provider, who would interpret the results in a subsequent consultation. in the future, it is possible that covid- diagnostic and serological tests will become increasingly available both on an at-home and consumer-initiated basis, for a number of reasons. first, there is consumer demand, which provides financial incentives for companies to offer such tests. second, there are public health benefits in expanding at-home testing capacity-this type of testing may allow for more individuals to get tested without exposing themselves and others to the risk of infection. third, fda has recently expressed its explicit support for at-home covid- testing, clarifying that such tests may be issued an eua as long as manufacturers provide adequate data and scientific evidence supporting the safety and accuracy of such tests. however, the development of such a market raises ethical concerns and regulatory challenges, which need to be addressed in order to reap the full potential of dtc testing. although covid- testing in general-even when not provided on a dtc basismay raise many ethical and regulatory issues, the five main concerns discussed in this section are particularly pronounced in the dtc space. more specifically, the athome covid- diagnostic testing model presents heightened challenges regarding the accuracy of tests compared to testing that involves sample collection from a healthcare provider. in addition, the absence (or minimal involvement) of a healthcare provider and, potentially of adequate information accompanying the tests, intensifies concerns about the possible misinterpretation of test results. furthermore, to-date, there has been a number of misleading claims made by companies advertising dtc covid- tests (and misinformation from other sources), as well as numerous cases of marketing of fraudulent dtc tests. privacy concerns are also more pronounced in the dtc context, since some companies may not be covered by the health insurance portability and accountability act (hipaa). finally, the provision of dtc tests by commercial providers may exacerbate inequalities in access to testing at the expense of communities that are disproportionately affected by covid- . the major ethical and regulatory concerns that surround the actual processes of dtc testing for both active covid- infection and serological testing mirror existing concerns about dtc health monitoring and disease evaluation tests already widely available in the usa. many of these existing tests, such as hiv tests or the monitoring of hbac levels for diabetes management, have proven track records in medical treatment. however, many others-such as food sensitivity tests and genetic tests for susceptibility to multifactorial disorders-are of uncertain quality, particularly because of their inconclusive clinical validity (i.e. the ability of a test to correctly identify that a particular variant is correlated with increased risk of disease or condition) and unproven clinical utility (i.e. the ability of the test to inform clinical management of a patient). in the covid- context, the public health value of accurate covid- tests is clear. however, there remain questions regarding the accuracy of dtc tests, which is dependent on various factors, including the quality of the sample collected, proper shipment, and stability of the specimen, as well as the sensitivity and specificity of the test. indeed, fda has recently acknowledged that covid- tests involving at-home sample collection may present unique issues regarding accuracy, and in recognition of these challenges it recently published an eua template to help provide guidance to manufacturers of such tests. regarding the quality of the sample, although many diagnostic covid- tests in the healthcare setting utilize nasopharyngeal swabs-which may be difficult for individuals to obtain themselves-such tests seem unlikely to come to the us dtc market. the currently available dtc at-home tests utilize shallow nasal swabs or saliva samples, which are easier for individuals to obtain. early studies have indicated that nasal swabs and saliva samples-even when self-collected-can effectively and reliably identify infections of the sars-cov- virus, suggested that saliva may actually be more sensitive than nasopharyngeal swabs. thus, while further research in this field is necessary, at-present, quality for selfcollected shallow nasal swabs and saliva samples does not appear to be a primary concern. with regard to the shipment and stability of sample, fda has noted that at-home tests may raise particular concerns due to the time lapse between the collection and the analysis. in addition, samples may be subject to conditions during shipment (e.g. high temperatures) that may compromise them. however, for some nasal swabs (foam or polyester) shipped in certain ways (in a dry tube or in saline solution), fda has recently indicated that preliminary data suggest that the samples appear to be stable. thus, at present, samples collected and shipped using these methods appear to alleviate stability concerns, although questions remain regarding stability for other forms of samples and shipment methods. in addition, the sensitivity (i.e. the ability of the test to detect the presence of the virus or antibodies) and specificity (i.e. the ability of the test to detect the absence of the virus or antibodies) of the test itself are also crucial for the reliability of results. while the pcr tests currently used in covid- diagnostic testing are considered to be of high accuracy, there is always a risk of false-positive or false-negative results, and those risks may depend on factors such as testing outside the diagnostic window, and the use of inadequately validated assays. in the case of serological tests for covid- , such concerns are more pressing, as their accuracy has not been well-established and the chance of such tests producing false-positive results may be high, especially in low prevalence populations. a recent preprint study performed by a consortium of laboratories in california found that of the antibody tests studied, one test produced false-positive results over % of the time, and three other tests more than % of the time. given that until recently there has been only limited oversight of these tests, the reliability of serological tests remains an important concern. although dtc covid tests are reviewed by fda before they enter the market this does not eliminate concerns about their accuracy. issues of unproven quality are potentially inherent to those tests that are marketed under an eua, as all fdaauthorized covid- tests currently are. for fda to issue an eua for a test, the federal food, drug, and cosmetic act requires, among other things, that fda conclude it is 'reasonable to believe' that the test 'may be effective in diagnosing' the disease. consistent with this statutory language, fda has explained that the standard for a product being issued an eua requires 'a lower level of evidence than the 'effectiveness' standard that fda uses for [standard] product approvals.' concerns about test quality have intensified following the us department of health and human services's (hhs) august statement that fda will not require premarket review for laboratory developed tests (ldts), including for covid- ldts, unless the agency first goes through notice-and-comment rulemaking to do so. fda describes ldts as tests that are "designed, manufactured and used in a single laboratory," and historically has exercised its discretion not to enforce premarket review requirements for many ldts. but fda also has enforced such requirements for dtc tests (even when they may meet the definition of an ldt), and hhs's statement did not explain whether it was intended to apply to dtc products that may meet the definition of an ldt. it, thus, is unclear what hhs intended its statement to cover and how fda will treat dtc ldts going forward. it is possible that fda will allow some dtc covid- tests that are considered ldts to be offered without an eua. as a result, more tests of uncertain quality may enter the market in the near future. in addition, issues regarding the quality of dtc covid- tests may be heightened because of the widespread, historic nature of the pandemic and the urgent need for expanding testing capacity-and accompanying political pressure. at the same time, however, it is critical that regulators, industry, and the public recognize the need to ensure high-quality standards. the promise of direct-to-consumer covid- testing • for all dtc health testing, the absence of a healthcare professional and, potentially of adequate information regarding the potential limitations of these products, has raised concerns about the risk of misinterpretation of results and of potentially inappropriate subsequent healthcare decision making. these concerns apply even for those tests that have met relevant quality standards. moreover, such concerns are particularly salient for covid- testing. for diagnostic testing, false-negative results could create a false sense of security and contribute to further spread of the virus, while false-positive test results could keep people out of work, school, or childcare, exacerbating economic and educational harms. additionally, although the interpretation of covid- diagnostic testing is relatively straightforward-indicating whether an individual has an acute manifestation of the infectionserological testing is far more difficult to interpret. for example, while preliminary data suggest that recovery from covid- might confer immunity to subsequent infection, it is still uncertain how protective such immunity is and how long it may last. in addition, while many manufacturers claim that their serological tests are of high sensitivity and specificity, many have not released any data supporting their claims. considering the potential unreliability of currently available serological tests and the uncertainty over the meaning of covid- immunity, it is of concern that several companies are marketing serological tests to employers interested in testing their employees, as such results could be used to make decisions about employees going back to work. misinterpreting or overestimating test results could expose individuals to risks of reinfection and could undermine public health mitigation efforts. in this regard, dtc covid- tests, whether diagnostic or serological, should be accompanied by clear guidance and information about their potential and limitations. during the pandemic, with millions of individuals fearful of being sick, but also desperate to resume work, the scale, and immediacy of the adverse impact of misinterpreting covid- test results are far greater than other commercially available dtc health-related tests. many concerns that have been previously raised regarding dtc promotion of healthrelated tests-such as misleading or inaccurate claims, exaggeration of benefits and minimization of risks pandemic, the market has been flooded by companies making unsubstantiated and often fraudulent claims, such as falsely stating that their tests have been approved by fda or that their serological tests can diagnose the disease. to-date, several state and local regulators have issued cease-and-desist orders to individuals and companies on the grounds that they have been illegally promoting and offering covid- tests. at a federal level, both fda and federal trade commission (ftc) have warned companies to stop making misleading claims, including about treating and preventing the coronavirus. in addition to misleading information coming from companies themselves, the public has been receiving an overwhelming amount of misleading information about serological testing from other sources. politicians in the usa and abroad have exaggerated the potential of such tests, touting widespread serological testing as a 'game changer' and a key to restarting the economy. some governments have reportedly considered issuing 'immunity passports' based on positive serological tests results. additionally, in a may statement, the governor of new york stated that detecting covid- antibodies means that, 'you can get to work, you can go back to school, you can do whatever you want.' yet, as explained above, it is still uncertain what positive serological test results mean for functional immunity, how protective any immunity is, and how long it may last. misinformation about covid- tests, whether from companies or other sources, is particularly concerning. misleading product promotion capitalizes on widespread anxiety caused by the pandemic and preys on the vulnerability of consumers, many of whom are likely concerned about their health. the massive amount of information (and misinformation) about covid- , and the quickly changing landscape, may make it particularly challenging for consumers to differentiate between legitimate tests and fraudulent products (which might mislead consumers about their covid- health status). moreover, misinformation regarding the potential benefits and limitations of the tests could lead individuals to misunderstand their covid- health status-even if companies selling the tests are not themselves providing misleading information. dtc testing by private companies in the realm of genetics has raised important questions regarding privacy and confidentiality of personal data. in the usa, companies may not be subject to laws intended to protect the privacy of health information, such as the hipaa. thus, the protection of personal data, including the duration of storage and the third party access to them, is largely determined by terms of service created by the companies themselves. similarly, many of the companies offering at-home covid- tests, whether diagnostic or serological, may not be covered by hipaa and the protection of personal data may, therefore, depend on companies' individual policies. in the covid- context, consumers may erroneously assume, in some cases, that privacy rules governing data in the healthcare setting (such as hipaa) and doctorpatient confidentiality also apply to dtc companies, giving them a false sense of security. furthermore, consumers may not realize that for infectious diseases, the limits of confidentiality may be narrower as compared to other types of tests. more specifically, companies may need to comply with relevant local and state regulations regarding the reporting of positive test results to authorities and may need to disclose protected health information without obtaining prior permission from the consumer. currently, several state and county health departments require healthcare practitioners and medical laboratories to report covid- cases, providing, amongst other information, the name and address of the patient. while the policies of some companies are more transparent than others, it is likely that consumers will click 'i agree' to terms and conditions without ever reading them. this may be especially the case with individuals ordering diagnostic tests, as it is likely that such tests will be purchased under conditions of urgency and anxiety that may not allow for careful review of the relevant contracts. in addition, given the scarcity of tests, some people may not feel that they have the option to refuse. policies regarding third-party access to data are particularly relevant, especially in view of risks of discrimination in the context of employment. more specifically, it is possible that employers may be interested in accessing serological test results, especially when they are the ones initiating the testing. this is because confirming that employees have immunity could be relevant for recruitment decisions. for these reasons, it is important for consumers to understand the limits of confidentiality of their health information and the risks of a privacy breach. in recent years, dtc health testing has been marketed to consumers as an opportunity to access a wide range of health information directly, often completely bypassing the mainstream healthcare setting. by offering consumers information on genetic susceptibility to multifactorial disorders, carrier status, reproductive health, and infectious diseases, many dtc companies have presented themselves as expanding access to testing and enabling consumers to take control of their health. however, there have been longstanding concerns that such testing could eventually lead consumers back to the mainstream healthcare system for consultations regarding their test results, creating downstream costs and using resources that, in some settings, may be scarce. for covid- tests, competition over scarce resources may be more direct and tangible. currently, there are shortages of basic elements of diagnostic tests, such as swabs and reagents, both in the usa and worldwide. such shortages are partly responsible for the inadequate testing capacity in the usa. despite an increase in the number of tests performed daily since the first month of the pandemic, testing is still not scaled up sufficiently to meet public health needs or consumer demand. in this regard, companies offering dtc covid- testing could provide an alternative for individuals and expand access to testing. however, given the scarcity of resources, they could also be in direct competition with other healthcare providers, such as hospitals. the use of scarce resources by companies offering dtc testing during a global pandemic could also raise concerns over fair allocation of such resources. previous research has indicated that consumers who purchase dtc health testing tend to be of higher socioeconomic status. for example, empirical studies of dtc genetic testing have shown that the majority of the consumer base is white, highly educated, and has a higher than average household income. consistent with such findings, in the context of covid- , it is possible that poor and marginalized communities will have less access to dtc tests, because of inadequate financial resources, limited information about the availability of such tests, companies' marketing strategies, or other reasons. this is particularly concerning given that racial and ethnic minority groups have been disproportionately affected by the pandemic. currently, several state and county health departments are expanding testing capacity by launching testing sites in underserved communities. in order to avoid two-tiered access to testing based on socioeconomic status or race, it is important that efforts to provide free testing to low-income communities, as well as to communities of color, are sustained and expanded across the usa. currently, issues of fair access to covid- testing are more pressing for diagnostic tests, as they have clear clinical utility and are considered more reliable compared to serological tests. however, considering the ongoing policy discussions in some countries regarding using serological test results as an 'immunity passport' that would allow individuals to return to work, ensuring equitable access to serological testing may become crucial in the near future. as this article highlights, many of the concerns surrounding dtc covid- parallel those surrounding other dtc health tests that are widely available in the usa. however, the scale of the present pandemic lends an increased urgency to existing issues. given the fast-changing landscape of the covid- pandemic, this article cannot predict or address all issues associated with dtc covid- testing that are likely to arise. there are, however, several recommendations that can help inform the ethical provision of dtc health tests during this public health crisis. first, consistent with its obligations under the federal food, drug, and cosmetic act, fda should reassess its euas and remove authorization for tests that are found to be of low quality. enabling testing to reach the market as quickly as possible is, of course, an important goal. but testing is not useful if consumers, healthcare professionals, and public health regulators cannot be confident in the results. ultimately, fda must ensure progress in studying and developing high-quality testing continues, and assure available testing meets the conventional-rather the lower, euastandards. second, all stakeholders should be working to educate policymakers and the public with accurate, non-misleading information about the limits and potential benefits of dtc testing. for example, companies should provide consumers adequate and clear information regarding their tests, in both communications about how to interpret test results and in promotional materials. ftc and states should continuously monitor the market and take action when necessary to protect consumers and ensure they have accurate and non-misleading information. in addition, for companies that are marketing dtc tests under an eua and that make misleading claims that have a negative public health impact, fda should make clear it will consider withdrawing the eua. third, with regard to privacy, it is crucial that companies provide transparent and easy-to-comprehend privacy policies that are not buried amongst other terms and conditions. considering the vulnerability of consumers and the ongoing public health crisis, the ftc should monitor the practices of such companies closely to ensure that such terms are not disproportionate and safeguard the rights of consumers to privacy. fourth, equitable access to high-quality dtc tests is critical. at a minimum, companies should make clear whether their tests are covered by health insurance and whether they provide options for individuals who cannot afford standard prices, whether or not they are insured. but more is likely to be needed-and if mechanisms for equitable access for covid- testing are successfully developed, they can inform models of access for other kinds of potentially beneficial dtc testing. ensuring a market of accurate and ethically marketed dtc covid- tests presents significant challenges for regulators and requires the buy-in of all stakeholders, including industry. at the same time, regulators and industry may be well-equipped to address many of these challenges, drawing on past experience regulating other dtc tests. regulators, industry, and the public also have an opportunity to think carefully about the risks and benefits of different models of dtc testing, and ultimately use the lessons learned from covid- to improve the dtc testing market. saliva is more sensitive for sars-cov- detection in covid- patients than nasopharyngeal swabs, medrxiv food and drug administration, supra note potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease test performance evaluation of sars-cov- serological assays antibody tests go to market largely unregulated, warns house subcommittee chair direct-to-consumer genetic testing: perceptions, problems, and policy responses all your data (effectively) belong to us: data practices among direct-to-consumer genetic testing firms the future of dtc genomics and the law hipaa and protecting health information in the st century privacy in the age of medical big data genomic privacy and direct-to-consumer genetics: big consumer genetic data-what's in that contract? health system implications of direct-to-consumer personal genome testing, public health genomi hipaa for professionals: faq reporting covid- /sars-cov- infections employers rush to adopt virus screening. the tools may not help much testing remains scarce as governors weigh reopening states testing challenge: why it's so hard to overcome testing shortages in the united states a dire warning from covid- test providers cities still lack testing capacity consumer perspectives on access to direct-to-consumer genetic testing: role of demographic factors and the testing experience: consumer perspectives on access to direct-to-consumer genetic testing design, methods, and participant characteristics of the impact of personal genomics (pgen) study, a prospective cohort study of direct-to-consumer personal genomic testing customers the impact of the covid- pandemic on marginalized populations in the united states: a research agenda covid- : disproportionate impact on ethnic minority healthcare workers will be explored by government amid ongoing covid- pandemic, governor cuomo launches new initiative to expand access to testing in low-income communities and communities of color denver launching coronavirus testing to help communities of color county expands coronavirus testing in hard-hit black, latino communities louiza kalokairinou is a postdoctoral fellow at the department of medical ethics and health policy, perelman school of medicine, university of pennsylvania. louiza received a phd degree in she worked as a policy officer in the research ethics and integrity sector of the european commission. louiza's research focuses the ethical, legal, and social aspects of direct-to-consumer health products and emerging technologies zettler is an associate professor of law at the ohio state university moritz college of drug enforcement & policy center housed at the college of law, and a member of the ohio state university comprehensive cancer center in addition to professor zettler's academic work, she served as an associate chief counsel in the fda's office of the chief counsel ashwini received a ba degree in public health/sociology from nyu and master of bioethics from the university of pennsylvania. she will continue her education at ucla this fall with a phd in health policy and management kyweluk is a postdoctoral fellow at the department of medical ethics and health policy, perelman school of medicine, university of pennsylvania. moira holds a joint phd/mph from northwestern university in medical anthropology. her research specialization is reproduction in the united states with a focus on assisted reproductive technologies, queer and transgender family building, reproductive health, and peri-conception genetic testing anna wexler is an assistant professor in the department of medical ethics and health policy, perelman school of medicine, university of pennsylvania. she is the principal investigator of the wexler lab, which studies ethical, legal, and social issues surrounding emerging technology, with a particular focus on do-it-yourself and direct-to-consumer medicine and science this study was supported by the office of the director, nih, under award number dp od . dr. kyweluk's work was supported by a postdoctoral training grant from the national human genome research institute grant number t hg . key: cord- -w lrz authors: sabit, maureen; wong, cecil; andaya, agnes; ramos, john donnie title: pollen allergen skin test and specific ige reactivity among filipinos: a community-based study date: - - journal: allergy asthma clin immunol doi: . /s - - - sha: doc_id: cord_uid: w lrz background: despite the clinical importance of pollen allergens among filipinos, few studies delve into the sensitization profiles of filipinos against pollen allergens. this study determined the sensitization profile of filipinos to pollen using skin prick test (spt) and pollen-specific elisa. methods: pollen from fifteen selected plant sources was collected and extracted for use in sensitization tests. volunteers were interviewed for their clinical history prior to blood sampling and spt. the blood samples collected were assessed using enzyme-linked immunosorbent assay (elisa). results: the best panel of pollen allergens for the skin prick test was mangifera indica ( %), acacia auriculiformis ( %), mimosa spp. ( %) amaranthus spinosus ( %), lantana camara ( %), pilea microphylla ( %) and dichanthium aristatum ( %). young adults had more sensitizations to pollen than among early childhood and elderly. there were more allergic subjects that have rhinitis ( %) than asthma ( %) and atopic dermatitis ( %). pollen-specific ige levels show low percent reactivity as compared to the skin test with cocos nucifera obtaining the highest ige reactivity ( %). conclusions: pollen allergens from both arboreal and herbaceous plants used in this study yielded positive reactivities for both skin tests and specific ige tests. allergy is a hypersensitive reaction characterized by an immune-mediated inflammatory response to common environmental protein allergens that are deemed to be harmless in non-allergic individuals [ ] . the global increase in the prevalence of allergic respiratory diseases and their effect on the quality of life of allergic patients is a health issue that needs immediate attention [ , ] . in the philippines, the reported overall prevalence of allergic rhinitis and allergic rhinoconjunctivitis is % and %, respectively [ ] ; whereas, work absence due to asthma is reported at . % [ ] . pollen is one of the most common and important sensitizing aeroallergens [ ] [ ] [ ] [ ] that cause respiratory allergies such as allergic rhinitis, allergic asthma, and atopic dermatitis. dissemination or dispersal of pollen, which occurs during a plant's pollination or flowering period, ensures survival and continuity of its lineage. small, lightweight pollen, which is produced in copious amounts by anemophilous (wind-pollinated) plants, are the major allergens in the atmosphere. several studies have shown that the incidence of pollinosis in urban areas is higher than the countryside due to unsuitable green space construction, urban heat island effect, and traffic pollution [ ] . allergy, asthma & clinical immunology *correspondence: mbsabit@ust.edu.ph; mhayen @gmail.com research center for the natural and applied sciences, thomas aquinas research complex, university of santo tomas, manila, philippines full list of author information is available at the end of the article in tropical asia, little information on pollen allergens is available [ ] , and information on the sensitization profiles of filipino allergic patients to pollen allergens is limited. sensitization to grass and weed pollen among filipinos was reported earlier [ ] and described anew by recent studies using immunobiological techniques [ , ] . it is in this context that this study was conducted. aqueous extracts of tree and weed pollen found to be abundant in the atmosphere were used to generate the sensitization profile of filipinos using skin tests. this study aims to determine the total ige and pollen specific-ige profiles of skin-test positive and negative subjects and correlate skin tests with pollen-specific ige reactivity. vegetation or the "green space" in a highly urbanized city of metro manila, is found only in parks, gardens, and trees planted along the road. ten barangays near the vicinity of a pollen trap (situated within the university of santo tomas, manila) were randomly chosen for this study. prior to sampling, an approval from the ust graduate school institutional ethics committee review board was obtained. a total of volunteers who have been living, working, or studying in the "university belt" for more than years prior to the conduct of this study were recruited. spt-positive subjects were designated as cases while spt-negative subjects were controls. all participants gave their informed consent prior to answering a standardized questionnaire. this questionnaire was adapted and modified by de guia [ ] from previous sources [ ] [ ] [ ] , and, validated these questionnaires for filipino patients. the fifteen plants chosen as sources of pollen were previously reported as widespread in metro manila, and most are representative of the plant families with a high prevalence of airborne pollen [ ] . . pollen samples were collected from the mature anthers of these plants and processed as described [ ] . flowers from trees and weeds were dried then passed through reducing sizes of mesh sieves ( , , and µm, respectively). the presence of pollen was confirmed under a stereomicroscope (bs- t digital biological trinocular microscope). pollen was stored in a tightly sealed container with a desiccant at °c. one gram (dry weight) of pollen was mixed with ml diethyl ether and placed on a shaker overnight. the defatted pollen was centrifuged at rpm for min, left to dry overnight, and mixed with ml phosphate buffered saline (pbs). the mixture was stirred overnight at °c and centrifuged at , rpm, °c for min. the supernatant was transferred to a dialysis tubing ( - kd mwco, supplied by spectrum labs, usa) and passed through a . μm millipore filter (whatman puradisc , pes sterile). ml aliquots of the dialyzed products were transferred to microcentrifuge tubes and stored at − °c until use. the total protein content of the pollen was analyzed using bio-rad protein assay kit ii (bio-rad laboratories inc, hercules, ca, usa). each crude pollen aqueous extract was diluted with the appropriate amount of pbs to get a final concentration of µg/ml for use in skin prick test (spt) and pollenspecific ige elisa. volunteer selection was made carefully following the guidelines as described [ ] . spt was performed on all participants using a panel of crude pollen extracts, house dust mites (hdm) suidaisia pontifica (sud), and blomia tropicalis (blo), and with histamine ( . %) in pbs and physiologic saline solution as positive and negative controls, respectively. a drop of each pollen extract was directly pricked on the participant's forearm using a mm-point sterile lancet. a white wheal measuring ≥ mm in diameter and a red flare around the pricked skin area was interpreted as positive spt [ ] . five ml peripheral blood of study participants was collected in edta tubes and then centrifuged to separate the plasma. samples were aliquoted and stored at − °c until further use. the total ige levels of cases (n = ) and controls (n = ) were determined following the manufacturer's protocol (human ige elisa core kit, komabiotech, south korea). for pollen-specific ige elisa, μg/ml aqueous pollen extracts diluted in carbonate-bicarbonate buffer were coated overnight at °c onto the wells of high-binding microtiter plates (corning costar, ny, usa). plates were blocked with % bsa (sigma-aldrich, saint louis, mo, usa) in pbs for h at room temperature. plasma samples from both cases and controls were dispensed in duplicates onto the wells and incubated for h at room temperature. plates were incubated with × dilution of an hrp-conjugated goat anti-human ige for h at room temperature. colorimetric reactions for all immunobiological tests were performed using tmb ( , ′, , ′-tetramethylbenzidine) and the reaction was stopped with m h so . absorbance was read at nm using bio-tek elx elisa reader (tecan, austria). data characteristics of test subjects (cases and controls) and positive reactions to different pollen allergens using skin prick test and specific ige elisa were presented as frequency (percentage) and compared using the chi square test of homogeneity or fisher's exact test or z-test for two sample proportions. the diagnostic performance of spt (positive and negative predictive values, specificity and sensitivity) with pollen, was computed. spearman's correlation coefficient was used to test the association of the different pollen based on pollen-specific ige elisa results. percent reactivity of pollen-specific ige and sensitization profile among age groups were graphically represented. frequency tables and graphs were created, and data analyzed using spss (v. ), ms excel and/or graphpad prism . five hundred forty-one study subjects from metro manila were recruited. seven percent ( %) of the study subjects were excluded because of non-cooperation, had taken antihistamine drugs before testing and backing out at the last minute. of the % that were positive to skin tests (n = ), % (n = ) were positive to both pollen and hdm, % (n = ) were positive only to pollen, and % (n = ) were positive only to hdm. subjects that tested positive to pollen (cases, n = ), who self-reported to having allergic asthma (aa), allergic rhinitis (ar), and atopic dermatitis (ad), were referred to as allergic ( %), while those who self-reported not to have allergic diseases were asymptomatic. of the skin-test negative subjects (to pollen), were asymptomatic and referred to as controls. table shows the characteristics of the test subjects (cases and controls). significant differences were shown in the percentage number of children ( - years old), young adults ( - years old), between gender and those with a family history of allergies between cases and controls. of asymptomatic cases (n = ), % have family members that were allergic. allergic asthma (aa) and ar were commonly reported in either the father or mother of the cases. several cases and controls have pets at home, and there were no significant differences between them. the most common household pet were dogs (cases- %, controls- %), cats and birds (cases- %, controls- %) and a combination of dogs, cats, and birds (for cases only- %). likewise, no significant differences were shown between cases and controls who self-reported to smoke or have family members who smoke. allergic rhinitis ( %) was prevalent among allergic cases, followed by aa ( %) and ad ( %). total ige values of ≥ iu/ml of subjects in cases and controls were % (n = ) and % (n = ), respectively. based on spearman's rho, there was no significant difference in the mean ige levels between gender (cases and controls) and presence of allergic diseases in cases, although, the highest mean was obtained from male allergic subjects ( . iu/ml) and those with aa ( . iu/ml) and ad ( . iu/ml). of the species of arboreal plants used for spt, most of the study subjects tested positive to three pollen sources: mangifera indica (man), acacia auriculiformis (aca), and lantana camara (lan) as shown in table . study subjects were also positive to the pollen of herbaceous species, namely, mimosa spp. (mim), amaranthus spinosus (ama), pilea microphylla (pil), and dichanthium aristatum (dic). wheal diameters of - mm were observed in subjects who tested positive to mim and man. based on sensitizations, % and % of positive subjects from skin tests and pollenspecific ige elisa, respectively, were sensitized to one allergen (monosensitization) while the rest of the test subjects were sensitized to two or more allergens (polysensitization). figures and show the sensitization profile of allergic subjects across age groups. male children ( - years old) have early sensitization than females. however, females show high sensitizations than males in all other age groups. overall, there was an increase in the number of sensitizations to young adults ( - years old) and then gradually declined in the older age groups. likewise, the number of polysensitized ( % males, % females) subjects show similar tendencies while monosensitization ( % male, % female) were more evident in younger age groups. the sensitivity and specificity of the skin tests were % ( % ci - %) and % ( % ci - %), respectively. the prevalence of the allergic disease in the population was % with a positive predictive value of % ( % ci - %), and a negative predictive value of % ( % ci - %). significant differences in positive reaction to skin tests and pollen-specific ige elisa were shown in pollen allergens ( table ) . fifty-four percent ( %) of skin ige of ≤ iu/ml (fig. ) . as shown in table recent sensitization studies in the philippines were mostly on specific-ige profiles of filipinos to selected grass species (pollen) and house dust mites [ , ] . studies on spt using pollen from grasses and weeds have also been described [ ] . after a few decades, in this study, other sources of pollen, particularly from trees were utilized for both spt and elisa tests. although m. indica, a. auriculiformis, and l. camara are entomophilous, there have also been published reports of their allergenicity [ , ] . skin prick tests (spt), which is an essential procedure to confirm sensitization in ige-mediated allergic disease in subjects with allergic rhinitis, asthma, and atopic dermatitis, can be performed from infancy to old age [ ] . likewise, spt is considered a safe diagnostic procedure as the occurrence of systemic reaction has decreased and cases of fatalities were extremely low [ ] . aside from time, cost and safety, spt had a high sensitivity to aeroallergens, mainly pollen and house dust mites [ ] . factors that influence the pollen threshold values for the development of allergic symptoms are as follows: time of the season, weather conditions, pollen allergenicity, air pollution and patient characteristics [ ] . the recruitment of study subjects was done near the end of the flowering season (from april to june) when most of the trees (e.g. m. indica, c. nucifera, eucalyptus spp., etc.) were in full bloom and bear fruits. the flowering of some plant sources are seasonal (e.g. m. indica, eucalyptus spp., etc.) but most flower all throughout the year (e.g. c. nucifera, d. meyeniana, l. camara, etc.). as previously reported [ ] , the concentration of airborne pollen decrease near the end of may up to the first weeks of june, due to the increasing amount of rainfall in the region. the high prevalence of allergic disease and high positive predictive value signify that there is a high probability that the amount of pollen in the air may have caused the allergic disease of the allergic subjects. although skin tests in this study detected only almost one-third of the study subjects with allergic disease (low sensitivity), it has a high probability (specificity) that it can discriminate those who do not have an allergic disease in any of the pollen allergens used. similarly, in another study, only . % of their study subjects were sensitive to pollen allergens [ ] . allergic cases who tested negative to the skin tests require another test or another panel of pollen allergen to confirm results. whereas, asymptomatics may develop allergic diseases later in life [ ] . in this study, there's a discrepancy between results from spt and pollen specific-ige (sige), particularly that of m. indica. a recent study [ ] made an assumption that tropical flora produces highly glycosylated allergens that hid or mask protein epitopes. as a result, ige binds to these non-allergenic, pollen-derived carbohydrate epitopes instead of the allergenic protein allergens. this ultimately resulted in a specific-ige negative response. likewise, spt-negative subjects that are positive to specific-ige elisa may be due to the presence of a crossreactive carbohydrate determinant or ccd [ ] [ ] [ ] , or the lack of pollen coat allergens, containing allergic epitopes [ ] . more than % of allergic patients that were asymptomatic have their ige bind to carbohydrate compounds instead of the allergen [ ] . in this study, some skin test-positive subjects were asymptomatic. ideally, a subject that has a positive clinical history would also have positive allergen-specific test results [ ] . instead, anomalies in having either positive or negative test results occur since the cause or presence of allergic disease are not revealed in all cases with positive clinical history. even if a patient was clinically allergic to an allergen if there were no recent exposure, then allergic symptoms may be caused by something else; or, a patient may be sensitized to an allergen but not clinically allergic to it [ ] . however, a significant number of allergic sensitizations may be missed if only one type of testing was performed [ ] . thus, spt and specific-ige testing should not be interpreted interchangeably but instead used as complementary [ ] . among asians, exposure to pollen in urban communities is less than in rural areas. studies suggest that early/childhood exposure to pollen (and keeping pets) can protect against allergic sensitization up to adulthood [ ] . in contrast, this protective effect of rural living had changed due to a shift in urban lifestyle in rural areas [ ] . locally, pediatric patients showed that house dust mites and cockroaches were the main allergens, followed by sorghum jalapense, a. spinosus, and m. indica [ ] . likewise, a. spinosus, m. indica, together with, mimosa and a. auriculiformis were less allergenic to children. although m. indica and a. auriculiformis belong to < % of the airborne pollen in manila [ ] , its [ , ] . alternatively, in this study, trees such as c. papaya and c. nucifera belonged to > % of airborne pollen in manila [ ] but showed low sensitization in skin tests. this contrasts with other studies, wherein c. papaya, and c. nucifera elicited a high response to spt [ , ] , which may be attributed to geographical location, climate and allergen exposure. a high percentage of test subjects in this study reported a history of rhinitis and asthma, which, are allergic diseases often associated with sensitization to aeroallergens [ ] . sensitization to pollen in this study peaked at the young adult stage ( - years old), and male sensitization started earlier than females, as is also shown in previous studies [ , , ] . a longitudinal study of an urban population in central italy [ ] revealed a significant increase in skin prick test reactivity, using the same sample population, across age groups and particularly in subjects < years old. at present, there is no accepted explanation for the sensitization shift between genders [ ] . in a review assessing the impact of age on atopy, immunosenescence or a lower expression of ige was observed as the cause of age-related decrease of positive skin test [ ] . exposure to environmental allergens increases over time as evidenced by the number of polysensitization, particularly in older age groups, as shown in this study. this polysensitization was also evident when pollen allergens were tested for cross-reactivity using an elisa inhibition assay. nearly all pollen, either closely or distantly related, had weak to strong associations and although of low percentage inhibition value, this may indicate the presence of cross-reactive proteins. cross-reactivity between closely related plants reflects phylogeny, shared antigens or epitope binding sites, while cross-reactivity in distantly related plants, is due to minor allergens (e.g., profilins, lipid transfer proteins, and pathogenesis-related proteins) [ ] . these minor allergens, called panallergens [ ] play a significant role in the distribution of the allergic response to conserved epitopes of different allergenic sources [ ] . in conclusion, pollen allergens from both arboreal and herbaceous plants used in this study yielded positive reactivities for both skin tests and specific ige tests. additionally, for a small community-based study population, it shows that filipinos living in a highly urbanized city are allergenic to local pollen. further sensitization studies should be done to assess if there would be differences between those living in urban and rural areas. moreover, longitudinal studies comparing populations using the same tests and methods should be undertaken at different periods to have a more conclusive set of data. likewise, an 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specific ige in young children variability of offending allergens of allergic rhinitis according to age: optimization of skin prick test allergens the impact of age on prevalence of positive skin prick tests and specific ige tests guidelines for using pollen cross-reactivity in formulating allergen immunotherapy types of sensitization to aeroallergens: definitions, prevalences and impact on the diagnosis and treatment of allergic respiratory disease pollen-cross allergenicity mediated by panallergens: a clue to the pathogenesis of multiple sensitizations publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations the authors wish to thank the following individuals for their assistance and technical support: nicole andreanna bulseco, vanessa maris cariño, romina bianca dinglasan, rencie espino, raymond michael baladad, ina marie de jesus, john darrel pamintuan, emmanuel tom rosales, and carol navidad. gratitude is also extended to the following institutions for the use of their facilities: university of santo tomas college of science, university of santo tomas graduate school, and university of santo tomas research center for the natural and applied sciences. ms designed the study, gathered all data, performed statistical analyses and interpretation of data, and drafted and revised the manuscript. cw contributed to data collection and interpretation of data. aa contributed to the design of the study and helped interpret data. jr contributed to the design of the study, helped in the interpretation of data and participated in the revision of the manuscript. all authors read and approved the final manuscript. there were no funding agencies used in the conduct of this study. the datasets during and/or analysed during the current study are available from the corresponding author on reasonable request. key: cord- -mqs xm authors: theagarajan, lakshmi n. title: group testing for covid- : how to stop worrying and test more date: - - journal: nan doi: nan sha: doc_id: cord_uid: mqs xm the corona virus disease (covid- ) caused by the novel corona virus has an exponential rate of infection. covid- is particularly notorious as the onset of symptoms in infected patients are usually delayed and there exists a large number of asymptomatic carriers. in order to prevent overwhelming of medical facilities and large fatality rate, early stage testing and diagnosis are key requirements. in this article, we discuss the methodologies from the group testing literature and its relevance to covid- diagnosis. specifically, we investigate the efficiency of group testing using polymerase chain reaction (pcr) for covid- . group testing is a method in which multiple samples are pooled together in groups and fewer tests are performed on these groups to discern all the infected samples. we study the effect of dilution due to pooling in group testing and show that group tests can perform well even in the presence of dilution effects. we present multiple group testing algorithms that could reduce the number of tests performed for covid- diagnosis. we analyze the efficiency of these tests and provide insights on their practical relevance. with the use of algorithms described here, test plans can be developed that can enable testing centers to increase the number of diagnosis performed without increasing the number of pcr tests. the codes for generating test plans are available online at [ ]. the novel corona virus has caused a pandemic in early . the reproduction rate of the corona virus is estimated to be between . and . [ ] . from an infected patient, covid spreads to . to . others on an average. as the virus spreads through respiratory droplets, it spreads at an exponential rate, especially, in densely populated locations. the infected patients become carriers at an early stage even before the onset of symptoms [ ] . thus, it becomes imperative to test a large number of people and identify early stage infections to contain the spread of covid- . the pcr based testing is considered to be one of the best techniques for early stage diagnosis [ ] . group testing is well known methodology in the combinatorics and compressed sensing literature [ ] . in group testing(gt), multiple samples are pooled together to form groups (fewer in number than the total number of samples). tests are performed on these groups and from the outcome of these tests, the infected samples are inferred. group testing relies on the fact that not all of the tested samples may be infected. thus, by employing group testing for covid- diagnosis, the number of samples tested can be increased, the tests performed can be made economical and the speed of detection can be improved. this can lead to efficient containment of the spread of covid- . in this article, we investigate group testing for covid diagnosis using pcrs from a practical view. we analytically study the effect of dilution, caused by pooling in group tests, on the accuracy of the tests. we present multiple group testing algorithms with which a test plan for diagnosis of a pool of samples can be generated. we analyze and present the scenarios in which the presented algorithms are appropriate. we show through simulations that group testing can provide considerable gains in the number of tests performed. finally, we provide some guidelines for performing covid diagnosis in practice. a practitioner can directly generate the test plans using the matlab codes that are available online at [ ] . certain key findings and discussions of this article can be listed as follows: • when the infection rate is less than %, group test can help to reduce the number of tests significantly. some examples on the gains obtained through group testing (with a sensitivity of more than %) are given below. number of samples to test infection rate % % % % % % number of tests required by group testing • replication or repeating a test is required to improve the accuracy of any qrt-pcr test outcome. we find that replicating the test twice could be sufficient to get high accuracy. further, group testing could provide inherent replication and reduce the number of replicates required. for details refer to sections . and . . • we also analyzed the effect of dilution caused by dividing a swab sample's content to smaller portions and mixing multiple samples together. this helped us to determine an upper limit on the number of samples that can be pooled together. it was found that up to samples can be pooled together without reducing the test accuracy. for details refer to section . . • it was found that different group testing strategies are optimal under different conditions. the diagnostician should adapt the test plan depending on the infection rate of a given cluster or local community. test plans that are optimal for a given infection rate are discussed in section . further guidelines to follow while testing for covid- through group testing are discussed in section . notations: . denotes the floor operation, i.e., largest integer lesser than or equal to the given number. . denotes the ceil operation, i.e., smallest integer greater than or equal to the given number. . denotes rounding off operation. |a| denotes the cardinality of the set a, i.e., the total number of elements in the set a. the real time or quantitative reverse transcription polymerase chain reaction (qrt-pcr) is the testing method used for early detection of covid. in rt-pcr, the viral rna molecules present in the test medium are first reverse transcribed into dna, which is referred to as the complementary dna (cdna). the cdna corresponding to the covid genes are amplified using pcr, which is performed through thermal cycling. in the high temperature cycle, the target cdna's double-helix strands are separated (referred to as the denaturation process). in the low temperature cycle, the primers bind onto the cdna strands (referred to as annealing) to initiate the polymerization through which the free nucleotides assemble on the dna strands to form a new double-helix dna (referred to as the elongation process). thus, in every cycle the number of dna particles present are doubled; refer fig. . after several cycles, the total number of target dna present is increased to an exponentially large volume. finally, fluorescent dyes that fluoresce in the presence of the target dna are used to visually identify the presence or absence of the virus. the number of thermal cycles determine the final volume of target dna present; hence, by increasing the thermal cycles (also referred to as amplification cycle), the sensitivity or the detection accuracy of qrt-pcr can be improved. a detailed procedure and reagents used in qrt-pcr for detection of covid can be found in [ ] . using qrt-pcr, it was found that virus particles are sufficient to successfully detect the presence of the virus in a test sample with very high accuracy (> . %) [ ] . however, this accuracy or goodness of test may vary with the qrt-pcr kit used. we define the following metrics to compare and analyze the goodness of tests. let x be a binary random variable that denotes the presence (x = ) or absence (x = ) of the virus in a test sample. let x t be a binary random variable that denotes the outcome of a test. definition -false negative rate : γ = pr(x t = |x = ) the rate or probability of the outcome of a test being negative when the virus is actually present in the sample. alternatively, the sensitivity is defined as the probability of the test outcome being positive when the virus is actually present in the sample; this is given by −γ = pr(x t = |x = ). it is desirable for the test to have a low value for γ. definition -false positive rate : β = pr(x t = |x = ) the rate or probability of the outcome of a test being positive when the virus is actually absent in the sample. it is desirable for the test to have a low value for β. definition -prior : α = pr(x = ) the rate of occurrence of the virus in a given population. the prior can be approximately computed, using previous history, as the ratio of the number of positive cases to the total number of tests performed. it is important to minimize sample bias in this heuristic computation. according to [ ] , the prior (at the time of writing this article) for united states of america is about . and for india is about . . among the countries where more than tests were performed, the lowest prior is for uae (about . ) and the highest is for spain (about . ). in real life, we are more concerned about the false negative rate (as opposed to false positive rate). it is very important to have the least γ to minimize the spread of covid and fatality caused by it. further, the value of these rates depend on the viral load or the number of viral rna copies present in the test (denoted by l). we denote the false negative and positive rates as a function of l using γ(l) and β(l), respectively. it was found in [ ] that γ( ) ≈ . . therefore, the goodness or efficiency of a testing technique is given by γ(l) and β(l). it is necessary to know these parameters for a given testing technique before we can analyze the efficiency of group testing using the same. often tests are performed multiple times on a single sample to confirm the outcome and account for any variability in the testing procedure, thereby improving the accuracy of the test. here, we shall analyze the improvement in accuracy when tests are replicated for a given sample. when the test is replicated r times, the outcome is declared based on the majority rule. to declare the final decision as negative, the apr should have a value greater than . the expressions to compute the sensitivity and apr due to replication are derived in appendix a. figure illustrates the improvement in accuracy for double and triple replication. from fig. a , one can choose the value of r, i.e., how many tests to perform depending on the γ of the testing technique and the γ r that is desired. for example, when γ is small (< . ), double and triple replicates give very similar performance; hence, double replication will suffice. figure b shows us that replication is necessary when the prior is more than % at a false negative and positive rates of % and %, respectively, for the testing technique. group testing(gt) refers to the idea of pooling multiple samples together and performing tests on certain subsets of these samples to discern the infected samples. first, we illustrate gt through a simple example given in fig. here, we have utilized only tests to diagnose samples -a % reduction in the number of tests. note that, if we had known that there was exactly one infected sample, then only tests would be required (tests and would not be required). this gt algorithm is referred to as the binary search and is the optimal gt when there is exactly one infected sample in a given pool. in general, to test a pool of n samples with up to one infected sample, we require at most log n tests and at least log n tests. this gain increases exponentially with n ; for example, n = requires at most tests with gt as opposed to tests without gt. the theory of group testing deals with the design and analysis of algorithms that tell us how to choose subsets (groups) of samples to pool together and test, and identify the infected samples. in other words, gt aims to minimize the number of tests (t ) required to identify at most d number of infected samples among n number of given samples (pool size); ≤ d < n and t ≤ n . in practice, the value of d is not known. nevertheless, depending on the value of the prior, an upper bound on the number of infected samples can be chosen as d for a given n . there are two paradigms of gt, namely, • combinatorial group testing (cgt): the combinatorial algorithms require the exact number (or an upper bound) of the infected samples d. as long as the chosen value of d is greater than or equal to the true number of infected samples, cgt algorithms always identifies the infected samples correctly. • probabilistic group testing (pgt): the probabilistic algorithms require an upper bound on α and identify all infected samples with certain probability p d . usually, the detection probability p d is very close to ; however, there still may be a non-zero probability of the infected cases going unidentified. for small values of α, the average number of tests performed in pgt is less than n ; however, there can exist cases for which the number of tests performed by pgt might be greater than n , albeit, the probability of occurrence of such cases will be relatively small. in pgt, there exists a trade-off between p d and the average value of t . from the above discussion, it can be seen that, due to their deterministic nature, cgt algorithms are preferred in practice to test for diseases. when an upper bound on d cannot be reliably established, pgt algorithms may prove to be more efficient as opposed to cgt. there exists pgt algorithms in which p d = . in the worst case (i.e., when d = n − ), the value of t can be greater than n , but the average value of t can still be much less than n . this is further discussed in section . cgt and pgt algorithms are further classified into • adaptive tests: here, the tests are performed sequentially. first a group is chosen randomly based on d n or α and tested, the outcome of this test determines the next group to test and so on. thus, the size and samples of a group are chosen adaptively based on previous group and its test outcome. the gt described in figure is an example of adaptive cgt. • non-adaptive tests: when the test plan is fixed for a given d and n , then it is known as the non-adaptive gt. here, a fixed number of tests are always performed irrespective of the number of infected samples present in the pool. an advantage of non-adaptive gt is that, if t n is the number of groups to be tested, then all the t n tests can be simultaneously run in parallel. the non-adaptive gt can be represented by a matrix of dimension t n ×n (referred to as the measurement matrix), and the samples can be represented by a n × vector with 's for uninfected samples and 's for infected samples. the measurement matrix consists of 's and 's, the 's in a row correspond to the samples included in a test and the 's in a column correspond to the number of times a particular sample is tested. the boolean or operation between the measurement matrix and the samples vector gives the gt outcomes. now, designing a non-adaptive gt algorithm becomes a problem of designing efficient measurement matrices and decoding algorithms to discern the positions of 's in the sparse samples vector with the given t n test measurements. the non-adaptive test algorithms can be studied with the aid of compressed sensing literature [ ] , [ ] . a key drawback of the non-adaptive gt algorithms is that it requires a large value of n (in the order of − ) to be efficient and provide reliable performance. also, when the number of testing kits are limited and the prior is small, sequential tests are more efficient and quicker in identifying and discarding uninfected samples than parallel tests. therefore, in this article, we shall limit our study only to adaptive tests. in this section, we shall discuss some limitations and surprising advantages of performing group tests for covid diagnosis in practice using qrt-pcr. a key question in the application of gt for covid testing is how small should d be, relative to n ? that is, what is the range of values of d n for which gt reduces the total number of tests required? this was first answered in [ ] ; gt is said to reduce the number of tests required when d n < − √ . as a general rule of thumb, considerable reduction in the total number of tests can be achieved when d n or the prior α is less than % ; in all other cases, it is best to perform individual tests. as discussed in section , typical value of α for covid is less than . . thus, gt can be utilized to efficiently increase the number of samples tested for covid with minimal number of tests performed. in group testing, dilution occurs in two stages, namely, preparation and pooling. we shall discuss the effects of these dilutions on the allowable sample size and goodness of test. the following discussion will also help us to determine a practically appropriate value of the pool size n that provides reliable test outcomes. when preparing the samples for gt, each sample needs to be divided into multiple portions for usage in multiple groups. in the example in fig. , each sample is required to be divided into portions since any sample could be involved in a maximum of groups. in general, a sample may be involved in at most log n groups while testing n samples [ ] . if each test is replicated r times, then a sample may have to be divided into r log n portions. however, we shall see in the next subsection that each test need not be replicated in gt as it could provide inherent replication. in practice, to test for covid, swabs from nasopharynx or throat [ ] are taken. the swab samples can be dissolved in liquid buffer media [ ] and this can be divided into multiple portions. when the samples are divided into multiple portions, the viral load gets distributed across the divided portions. therefore, each sample can be divided only into certain number of portions such that the viral load in each portion can still be detected reliably by qrt-pcr. the swab from nasopharynx contains − corona viral particles [ ] , if l is the amount of viral load required for reliable detection, then each sample can be divided into at most v l l portions, where v l is the amount of viral particles in the swab. as discussed in section , the false negative rate γ(l) depends on the viral load in the test sample. if γ * is the required false negative rate for each test, then the corresponding viral load is given by the inverse function γ − (γ * ), and each sample can be divided into at most v l γ − (γ * ) . in figure , using the γ(l) from [ ] for qrt-pcr, we plot the number of portions into which a swab containing v l viral load can be divided to achieve a given false negative rate with three replicates. it can be seen that, when the swab has a viral load of , we can still obtain about portions for γ = . . when portions of n swabs, of which d are infected, are mixed or pooled together for a qrt-pcr test, the viral load in d samples are diluted by the n − d virusfree samples. this dilution is referred to as the pooling dilution. the effect of this dilution on the performance of virus detection has been studied in [ ] . based on the probit model described in [ ] , the effect of pooling dilution was derived in [ ] . though the model derived in [ ] is for testing hiv, the authors mention that the model is applicable to other viral tests. simplifying the model in [ ] for covid, the sensitivity after pooling dilution is given by where Φ(.) is the cdf of the normal distribution, χ is the number of rna copies per viral particle (χ = in the case of corona virus), d is the number of infected samples, v p is the viral load in each infected sample, v and v are the viral loads corresponding to a sensitivity of . and . , respectively, for the considered testing the maximum number of groups in which a sample will be involved may vary depending on the gt algorithms. it can be proved that log n are sufficient to identify an infected sample among an arbitrary number of infected samples [ ] . further, once identified, as infected or uninfected, that sample is not used in any subsequent groups for testing. technique, i.e., v x = γ − ( − x). in fig. , we show the reduction in sensitivity of the pooled test when different number of samples (n ) are pooled together with different number of infected samples (d). it can be seen that the pool size of still provides a very high sensitivity after pooling dilution even when a single sample is infected. a similar conclusion on the pool size was reported through experimentation in [ ] . in general, if t is the number of tests for covid that are to be performed on a swab with viral load v l with r replicates to achieve a sensitivity of − γ * , then the maximum pool size can be derived as to achieve a sensitivity of %, the above equation can be simplified to n = v l rt v . for t = log n , we get where w (.) is the lambert w function. this formulation includes the effect of dilution in both the sample preparation and pooling stages. example: for a swab containing a viral load of viral particles, and a testing technique that requires viral particles to achieve % sensitivity, the maximum pool size for % sensitivity of the group test should be n = . as seen from the above example, an efficient group test which performs the least number of total tests (t ) per sample can enable us to increase the pool size, which, in turn, increases the testing speed and cost. therefore, employing an efficient gt algorithm for covid testing is the key component in pooling tests. we shall discuss some practically relevant algorithms in section . in group testing, samples that belong to a group, which has a test outcome of positive, are often tested again in smaller groups. this ensures that multiple tests are performed for some samples. this can be observed in the example described in fig. ; sample is involved in tests that are positive. in gt, almost every sample that tests positive is replicated at least twice. this inherent replication reduces drastically the false positive rates of gt without an explicit replication of the individual tests. the exact amount of reduction of the false positive rate depends on the gt algorithm. note that the group tests whose outcome are negative may not be replicated in gt and may require explicit replication to reduce false negative rates. therefore, the false negative rates or the sensitivity would suffice to be an appropriate metric to evaluate group tests and one can focus on reducing γ to improve gt. in this section, we discuss two combinatorial group tests and a probabilistic group test which could be practically useful in testing for covid- . the generalized binary splitting (gbs) and multi-stage testing (mst) are the cgt algorithms, and nested testing (nt) is the pgt algorithm that we describe in the following subsections. the generalized binary splitting (gbs) is the most commonly used adaptive algorithm in the cgt literature [ ] . gbs is the generalization of the binary splitting procedure (bsp). first, we describe bsp, and generalize it to obtain gbs. the binary splitting procedure assumes that there exists at least one infected sample in a given pool and the goal of bsp is to identify exactly one infected sample in the least number of tests. that is, bsp works on a pool of size n with d ≥ and identifies an infected sample in exactly log n tests. the steps in bsp are given below: • step split the n samples into two halves, say groups g and g . • step test g . • step when the test is positive: (i) continue performing all future tests with the samples from only g , (ii) set n = |g |, and (iii) if the number of samples in g is , then one infected sample has been identified and the algorithm is terminated. • step when the test is negative: (i) continue performing all future tests with the samples from only g , (ii) set n = |g |, and (iii) if the number of samples in g is , then one infected sample has been identified and the algorithm is terminated. note that, since d ≥ , if g tests negative, then g must test positive. • step with the updated n and samples pool, goto step . the gbs algorithm simply attempts to perform the bsp d times to identify at most d infected samples in a given pool of size n . the pseudocode and the steps in gbs algorithm are given in algorithm . analysis: since the outcome of a test performed at each step determines the next group for testing, the total number of tests varies for different inputs for a given n and d. the number of tests performed in the worst case, i.e., the maximum value that t can attain in gbs is given by t ≤ log n d + d. figure shows the maximum number of tests required by gbs with each test replicated twice for different values of n and d. it can be seen that gbs testing requires lesser number of tests, even in the worst case, than the conventional testing, which is n . in gbs, each sample may be involved in up to log n d + tests; the sample preparation stage should provide at least log n d + portions for each sample. practical considerations: when employing gbs in practice, the following points need to be kept in mind. • the tests in gbs are sequential. that is, all the group tests have to be performed adaptively and in-order to obtain the final result. • the gains of gbs are higher for large values of n. from simulations, we observed that gbs is suited for d n ≤ % and the average number of tests required can be reduced by up to % of that of conventional tests. • a key thing to note in gbs is that the algorithm can fail if the value of d is underestimated. if the pool contains lesser number of infected samples than d, then gbs identifies all infected samples perfectly. • inherent replication: in gbs, when a group is tested positive, often it gets tested again in the subsequent groups, thereby providing inherent replication. however, due to bsp, there exists scenarios where no samples are involved in multiple tests. therefore, in practice, one has to explicitly watch out for such samples and replicate the test, if required. • at the end of gbs tests, the n − d samples, that are marked as uninfected, can be pooled into one group and tested. this ensures that d is not underestimated. some of the disadvantages of gbs are overcome by the multi-stage testing algorithm, which is described in the next subsection. a disadvantage in gbs tests is that the number of group tests that a particular sample undergoes is difficult to compute. to overcome this issue, we can employ c. h. li's multi-stage testing (mst) [ ] . in mst, each sample undergoes exactly s number of tests. the value of s can be chosen as dictated by any practical restrictions; however, there is an optimal number of stages that would minimize the total number of tests performed, this is given by [ ] s = arg min the pseudocode of the mst algorithm is given in algorithm . it can be explained as follows. maintain three bins: infected samples' bin (isb), uninfected samples' bin (usb) and queued samples' bin (qsb). initially, all n are in qsb. in the ith stage (i = , , · · · , s), form g i groups with all samples in qsb and test them. the samples that belong to groups which tested negative are moved to usb. if the group size is more than one, then the samples that belong to groups that tested positive are retained in qsb, else they are moved to isb. proceed to i + th stage and repeat the above steps till the group sizes become . analysis: the group size g i is computed as g i = n i− /k i , where k i = δ − i s is the average number of samples in a group. in practice, some groups of g i may contain k i samples and the rest may contain k i + samples. note that, in the last stage, all groups contain exactly one sample, i.e., k s = . the total number of tests performed in mst is t = s i= g i . the value of t is not fixed for a given n and d as it depends on the group test outcomes. however, we can determine the value of t in the worst case, i.e., the maximum value that t can take for a given n and d. this is given by t ≤ ed ln δ [ ] . practical considerations: when used in practice, mst has the following advantages. • all groups in each stage can be tested in parallel. thus, despite being an adaptive gt, testing can be sped up using mst. • when more than d groups test positive at any stage, then it can be inferred that the estimate of d is incorrect. in this case, the remaining samples in qsb can be tested with an mst test plan for the updated value of d and n (the number of samples in qsb will be the new value of n ). this ensures that the tests performed in all previous stages are still useful even when the value of d is incorrect. • when the true number of infected samples is less than or equal to d, mst identifies all infected samples. • since the number of stages s is known, the number of times any sample will be tested is at most s. thus, in the sample preparation, it is sufficient to divide each swab content to only sr portions, where r is the number of replicates. • inherent replication: since all the samples in qsb at the end of stage-i are tested again in stage-i + , the tests for infected samples are automatically replicated. therefore, only those groups that test negative at each stage needs replication. the groups that test positive are replicated inherently at least s times, thereby increasing the test accuracy and reducing false positives. this inherent replication further reduces the total number of tests required. we derived that the total number of tests reduced due to inherent replication in mst is at least k • the maximum number of tests required by mst is always bounded above by n , i.e., t ≤ n . in fig. a , we plot the optimal number of stages required in mst for different values of d and n . note that, when the number of stages increase, the inherent replication for infected samples increase and improves the accuracy without any additional tests for replication. in fig. b , we plot the number of tests required by mst in the worst case scenario for different values of d and n with double replication. for n = , the maximum number of tests required for mst saturates at as opposed to in the conventional testing with double replicates. it can be seen that mst requires uniformly lesser number of tests than the conventional testing. though these numbers represent the worst case scenario, simulations show that the average number of tests required to detect infected samples could be % less than the conventional testing. gbs vs mst: figure shows the total number of tests required in the worst case for gbs and mst at different values of n and d = , · · · , . the number of tests required by conventional testing is also indicated for baseline comparison. it can be seen that for small values of δ, gbs outperforms mst. as d increases for a fixed n , gbs may sometimes require more number of tests than the conventional testing; however, mst always requires less than or equal number of tests as conventional testing. in general, for large values of n (> ), gbs may be appropriate, and mst may be appropriate in the other regime. figure can be used as a guideline to choose the best test for a given value of n and d. the value of d played an important role in the adaptive cgt algorithms discussed in the previous subsections. when the value of d is an underestimate, then the test plan provided by cgt may fail or may turn out to be suboptimal. this shortcoming can be addressed by the usage of pgt algorithms. here, we shall describe a probabilistic group testing algorithm known as the nested testing (nt) [ ] . the nt algorithm takes n and α as the input and provides an adaptive test plan that minimizes the average number of total tests required to diagnose n samples. the actual number of infected samples in a pool or its estimate is not required for nt, only the prior probability of the presence of an infected sample is needed. nested testing is an optimal pgt which identifies all infected samples without failure [ ] . the algorithm proceeds by testing a group of samples from ub and moving them to pib, if they test positive, then transferring the diagnosed samples to db and returning the rest to ub, and repeating the whole process till all samples are diagnosed. analysis: the nt algorithm models the presence of the virus in each sample as an independent bernoulli random variable with probability α. thus, nt can identify any number of infected samples in a pool, i.e., ≤ d ≤ n . the probability pr(d = i), i = , · · · , n , is given by the binomial distribution; nested testing exploits this fact to identify the group that has the highest probability to contain infected samples and tests it. the nt algorithm gives the least number of tests for which pr(d = i) is the maximum. when the number of infected samples is i, such that pr(d = i) is the least, the total number of tests required by nt may be more than n . however, when the nt test plan is applied to multiple pools of size n , the average number of tests required per pool will be lesser than n . the average number of tests required by nt is given by g( , n ) , where g() is as given in ( ) . figure plots the average number of tests required by nt for different values of n and α. it is clear that, for smaller values of the prior probability, nt can provide large gains in terms of the average number of tests performed without any knowledge of d. practical considerations: when used in practice, nt has the following advantages. • nested testing can identify all infected samples irrespective of the actual value of d. the probability of detection of infected samples by nt is . • a key condition for nt to perform well in practice is the availability of independent samples. that is, the probability of each sample being infected should be independent of the other samples in the pool and equal α. this can be achieved in practice through randomization of samples. that is, constituting a pool with samples from reasonably separated geographical locations. • the value of the prior α can be estimated based on the past history as discussed in section . further, this value should be continuously updated based on the outcomes of the tests performed each time. • inherent replication: in nt, an infected sample has very high probability of getting tested in at least two groups. hence, nt can ensure at least double replication for samples that test negative. • to create an nt test plan, the algorithm needs to evaluate the expression in ( ) group testing is a promising method that can be effectively utilized to ramp up the number of tests performed in covid- diagnosis. gt can help us quickly identify several early stage infections. by reducing the number of tests performed, gt can make the testing less expensive and economical. the following are some guidelines that can be followed in employing gt for covid- diagnosis. • before employing pooling, the sensitivity of the testing technique needs to be characterized. some qrt-pcr kits are known to provide accurate results with smaller viral load, whereas some are known to require a large amount of viral load to detect the virus. this sensitivity characteristics, i.e., γ(l), needs to be understood before the formulation of gt test plans. the knowledge of γ(l) would help us to decide the optimal pool size and number of replications required. • when the testing speed is a primary factor, it may be better to employ mst as it enables to perform parallel group tests. • in cgt algorithms such as gbs or mst, randomization is not required. the statistical relation between the samples are irrelevant in cgt group tests. however, the estimate of the upper bound on the number of infected samples in a pool is an important parameter that needs to be accurate. the value of d can be estimated by observing the history of a location or cluster. when more samples from a location test positive, then the estimate of d should be correspondingly increased and vice versa. • pgt algorithms such as nt has the advantage of not requiring the exact value or an upper bound on the number of infected samples in a pool. pgt algorithms require the prior probability values (α). once again, this can be obtained from the history of the tests performed for a location or cluster. the ratio of the number of samples tested positive to the total number of tests performed can give us this estimate (refer section ). this estimate needs to be update continuously over time. • randomization could significantly reduce the number of tests performed in pgt. when samples from a small community or cluster are pooled together, most of them are likely to have a similar test outcome. however, pgt works best when the samples are independent. hence, the testing center should randomize by picking samples from different communities or clusters to form a pool. this randomization can bring down the average fraction of samples that are positive in a pool and the dependence among the samples. • in practice, pgt tests are suited well for locations where the infection rate is higher and the cgt tests are suited well for locations where the infection rate is small. this is because, pgt does not need the value of d and an underestimated value could cause failure of cgt tests. • when choosing a gt algorithm to perform diagnosis, the practitioner can intelligently switch between gbs, mst and nt, depending on the estimate of d and α, and their accuracy. the performance plots provided in section can be utilized in choosing the best test for a given scenario. • from the study so far, it is clear that considerable reduction in the total number of tests can be achieved when d n or the prior α is less than %. • note that when d > n or α > , group testing can still be helpful. under this condition, the goal of gt would be reversed, i.e., to identify the uninfected samples rather than the infected samples. all our discussions so far remain applicable with this switch. • the matlab codes for simulating the results and generating group test plans are available online at [ ] . where x t is the random variable denoting the outcome of the tth replicate. when the test is replicated twice, pr(x = , x = |x = ) = γ . for triple replication, pr(x + x + x ≤ |x = ) = γ ( − γ) + γ and pr(x = , x = , x = |x = ) = γ . for a given set of test replicate outcomes x , · · · , x r , the probability of the sample actually containing the virus is given by pr(x = |x , · · · , x r ) -this is referred to as the a posteriori probability. the a posteriori probability ratio (apr) pr(x= |x ,··· ,xr) pr(x= |x ,··· ,xr) is easier to compute than the individual a posteriori probabilities. the apr for a given set of outcomes is ap r = pr(x = |x , · · · , x r ) pr(x = |x , · · · , x r ) = pr(x , · · · , x r |x = ) pr(x , · · · , x r |x = ) where m is the number of negative outcomes (i.e., x t = ) in r replicates. divide p i− into g i disjoint groups -g , g , · · · , g gi such that g ∪ g ∪ · · · ∪ g gi = p i− test groups g , g , · · · , g gi : discard groups that tested negative test group g ⊆ p if test outcome is positive then : identify an infected sample in g with bsp (since the group tested positive, it must contain at least one infected sample) update n = n − − g (where g is the number of uninfected items diagnosed from bsp, remove these from the pool) test the n samples individually : end if available online: matlab codes for test plan generation pattern of early human-to-human transmission of wuhan novel coronavirus ( -ncov) sars-cov- (covid- ) by the numbers coronavirus and the race to distribute reliable diagnostics group testing and sparse signal recovery diagnostic detection of -ncov by real-time rt-pcr detection of novel coronavirus ( -ncov) by real-time rt-pcr coronavirus disease (covid- )-statistics and research boolean compressed sensing and noisy group testing on the cut-off point for combinatorial group testing combinatorial group testing and its applications transport of viral specimens a methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution refinement of a viral transmission risk model for blood donations in seroconversion window phase screened by nucleic acid testing in different pool sizes and repeat test algorithms evaluation of covid- rt-qpcr test in multi-sample pools born again group testing: multiaccess communications group testing to eliminate efficiently all defectives in a binomial sample the author thanks namrata m. nilavar, indian institute of science, bangalore, for useful discussions. hence, the false negative and positive rates for r tests are given by (each replicate is assumed to be independent of the other) compute h =g( , |u|) using ( ) test a group g ⊆ u of size h :if test is negative then :else :if h == then update d = d + g and make p empty while p is not empty do compute g =g(|p|, |p ∪ u|) using ( ) test a group g ⊆ p of size g : if test is positive then g( , m) = g( , m − ), g( , ) = , g( , ) = . key: cord- -pbliko k authors: cohen, tomer; finkelman, lior; grimberg, gal; shenhar, gadi; strichman, ofer; strichman, yonatan; yeger, stav title: a combination of 'pooling' with a prediction model can reduce by % the number of covid- (corona-virus) tests date: - - journal: nan doi: nan sha: doc_id: cord_uid: pbliko k we show that combining a prediction model (based on neural networks), with a new method of test pooling (better than the original dorfman method, and better than double-pooling) called 'grid', we can reduce the number of covid- tests by %. the search for carriers of covid- is done primarily through testing using rt-pcr's. these tests are the most common way to empirically identify carriers of the virus, and urgently need to be conducted on a large scale. today, patients are granted a test if deemed necessary by the government and are carried out individually, i.e., every sample is tested separately. the problem is that the number of samples gathered today supersedes the amount of tests that can be conducted daily; moreover, the world-wide shortage in equipment and resources prevents a much-needed increase in the number of daily tests. as a result, the testing system today is at full capacity, and falls short of the need. two recent developments are relevant to the solution that we describe here: . data regarding tests and the patients behind them has been gathered (over , tests in israel as of mid. april, ) that enables us to build a prediction model of who is likely to be positive; . a new study [ ] has shown that it is possible to combine up to samples in one 'pool ' and identify whether at least one of them is positive with a single test. pooling in general (in the context of other tests) is an old idea due to dorfman [ ] . a simple calculation shows that creating random pools of samples will not be efficient in identifying positive patients, with the current rate of positive samples in israel --~ %. with this rate, less than % of the pools will succeed, and the rest will have to be re-tested one by one. our method solves this problem by identifying those samples that have a much smaller chance of being positive and putting them in one pool. furthermore, it recommends the optimal size of the pool, given the probability that samples in that pool are positive. by using the meta-data of the tests, which was gathered by the ministry of health, we created an algorithm (based on machine learning, and specifically a 'neural network'), that predicts the probability of a patient being negative or positive for the virus based on his/her data: whether they cough, has a sore throat, shortness of breath, or a headache, as well as his/her age group, gender, and likely cause for the sickness. based on this data our model predicts with an accuracy of . % the outcome . for each patient, the outcome of the neural network is a number indicating the likelihood that this patient is positive. hence by sorting the patients according to this value, we can pool together tests with almost a uniform probability of being positive. in appendices a -c, we survey three different ways to use this data -the first-of-which is a known method due to dorfman [ ] -which we'll call here `single pooling' (appendix a): according to this method, if the pool turns out to be positive, all samples in that pool need to be re-tested individually, as shown in the following diagram: the expected number of tests can be calculated, based on the probability of the samples in the pool to be positive, and the size of the pool (see appendix a for details). we show that for each value of there is an optimal pool size. for example, for patients with % probability of being positive, the optimal pool size is . for probabilities higher than some threshold, it is not cost-effective to use pooling at all. we calculated that if this method had been used on all tests carried thus far in israel (see appendix e for data), we would reach full accurate classification of all the patients with about % of the tests. the best method that we found is called ' d-pooling' (or 'matrix pooling') [ ] [ ], and is described in appendix c -it can do the same thing with only % of the tests. appendix d includes a table comparing the required number of tests per patient with the various methods, as a function of , and also a comparison to a recently introduced method called double-pooling [ ] . . challenges: changing the process, and the overhead of re-testing. our solution does not require new equipment. it requires, however, a change in the current process. first, the samples corresponding to patients that are selected for pooling, will have to be duplicated for potential repetition of the test, in case the pool turns out to be positive. the dataset that we used was published by the moh. it has a known bias which likely distorts the result: positive cases are much more likely to include the clinical data mentioned above than negative ones, since for negative cases this data was not always entered retroactively. in itself this may have contributed to the success of the prediction model, since the very fact that there is no clinical data is a good predictor of the result. this problem will disappear if the data collection process will improve. the numbers that we present here will likely not be as good in practice because of this reason. a detailed discussion of this matter appears in [ ] . second, the tests that are currently given to the lab in some arbitrary order, will have to be resorted, based on the recommendation of our system. the total number of tests is not the only objective. one should also consider • the number of test iterations. each such test takes time (several hours on the pcr machine), which leads to a delay in the response time to the patient. • the amount of sample duplication. if a sample will potentially need to be retested, it has to be duplicated. in appendix d we consider these objectives when comparing the various methods. in appendices a -c we describe different pooling methods, with a decreasing number of expected tests. appendix d compares the efficiency of the various methods. the raw data can be downloaded from [ ] . appendix a: the single pooling method [ ] in this model a sample can only be part of a pool once. that is, if the pooled sample fails, then all samples in the pool are re-tested individually. let be the probability of a test to be positive, the pool size, and the population size. the expected number of tests, as a function of the probability of a test to be positive and the pool size is calculated as follows: in the case of a failure there are + tests (left part of ( )) for samples, and in case of success there is a single test for samples (right part of ( )). the overall number of pools is / . let us take two numeric examples: for = . , = , = , the average number of tests is . . for = . and the same values of , , the expected number of tests drops to . . it is clear that from some threshold for the value of , it is not cost-effective to use pooling at all. the plots in figure are based on ( ), divided by , so it reflects the expected number of tests per patient. it is evident that for each probability, there is an optimal pool size -the size that brings to minimum the expected number of tests. for example, for = . , the optimal pool size is , and we saw earlier that this implies . tests per patient. appendix b: the binary-tree method one can extend the idea presented in appendix a to multiple levels of pooling. this is sometimes called 'multi-stage pooling' [ ] . that is, given a pool of size that fails, split it to two and retest, until reaching the leaves of the search tree. a small optimization is achieved as follows. suppose that a node at level in the binary tree is positive, and we then check, e.g., the left child node at level − . if that node is negative, not only that we can skip the whole subtree under that node, we can also skip the other node at level − , because it is bound to be positive. the plots in figure below are based on simulations, including this optimization. p: some of the data from our simulation with = appear in table below, where the optimal pool size (the value of ) is highlighted for each value of . one may observe that above a certain probability ( = . ) pooling is not cost-effective. the main disadvantage of the binary tree method is that it imposes log iterations (the height of the binary tree). furthermore, if the optimization mention above is activated, it doubles the number of iterations (because one cannot test the two sibling nodes simultaneously). see appendix d for further discussion. another method of pooling is based on a matrix of pools. we arrange an × matrix of samples. we then pool together each column and each row, hence pools of samples each. this implies that each sample participates in two pools (i.e., row and column pools). suppose that out of the samples are positive. this means that in the worst case pools will test positive (as each such sample makes a separate row and column positive), and correspondingly there will be samples that are potentially positive and hence need to be re-tested. there is a limit, however, on the number of additional tests: it cannot surpass . hence the worst case can only happen times. the grid (also can be seen as a matrix) in figure is for = . each of the junctions is a sample. correspondingly, pools will be tested. for example, the samples in the first row form a pool, and the samples in the first column form another pool. suppose there are positive cases from those samples, and they are located at ( , ) and ( , ) (marked in red). correspondingly, row-pools , , and column pools , are positive (marked by 'x'). but this leaves us with candidate samples, which must be retested individually. so altogether, in this case we need tests, for people. a more fortunate case is when the positive cases happen to be on the same row or column. for example, if those two positive cases were on the same row, we would not need more tests at all as they would be uniquely identified. eq. ( ) below expresses the expected number of tests with the d-pooling method, in the worst case. as before, is the probability for a positive test, is the size of the population, and , in this case, is the number of columns/rows in the matrix. recall that the worst case is when each positive sample is a singleton on its row and column. in that case the number of added tests is = ( ) . hence, we have this expression is relevant only when ≤ . since = , this happens when ≤ , or ≤ / . furthermore, it is relevant only as long as (# ) < , which implies that eq. ( ) is a strictly tighter bound than the former ≤ / . plotting ( ) for different values of and where = (see figure ) , shows that here, too, for each value of , there is an optimal matrix size. we note that for these results to apply, we must have ≤ (otherwise we do not have enough samples to fill the matrix). for example, for = . the optimal value of is , which means that we can use the result only if ≥ (here the results were computed, as mentioned, with = ). we also simulated this method, in order to get the actual statistics rather than the worst-case scenario. we included the following (small) optimization in the simulation: suppose that the number of positive rows is . for each positive column, if the first − samples turns out to be negative, there is no need to test the last one, as it is bound to be positive. the same argument applies to each row. in the best-case scenario all the positive cases are in the last row and last column -in such a case we save − tests (- because of the bottom corner). the downside of this optimization is that it adds an iteration. see appendix d for a discussion. there are other possible optimizations, which are discussed in [ ] [ ] and we did not include in our simulation. for example: test rows only; if none of them is positive -stop; if exactly one row is positive, check all samples in that row individually; otherwise -continue as usual. appendix d: comparing the methods table below compares the three methods in terms of their tests per patient (tpp): the ratio between the expected number of tests and the population size . note that each cell was calculated with the optimal pool size for the given value of . for example, for = . the optimal value of in the binary-tree method is , whereas the optimal value of in the dpooling method for this probability is . the last line of the table refers to results of simulating the d-pooling method, which is expected to be better (and indeed our results show that it is) than the worst-case as formulated in ( ). it is clear from the table that the actual (i.e.., simulated) d-pooling method is the most efficient one in terms of minimizing the number of tests. finally, let us compare the d-pooling method to a recently introduced method called doublepooling [ ] . citing [ ] : "given a probability of a positive test, pick an optimal size ( ) for the pool size. divide the population to be tested into non-overlapping pools of size s (the division is assumed to be random) twice. thus, now every patient belongs to two pools and is tested in two parallel rounds, a and b. for every patient if both the pools test positive then test the patient individually. otherwise consider that patient cleared.". using their analysis (which we independently verified via simulation), the tests-per-patient of double-pooling is the following: hence both the d-pooling method and the binary-tree method are more efficient than double-pooling. both the d-pooling-and the double-pooling method require two steps. so far we only compared the methods by the expected number of tests per patient. let us now compare them by the number of iterations, and the number of sample duplication that is necessary (this represents the number of times a patient will be retested in the worst case): sample duplication single pooling binary tree log , (or log with the optimization). log d-pooling (or , with the optimization). appendix e: the current distribution of samples in israel in figure , the horizontal axis shows the value predicted by our neural network, multiplied by . the vertical axis shows the accumulated percentage of the population that falls under this value. for example, over % of the population are classified by our neural network as having less than % chance of being positive. the raw data is accessible from [ ] . evaluation of covid- rt-qpcr test in multi-sample pools / idan yelin, noga aharony the data used in the analysis of the algorithms the data from the ministry of health the detection of defective members of large populations a note on double pooling tests (preliminary version improved matrix pooling the use of a square array scheme in blood testing the blood testing problem appendix c: the d-pooling method [ ] [ ] key: cord- -bpx qr i authors: eisty, nasir u.; perez, danny; carver, jeffrey c.; moulton, j. david; nam, hai ah title: testing research software: a case study date: - - journal: computational science - iccs doi: . / - - - - _ sha: doc_id: cord_uid: bpx qr i background: the increasing importance of software for the conduct of various types of research raises the necessity of proper testing to ensure correctness. the unique characteristics of the research software produce challenges in the testing process that require attention. aims: therefore, the goal of this paper is to share the experience of implementing a testing framework using a statistical approach for a specific type of research software, i.e. non-deterministic software. method: using the parsplice research software project as a case, we implemented a testing framework based on a statistical testing approach called multinomial test. results: using the new framework, we were able to test the parsplice project and demonstrate correctness in a situation where traditional methodical testing approaches were not feasible. conclusions: this study opens up the possibilities of using statistical testing approaches for research software that can overcome some of the inherent challenges involved in testing non-deterministic research software. research software can enable mission-critical tasks, provide predictive capability to support decision making, and generate results for research publications. faults in research software can produce erroneous results, which have significant impacts including the retraction of publications [ ] . there are at least two factors leading to faults in research software: ( ) , the complexity of the software (often including non-determinism) presents difficulties for implementing a standard testing process and ( ) the background of people who develop research software differ from traditional software developers. research software often has complex, non-deterministic computational behavior, with many execution paths and requires many inputs. this complexity makes it difficult for developers to manually identify critical input domain boundaries and partition the input space to identify a small but sufficient set of test cases. in addition, some research software can produce complex outputs whose assessment might rely on the experience of domain experts rather than on an objective test oracle. finally, the use of floating-point calculations can make it difficult to choose suitable tolerances for the correctness of outputs. in addition, research software developers generally have a limited understanding of standard software engineering testing concepts [ ] . because research software projects often have difficulty obtaining adequate budget for testing activities [ ] , they prioritize producing results over ensuring the quality of the software that produces those results. this problem is exacerbated by the inherent exploratory nature of the software [ ] and the constant focus on adding new features. finally, researchers usually do not have training in software engineering [ ] , so the lack of recognition of the importance of the corresponding skills causes them to treat testing as a secondary activity [ ] . to address some of the challenges with testing research software, we conducted a case study on the development of a testing infrastructure for the par-splice research software project. the goal of this paper is to demonstrate the use of a statistical method for testing research software. the key contributions of this paper are ( ) an overview of available testing techniques for non-deterministic stochastic research software, ( ) implementation of a testing infrastructure of a non-deterministic parallel research software, and ( ) demonstration of the use of a statistical testing method to test research software that can be a role model for other research software projects. in a non-deterministic system, there is often no direct way for the tester (or test oracle) to exactly predetermine the expected behavior. in parsplice (described in sect. . ), the non-determinism stems from ( ) the use of stochastic differential equations to model the physics and ( ) the order in which communication between the procedures occurs (note however that even though the results from each execution depends upon message ordering, each valid order produces a statistically accurate result, which is the key requirement for the validity of parsplice simulations). in cases where development of test oracles is difficult due to the nondeterminism, some potentially viable testing approaches include metamorphic testing, run-time assertions, and machine learning techniques [ ] . after describing the parsplice project, the remainder of this section explains these techniques along with their possible applicability to parsplice. parsplice (parallel trajectory splicing) [ ] aims at overcoming the challenge of simulating the evolution of materials over long time scales through the timewise parallelization of long atomistic trajectories using multiple independent producers. the key idea is that statistically accurate long-time trajectories can be assembled by splicing end-to-end short, independently-generated, trajectory segments. the trajectory can then grow by splicing a segment that begins in the state where the trajectory currently ends, where a state corresponds to a finite region of the configuration space of the problem. this procedure yields provably statistically accurate results, so long as the segments obey certain (relatively simple) conditions. details can be found in the original publication [ ] . the parsplice code is a management layer that orchestrates a large number of calculations and does not perform the actual molecular dynamics itself. instead, parsplice uses external molecular dynamics engines. the simulations used in parsplice rely on stochastic equations of motion to mimic the interaction of the system of interest with the wider environment, which introduces a first source of non-determinism. a basic parsplice implementation contains two types of processes: a splicer and producers. the splicer manages a database of segments, generates a trajectory by consuming segments from the database, and schedules execution of additional segments, each grouped by their respective initial state. producers fulfill requests from the splicer and generate trajectory segments beginning in a given state; the results are then returned to the splicer. the number of segments to be scheduled for execution in any known state is determined through a predictor statistical model, built on-the-fly. importantly, the quality of the predictor model only affects the efficiency of parsplice and not the accuracy of the trajectory. this property is important because the predictor model will almost always be incomplete, as it is inferred from a finite number of simulations. the unavailability of the ground truth model (which is an extremely complex function of the underlying physical model) makes assessment of the results difficult. in addition, this type of stochastic simulation is not reproducible, adding to the difficulty of testing the code. therefore, in this case study we create a basis for the parsplice testing infrastructure using various methodical approaches and apply the test framework to the continuous integration process. metamorphic testing operates by checking whether the program under test behaves according to a set of metamorphic relations. for example, a metamorphic relation r would express a relationship among multiple inputs x , x ,.., xn (for n > ) to function f and their corresponding output values f(x ), f(x ),.., f(xn) [ ] . these relations specify how a change to an input affects the output. these metamorphic relations serve as a test oracle to determine whether a test case passes or fails. in the case of parsplice, it is difficult to identify metamorphic relations because the outputs are non-deterministic. the relationship between the x 's and the f 's is therefore not direct but statistical in nature. an assertion is a boolean expression or constraint used to verify a necessary property of the program under test. usually, testers embed assertions into the source code that evaluate when a test case is executed. later testers use these assertions to verify whether the output is within an expected range or if there are some known relationships between program variables. in this way, a set of assertions can act as an oracle. in the context of parsplice, assertions can be used to test specific functions, but not to test the overall validity of the simulations, would protect only against catastrophic failures, such as instabilities in the integration scheme. machine learning is a useful approach for developing oracles for non-deterministic programs. researchers have shown possibilities of both black-box features (developed using only inputs and outputs of the program) and white-box features (developed using the internal structure of the program) to train the classifier used as the oracle [ , ] . it is possible to test parsplice with machine learning techniques. for example, we could fake the molecular dynamics (md) engine with our own model to produce output data to use as a training set and consider the actual output data as a testing set. due to the amount of effort required to use this approach in parsplice, we determined that it was not feasible. to implement the testing framework, the first author spent a summer at los alamos national laboratory working on the parsplice project. the testing framework is based on the multinomial testing approach (described in sect. . ), implemented using a progress tracking card (ptc) in the productivity and sustainability improvement plan (psip) methodology. the testing approach is integrated with the cmake/ctest tool for use in the runtime environment and continuous integration. in this section, we describe the psip methodology, the multinomial test approach, and results that verify the implementation of the testing framework. the psip methodology provides a constructive approach to increase software quality. it helps decrease the cost, time, and effort required to develop and maintain software over its intended lifetime. the psip workflow is a lightweight, multi-step, iterative process that fits within a project's standard planning and development process. the steps of psip are: a) document project practices, b) set goals, c) construct progress tracking card, d) record current ptc values, e) create plan for increasing ptc values, f) execute plan, g) assess progress, h) repeat. we created and followed a ptc containing a list of practices we were working to improve, with qualitative descriptions and values that helped set and track our progress. our progress tracking card consists of scores with a target finish date to develop the testing framework. the scores are: -score -no tests or approach exists -score -requirement gathering and background research -score -develop statistical test framework -score -design code backend to integrate test -score -test framework implemented into parsplice infrastructure -score -integrate into ci infrastructure we were able to progress through these levels and obtain a score of by the end of the case study. the multinomial test is a statistical test of the null hypothesis that the parameters of a multinomial distribution are given by specified values. in a multinomial population, the data is categorical and belongs to a collection of discrete nonoverlapping classes. for instance, multinomial distributions model the probability of counts of each side for rolling a k-sided die n times. the multinomial test uses pearson's χ test to test the null hypothesis that the observed counts are consistent with the given probabilities. the null hypothesis is rejected if the pvalue of the following χ test statistics is less than a given significance level. this approach enables us to test whether the observed frequency of segments starting in i and ending in j is indeed consistent with the probabilities p ij given as input to the monte carlo backend. our multinomial test script uses the output file of parsplice as its input and execute the test and post-processes the results by performing pearson's χ to assess whether to reject the null-hypothesis. a key insight from the theory that underpins parsplice is that a random process that describes the splicing procedure should rigorously converge to a discrete time markov chain in a discrete state space. in other words, the probability that a segment added to a trajectory currently ending in state i leaves the trajectory in state j should be a constant p ij that is independent of the past history of the trajectory. one way to test parsplice would be to verify that the splicing procedure is indeed markovian (memory-less). however, taken alone, such a test would not guarantee that the splicing proceeds according to the proper markov chain. a more powerful test would assess whether the spliced trajectory is consistent with the ground-truth markov chain. a key obstacle to such a test is that this ground-truth model is, in practice, unknown and can only be statistically parameterized from simulation data. to address this issue, we replaced the molecular dynamics (md) simulation backend with a simpler monte carlo implementation that samples from a pre-specified, markov chain. that is, we replaced the extremely complex model inherent to the md backend with a known, given model of predefined probabilities. the task then becomes assessing whether the trajectory generated by parsplice, as run in parallel on large numbers of cores, reproduces the statistics of the ground truth model. in this context, this technique is the ultimate test of correctness, as parsplice is specifically designed to parallelize the generation of very long trajectories that are consistent with the underlying model. statistical agreement between the trajectory and the model demonstrates that the scheduling procedure is functional (otherwise, the splicing the of trajectory would halt), the task ordering procedure is correct, the tasks executed properly, the results reduced correctly, and the splicing algorithm was correct. the statistical assessment to test parsplice can be conducted using the multinomial test approach. our null hypothesis was that the observed counts generated by parsplice are consistent with the probabilities in the model. if the p-value from the multinomial test is less than . , we reject the null hypothesis and conclude that the observed counts differ from the expected ones. conversely, if the p-value is greater than . , we do not reject the null hypothesis and can conclude that the test passes. for the sake of verifying our multinomial test, we ran parsplice in different time frames and observed the result. figure shows the p-values obtained from running parsplice for , , , , , , , and min. we can see that in all cases, the p-values are greater than . , which indicates that the tests passed during these instances of the execution. in this paper, we describe a case study of the parsplice project in which we followed the psip methodology to develop a testing framework to address the difficulties of testing non-deterministic parallel research software. we first considered applying traditional industrial testing approaches. however, the nondeterminism of parsplice made these approaches unusable. then we identified testing techniques specially designed for non-deterministic software. once again, those techniques did not fit parsplice. finally, we identified a statistical testing approach, multinomial testing, that would work for parsplice. the multinomial testing approach is ideal for parsplice given its constraints, i.e. time, non-determinism, and the existing continuous integration system. the lessons learned from this case study can be valuable to the larger research software community because, like parsplice, many research software projects have stochastic behavior which produces non-deterministic results. the approach we followed to develop the test framework can be a model for other research software projects. we plan to extend the testing infrastructure in a more methodological way with as many possible testing techniques installed in the system. pat: a pattern classification approach to automatic reference oracles for the testing of mesh simplification programs fault-based testing in the absence of an oracle engineering the software for understanding climate change automating image segmentation verification and validation by learning test oracles improving the development process for cse software techniques for testing scientific programs without an oracle testing scientific software: a systematic literature review a scientist's nightmare: software problem leads to five retractions long-time dynamics through parallel trajectory splicing some problems of professional end user developers software development cultures and cooperation problems: a field study of the early stages of development of software for a scientific community key: cord- -evh b o authors: brokopp, charles; resultan, eric; holmes, harvey; wagner, michael m. title: laboratories date: - - journal: handbook of biosurveillance doi: . /b - - / - sha: doc_id: cord_uid: evh b o nan results from laboratory testing are an important source of information for biosurveillance systems. clinical laboratory tests are vital for the correct diagnosis and treatment of individuals. clinical laboratories analyze blood, urine, mucus, saliva, respiratory secretions, cerebrospinal fluid, semen, vaginal secretions, sweat, feces, fluid aspirated from joints, and tissues from humans and animals. the tests performed include cell counts; analytical chemistries, including drug and toxin tests; and examinations to detect and identify microbes and markers of current and past infection. environmental testing is critical to the detection of outbreaks, the prevention of disease, and the monitoring of the environment. environmental laboratories analyze samples of water, food, air, soil, plant material, and unknown powders, as well as samples taken from surfaces for evidence of bacterial, viral, toxin, or chemical contamination. data produced by laboratories are important for biosurveillance of virtually every disease caused by biological agents, chemicals, or toxins. data collected during the preanalytical, analytical, and postanalytical phases of testing can be captured and incorporated directly into biosurveillance systems. preanalytical data, such as the type of test ordered and the reason for a test, can provide an early clue to the existence of an outbreak. similarly, analytic results, such as the initial gram stain of a cerebrospinal fluid specimen, can potentially confirm a diagnosis when combined with other clinical information, as it did in the first case of inhalational anthrax in the postal attack. the actual results of tests are obviously foundational to biosurveillance. the range of tests offered by an individual laboratory varies significantly among laboratories in the united states. many small laboratories perform a limited number of tests that are needed on an urgent basis or for screening purposes. larger laboratories provide more complex confirmatory analyses. the majority of clinical laboratories in the united states are small laboratories located in physician offices; however, the larger laboratories account for a high volume of all tests performed. table . describes the clinical laboratory tests that contribute to the diagnosis of inhalational anthrax. anthrax, as well as many other infectious diseases, is diagnosed after the performance of presumptive and confirmatory tests in combination with the clinical presentation. clinical specimens, such as blood, cerebrospinal fluid, urine, sputum, throat swabs, and skin scrapings, are used to isolate a causative agent that is later subjected to further testing with confirmatory procedures to make the final identification. preliminary tests results are sometimes released before the confirmatory tests results become available. when preliminary results are reported, the report often contains a statement about when final results will be available. laboratories that produce the types of data most useful for biosurveillance include clinical laboratories operated by the human or animal health systems, commercial laboratories, and governmental laboratories. laboratories typically specialize in either human or animal testing. commercial laboratories are free-standing laboratories that are not associated with hospitals or healthcare facilities and that often provide a broad range of services over a wide geographical area. governmental laboratories exist at the federal, state, and local level and often provide testing that is not readily available from other laboratories. we describe each of these types of laboratories in this chapter. laboratories that test for biologic agents are classified as biosafety level , , , or , with biosafety level providing the highest degree of protection to personnel and the environment. most clinical laboratory work is performed at level . these biosafety levels combine the use of laboratory safety practices, safety equipment, and laboratory facilities to provide greater levels of safety for the more dangerous organisms. each level is specifically appropriate for handling various biologic agents (cdc, ) . there are more than , clinical laboratories in the united states in which clinical laboratory scientists, pathologists, the centers for medicare and medicaid services (cms) registers all clinical laboratories in the united states that examine materials derived from the human body for diagnosis, prevention, or treatment. cms administers the program for the secretary of health and humans services in conjunction with the centers for disease control and prevention (cdc) and the food and drug administration (fda). cms regulates laboratories and establishes criteria for other organizations, such as state health departments, that also regulate laboratories to ensure compliance with the federal clinical laboratory improvement act (clia). clia was first enacted by congress in and set guidelines for large independent laboratories. in , congress amended clia to expand the type of laboratories that must comply; clia further established quality standards for laboratories to ensure accuracy, reliability, and timeliness of test results. in august, , , laboratories were registered with the cms (centers for medicare and medicaid services, ) . table . shows the distribution of these laboratories by type. more than % of these laboratories are located in physician offices. skilled nursing facilities ( . %), hospitals ( . %) ,and home health agencies ( . %) accounted for an additional % of laboratories. the remaining clinical laboratories are found in community health clinics, health maintenance organizations, blood banks, industrial facilities, medical technologists, and laboratory technicians perform billion or more diagnostic tests annually (centers for medicare and medicaid services, ) . the american society for clinical pathology (ascp) currently certifies more than , laboratory professionals who primarily work in clinical diagnostic and research laboratories. clinical laboratory services in the united states are delivered either by commercial clinical laboratories or by "in-house" laboratories at healthcare facilities (hospitals, clinics, physician offices), departments of health, veterinary hospitals, and clinics. individual veterinarians and physicians and the staff within their offices also conduct laboratory testing and produce results that are important for biosurveillance. professional laboratorians provide services that include simple, rapid screening tests; more advanced diagnostic tests; and complex confirmatory analyses. clinicians use the information provided by laboratories to establish diagnoses and to make treatment decisions on virtually every patient. the demand for testing is increasing as the population ages and requires more health care, including analytical services. new tests are frequently introduced that improve diagnosis and care. the emergence of new diseases, the threat of bioterrorism, and the need for better biosurveillance systems have increased the demand for qualified laboratory professional in all fields, especially infectious disease testing. although the demand for more laboratory professionals is increasing, the number of established laboratory professional training programs is decreasing. test kits determined by the fda to be sufficiently simple to perform that there is little risk of operator error. laboratories that perform waived tests must enroll in the clia program, pay certification fees, and follow the manufacturers' test instructions. however, laboratories that perform only waived tests do not undergo inspections or need to comply with other clia requirements for larger laboratories. laboratories that perform tests that use a microscope to examine specimens that are not easily transportable during the course of a patient visit are required to enroll in a clia program, pay applicable fees, and maintain certain quality and administrative requirements. these laboratories, known as provider-performed microscopy providers (ppmps), represent % of the registered laboratories and are not subject to routine inspections. the remaining clinical laboratories must either be accredited by of approved clinical laboratory accrediting organizations (american association of blood banks, american osteopathic association, american society of histocompatibility and immunogenetics, college of american pathologists; commission on office laboratory accreditation, joint commission on accreditation of healthcare organizations) or obtain a compliance certificate directly from cms. in august , these six organizations had accredited , ( . %) laboratories, and cms had certified , ( . %) laboratories. the balance of the clinical laboratories ( , ) were either waived test providers or ppmps (centers for medicare and medicaid services, ) . accreditation of clinical laboratories helps ensure that laboratories meet or exceed clinical standards established by governmental and nongovernmental associations. cms, insurance companies, and healthcare plans require laboratories to be certified or accredited by these organizations for reimbursement of laboratory services. table . shows the annual test volume of the , clinical laboratories that were certified by cms in august . over % of these laboratories perform fewer than , tests per year. only of these laboratories performed , or more tests per year. these laboratories represent only . % of all laboratories, yet they perform approximately % of all tests. two state health departments have developed and currently administer state clinical laboratory improvement programs that cms deems equivalent to the cms program. laboratories in washington and new york must meet the standards of these state programs. approximately additional states have laboratory licensure programs. they receive funding from cms to implement the federal clia program. in states that do not have clinical laboratory regulatory programs, the laboratories must choose between accreditation through one of the six approved organizations or submitting to inspection and certification by cms. environmental testing laboratories perform physical, chemical, and microbiological analysis of specimens collected in the environment. for example, a water sample may undergo physical testing (temperature, turbidity, odor, color), chemical testing (nitrates, sulfates, pesticides, metals), and microbiological testing (total plate counts, coliforms, giardia, cryptosporium). environmental testing laboratories provide a wide range of testing that is in many ways similar to the testing performed in clinical laboratories. sanitarians or water quality technicians often perform basic tests (e.g., for temperature, ph, volatility, and physical appearance) at the site where samples are collected. they transmit the results of these simple tests to the laboratory along with the samples, where chemists and microbiologists perform additional presumptive and confirmatory testing. results from the simple tests may suggest the need for more definitive testing, using instruments such as atomic adsorption spectrophotometers, gas chromatographs, and mass spectrometers. laboratories perform much of the routine environmental testing in batches of to samples on semiautomated or fully automated instruments. the raw analytical data are captured, processed, and reported by using software that interfaces directly with the instrument and the laboratory's data management system. environmental laboratories are certified by accreditation authorities recognized by the environmental protection agency (epa) as part of the national environmental laboratory accreditation program (nelap). at least states currently are recognized by the epa as environmental laboratory accrediting authorities. these state programs apply nationally recognized standards to the laboratories that they accredit so that there is some consistency in the quality of tests performed by accredited laboratories. commercial laboratories are an important component of the medical delivery system in the united states. a commercial laboratory is a laboratory that is free-standing; that is, it is not associated with a hospital or other healthcare organization. commercial laboratories may specialize in clinical specimens, environmental specimens, or both. commercial laboratories can be important partners for organizations that wish to develop biosurveillance systems because of size of the laboratories and their use of information technology. commercial laboratories have grown significantly in size during the past decade as a result of mergers and consolidations, and they may offer tests that are not readily available. many of these laboratories began as specialized reference laboratories, offering tests that could not be economically provided by smaller laboratories. small laboratories merged with larger laboratories that were, in turn, purchased by large laboratory corporations. regional consolidation of clinical laboratories that provided services to healthcare organizations led to the formation of large commercial laboratories. these commercial laboratories, such as lab corp, arur and quest, have developed service systems that allow them to provide clinical testing at their headquarters and at distributed sites around the country. large commercial laboratories have established elaborate courier systems that collect samples locally for overnight distribution to the appropriate laboratory in their network. although a sample may be transported to a distant laboratory, the results, nevertheless, frequently become available overnight. the commercial laboratories use information systems referred to as laboratory information management systems (limss) to track tests and results. these systems monitor test requests, capture test results, and electronically report the results, often within hours of the sample being received. as discussed in chapter , clinical laboratories are required to report notifiable diseases to local health departments. the large, multistate commercial laboratories face challenges in complying with notifiable disease reporting requirements that vary by state. further, reporting requirements frequently change as new diseases of public health interest are identified and many states have expanded laboratory reporting requirements to include suspected cases of notifiable diseases. commercial laboratories are increasingly using electronic laboratory reporting to satisfy these complex and changing requirements. commercial laboratories may specialize in environmental testing. these commercial environmental laboratories provide testing on a variety of samples, such as water, air, hazardous materials, dust, and soil. these laboratories often contract with governmental agencies, such as epa, department of defense (dod), and u.s. department of agriculture (usda) at the federal level and with environmental and regulatory agencies at the state and local level. federal, state, and local government agencies, such as health departments, operate laboratories or contract with commercial laboratories for testing related to diagnosis, regulatory compliance, investigations, and environmental monitoring. since the early s, governmental laboratories have performed testing that led to the identification of outbreaks of diphtheria, cholera, smallpox, and typhoid fever. during the th century, these laboratories, in conjunction with academic laboratories, helped develop vaccines and contributed to the detection of polio, rubella, measles, and whooping cough. the response to west nile fever in the united states and the release of viable bacillus anthracis in required these laboratories to develop procedures quickly for diagnosis and identification of agents that they had not previously encountered. governmental laboratories are key to the recognition of new and emerging infectious diseases and are vital to surveillance efforts. the department of health and human services (dhhs), usda, department of energy (doe), dod, and departments of commerce and justice, and the epa operate or fund clinical, environmental, forensic, and research laboratories. federal laboratories provide reference testing and are often involved with the development of new technologies, as well as the transfer of these technologies to other laboratories. many federal laboratories collaborate with international partners and serve as reference centers for specialized testing. federal laboratories often provide training, confirmatory testing, and reference materials for other governmental laboratories. the dhhs laboratories that are associated with disease detection, control, and surveillance activities are found at the national institutes of health (nih), cdc, and fda. the nih, headquartered in bethesda, maryland, conducts research on acute and chronic diseases, develops new therapies and immunizations, and develops new laboratory and diagnostic technologies for many infectious and noninfectious diseases and health conditions. much of the nih work is done through extramural grants and contracts with universities, private companies, and other governmental organizations. the cdc's laboratories focus on infectious diseases, occupational diseases, and environmental causes of diseases. the cdc specialized laboratories are in colorado, ohio, west virginia, and puerto rico, in addition to its headquarters in atlanta, georgia. the cdc has led the development of rapid national laboratory reporting systems that have been successfully used to identify multistate outbreaks of diseases ( bean et al., ; hutwagner et al., ) . cdc-based scientists have developed and used new technologies to identify outbreaks of disease in cooperation with state and local public health laboratories. one such example of the successful application of a new technology is known as pulsenet (discussed in chapters and ; http:// www.cdc.gov/pulsenet/). pulsenet is a national network of public health laboratories that perform dna "fingerprinting" of foodborne pathogens and clinical isolates to allow matching of isolates. this epidemiological typing method is the basis for detecting clusters of disease that are geographically diffuse, and for linking bacteria found in a specific food to bacteria found in one or more persons with a particular disease. pulsenet permits recognition of outbreaks that previously went undetected. a multistate outbreak of listeriosis in was identified only after the isolates of listeria monocytogenes were tested by using pulsed-field gel electrophoresis and determined to all have a common pulsenet pattern (cdc, ) . fda laboratories focus primarily on monitoring the food supply and ensuring the purity and potency of drugs and other pharmaceuticals. these regulatory laboratories frequently become involved in the investigation of food contamination (including ground beef, poultry) and the adulteration of drugs. fda maintains regional laboratories in washington, new york, colorado, michigan, kansas, california, georgia, and arkansas, as well as specialized laboratories in ohio, pennsylvania, puerto rico, and massachusetts. the fda laboratories provide testing to support investigation and compliance activities. fda's electronic laboratory exchange network (elexnet) is a web-based system for real-time sharing of laboratory data derived from foods. this system allows public health officials to compare laboratory findings and to identify outbreaks earlier. the usda operates laboratories that support many of their regulatory, monitoring, and investigative programs. usda laboratories conduct research on animal and plant diseases and provide testing of animals and agricultural products. the usda's national veterinary services laboratories (nvsl) located in ames, iowa, tests for domestic and foreign animal diseases, and function as the primary animal disease reference laboratory. the nvsl provides diagnostic support for disease control and eradication programs, import and export testing of animals, and laboratory certification for selected animal diseases. diseases, such as anthrax, rabies, brucellosis, and bovine spongiform encephalopathy (mad cow disease), may impact both animals and humans and, therefore, constitute priorities at this laboratory. a former usda laboratory, the foreign animal disease diagnostic laboratory (faddl), which is located on plum island off long island, new york, was recently transferred to the department of homeland security after supporting years of research on some of the most dangerous animal pathogens. the doe oversees the operation of doe national laboratories, many of which were established to support the production, use, and response to nuclear materials. after the end of the cold war, the focus of some of the doe laboratories shifted to other projects, including the human genome project and the development of technologies and assays to support homeland security initiatives. the doe national laboratories develop new technologies for countering biologic and chemical threats, including systems for the detection, modeling, and response to terrorist attacks (see www-ed.fnal.gov/doe/ doc_labs.html). the dod has established laboratories worldwide in locations such as peru, indonesia, egypt, thailand, and kenya. dod laboratories serve the needs of the armed forces and function as screening or sentinel laboratories for infectious diseases. the u.s. army medical research institute of infectious diseases (usamriid) has the capability to detect unusual biological agents that often require advanced testing techniques. this laboratory, located in maryland, is a member of the laboratory response network (lrn; discussed later) and one of a few laboratories worldwide that can isolate and identify the most dangerous human agents, such as ebola, smallpox and marburg viruses. the epa operates regional environmental testing laboratories across the united states. these laboratories have a research and environmental monitoring mission: they analyze air, drinking water, ground water, surface water, soil, sediment, and hazardous materials for biological, chemical, and radiological materials that are toxic to the environment. epa develops standard methods for the analysis of environmental samples. epa maintains large databases of environmental monitoring data produced by its own laboratories and others. its office of research and development (ord) directs laboratory activities at locations, including the national center for environmental assessment in research triangle park, north carolina. although the capability and capacity of the federal laboratories described above is large, this capacity was challenged by the volume of environmental and clinical samples generated during the anthrax postal attack. the distribution of anthrax spores in mail during october led to an unprecedented demand for quality testing throughout the united states owing to discovery of real and suspected contaminations. although few of the more than , environmental samples tested contained b. anthracis, the existing network of public and commercial laboratories was barely able to meet the demands for testing, and there were significant delays caused by the sheer volume of samples. the concept of a high-throughput laboratory capable of testing thousands of biologic, chemical, or radiological samples would require the laboratory to be equipped with the latest automated instrumentation and supported with an efficient lims (layne and beugelsdijk, ) . the establishment of high-throughput laboratories to support the nation's homeland security needs is a reasonable concept, especially if the major federal partners were to colocate resources on a national interagency homeland security laboratory campus. approximately of the more than , laboratories in the united states are classified as state public health laboratories. included in this number are about regional or branch laboratories that are administered as part of the state public health laboratory. more than , laboratory professionals are employed by state public health laboratories. each state and five territories operate a state public health laboratory. one major function of theses laboratories is to provide diagnostic and analytical services for surveillance of infectious, communicable, genetic, and chronic diseases. state (and local) public health laboratories provide testing to support many public health programs (tuberculosis, sexually transmitted diseases, hiv, immunizations, and newborn screening). areas of analysis include clinical and environmental chemistry, immunology, pathogenic microbiology, virology, and parasitology. state laboratories serve as reference laboratories, and they provide confirmatory testing of specimens submitted from other laboratories. the state public health laboratories frequently measure toxicants in human samples to document exposures to chemicals found in the diet or environment. this specialized testing requires expensive equipment (mass spectrometers, chromatographs) and well-trained chemists. the capabilities, responsibilities, and practices of the state public health laboratories vary. during recent years, many of these laboratories have received substantial federal funding to increase staff, equipment, and capabilities to respond to biologic and chemical threats, as part of the dhhs' cooperative agreement on public health preparedness and response for bioterrorism. a large percentage of the state public health laboratories have used some of the federal funding to build, remodel, and upgrade facilities. funding for state laboratories is generally a mix of state and federal funds. many states rely on fees, reimbursements, and service contracts to carry out their mission. some states have regional or district laboratories to provide the necessary services throughout an entire state. state public health laboratories partner with public health laboratories operated by counties or cities to meet the needs of their communities. state public health laboratories are generally better prepared to respond to an incident requiring biologic testing as opposed to an incident requiring chemical testing. although research is not the primary mission of public health laboratories, several state public health laboratories have developed close ties with academic institutions. the opportunity to work on surveillance projects with faculty and students from schools of public health and academic training programs for laboratory professionals has been beneficial to these laboratories. arrangements with academic centers afford opportunities to improve laboratory services and surveillance systems. flexible funding and other resources, such as grants, faculty, and students, help support special research projects and training opportunities within public health laboratories. state laboratories provide services to health departments; healthcare organizations; local, state, and federal law enforcement; local hazardous materials (hazmat) teams; civil support teams; and other private and governmental laboratories. state laboratories analyze thousands of water and air samples daily. state laboratories involved in the analysis of drinking water and other environmental samples are accredited by the nelar certified by epa office of drinking water programs, or accredited by state-specific accreditation programs. state public health laboratories are the backbone of the laboratory response network (lrn), which we discuss below. the lrn also includes laboratories under the jurisdiction of federal agencies discussed in this chapter. at the time of publication, state and local public health laboratories make up the laboratories that are members of the lrn. of these, state, territorial, and metropolitan public health laboratories are part of the lrn's chemical testing network. more than , local public health laboratories provide support for city and county public health programs. these laboratories offer onsite testing for child health screening, tuberculosis, refugee screening, food safety, sexually transmitted diseases, and lead poisoning prevention, as well as epidemiologic investigations and environmental monitoring. local public health laboratories often forward specimens to their state laboratories for tests that are not available locally. approximately % of the local public health laboratories only perform waived tests. another % perform moderate complexity testing, and % perform highly complex testing (association of public health laboratories, ) . many state and locally operated laboratories in addition to clinical and public health laboratories produce test results that may be useful for surveillance. forensic laboratories and toxicology laboratories are frequently associated with departments of public safety or with state or local medical examiners. these forensic laboratories may be positioned at the federal, state, or local level, depending on the jurisdiction. medical examiners contribute to biosurveillance by elucidating unusual causes of death (see chapter ). medical examiners and forensic pathologists frequently rely on laboratories to establish the exact cause of death. readers may understand laboratories as only providing test results after the analysis of samples that are submitted. this view of laboratories only focuses on one of their products and overlooks services provided by the professionals who work in the laboratories. laboratory professionals provide consultation on the selection of the most useful tests for screening, diagnosis, and verification of disease. they provide information on the proper handling and transportation of samples. development of new technologies, evaluation of technologies, and the application of technologies are other important services provided by laboratory professionals. laboratories evaluate test kits for ease of use, storage conditions, and performance characteristics. laboratories train individuals to perform testing and educate and inform users of laboratory services. laboratories may also operate laboratory-based surveillance systems for respiratory and enteric diseases. laboratories employ many analytic technologies to provide testing for diagnosis and surveillance. these tests range from simple screening tests to presumptive diagnostic tests and confirmatory tests. simple laboratory tests are used to screen biologic samples for the presence of biological agents or other substances that might indicate a disease, an infection with a biologic agent, or a contamination with a toxin or other chemical. the classical approach to identification of biologic agents involves direct examination of stained materials by microscopic examination for the presence of agents (dhhs/cdc, n.d.; york, ) . microscopic examination relies on staining characteristics and the size and shape of the organisms found. with few exceptions, it is rarely possible to identify an agent based only on microscopic characteristics. direct stains may help eliminate organisms from further consideration, but they are usually not sufficient without further testing to identify a pathogen. wet mounts are used for the direct microscopic examination of clinical materials for fungi and parasitic agents. additional simple assays take advantage of the ability of an organism to metabolize chemicals or produce chemical reactions that result in color changes of a substrate. recently, many assay kits have been developed for waived tests. these waived test kits can produce reliable results in most cases; however, one must understand the limitations of these kits and the need for confirmatory testing. field test kits, often referred to as handheld assays, have become popular with first responders who have a need to know if an unknown material contains a biologic agent or toxic chemical. simple immunologic reactions, coupled with a colorimetric indicator, form the detection systems for many handheld assays. validating the performance of handheld assays in comparative studies is a task generally reserved for governmental agencies or contract laboratories (emanuel et al., ) . the major advantage of the simple assays is that they are quick, as a result may be available in to minutes. the short turnaround time makes these tests ideal for use by surveillance systems provided one understands the limitations of the tests and that a method for confirmatory testing is available. presumptive diagnostic tests are procedures that, when properly performed, may indicate the presence of a particular agent or closely related agents. presumptive diagnostic tests for biologic and chemical agents are more complex and require more time to perform than do the simple tests described above. most bacterial and viral agents can readily be grown in culture media or cell culture if the appropriate conditions are met. these conditions include the appropriate temperature, ph, and a source of energy (e.g., glucose). inhibitory substances, such as antibiotics, are often placed into the growth media to prevent the growth of unwanted organisms. growth of organisms in cell culture or artificial media takes hours to or more days, depending on the organism. once organisms are detected on or in growth media, various techniques are used to determine the genus and species of the organism. for bacteria, the differential growth on select media, metabolism of various carbohydrates and other chemicals, and the presence of selected enzymes are often used for identification. special stains that incorporate florescent dyes coupled with antibodies to selected organisms are used for identification of bacteria and viruses. laboratories use immunologic assays to identify many biologic agents and for the subspecies typing that is needed for epidemiological purposes. immunologic assays generally involve the use of a specific antibody that can attach to or react with the outer-surface structures of an agent. other immunologic assays are used to detect antibodies in biological materials after infection with biological agents. after the isolation and identification of many organisms, drug-susceptibility testing determines the organism's susceptibility to drugs that are used to treat infections with the organism. a definitive or confirmatory test is a test that will identify with a very high degree of certainty the true identity of an agent. these tests have a very low likelihood of providing a falsepositive result. many of the definitive and confirmatory assays used today are molecular assays, which detect genetic material that is specific to a bacterium, virus, protozoa, or other organism. nucleic-acid-based assays rely on the unique differences found in the structure of single strands of dna and rna. the unique pattern of bases is specific for a single organism or closely related organisms. the nucleic-acid-based assays involve the use of probes, which are strands of dna or rna that match distinctive dna or rna patterns of the organism being tested and will bind with that dna or rna if it is in the clinical specimen. once the binding occurs, the binding can be detected by using electrochemical, colorimetric, and optical systems (committee on research and development needs for improving civilian medical response to chemical and biological terrorism incidents, ) . this binding provides extreme selectivity between the known probes and the material found in clinical specimens. the use of a technique known as polymerase chain reaction (pcr) makes it is possible to amplify trace quantities of dna or rna in a clinical specimen to enable the detection of as few as , bacteria or viruses. the high specificity and sensitivity of molecular assays makes them especially suited for detecting minute quantities of biologic agents and toxins. the use of genetic fingerprints has become a valuable tool for microbial forensics (murch, ) . by identifying distinct features of genes using sequencing techniques, it is possible to identify individual strains of organisms and to use this information as epidemiological markers. molecular techniques allow investigators to link strains from various sources and to form associations that often unravel the mystery of disease outbreaks. libraries of genetic patterns, or fingerprints, make it possible to trace the origin of many outbreaks. not only does sequencing identify dna or rna patterns unique to a particular organism, but, in many cases, these probe technologies are simpler, faster, and less technology-dependent than are other traditional assays. many biotechnology companies are pursuing production of microarray systems that will test for to , or more different dna fragments simultaneously. the technology embeds the probes on a single glass or nylon substrate called a microchip. by using these arrays and various detection systems onto which the clinical specimen is applied, the individual components of the microchip will react with dna fragments in the specimen and be detected. as this technology develops, it will become more common to use the microarray systems for screening and detection of diseases. simultaneous pcr assays for multiple respiratory viruses now have sufficient sensitivity and specificity to be a valuable tool for diagnosis of respiratory viral infections (hindiyeh et al., ) . in the future, pcr assays will be able to screen a single specimen for a multitude of biologic agents. a lims is a computer system that a laboratory uses to track specimens and manage analytical data. the function of a lims can perhaps best be explained by tracing a single test-a white blood count--from the time that a clinician orders the test until the time the clinician receives the result of the test. a clinician requests (orders) that a laboratory perform a white blood count on a blood sample from a patient in one of several ways. the clinician writes the order on paper, gives a verbal order to a nurse, or enters the order directly into a computer system. a lims may receive this order in one of several ways: directly, if the lims provides an order-entry component that either the clinician uses directly or the nurse or ward clerk uses on her behalf; indirectly, if a paper order form accompanies the specimen; or electronically, from an order-entry system embedded in another information system (such a point-of-care system as discussed in chapter ). we will trace the most automated path in which the lims receives the order electronically. the received order sets up a specimen-tracking process that is a central lims function. the lims (or a point-of-care system) controls a printer, which is often located in the clinical area from which the order originated. the printer generates a bar-coded label. a phlebotomist attaches the label to a "purple top" vial (containing magnesium citrate or ethylenediaminetetraacetic acid [edta] to prevent the blood from coagulating). the phlebotomist draws the blood after checking carefully that the identification on the labeled tube matches the patient, and sends the sample to the laboratory. oftentimes, the labeled specimen is transported by pneumatic chute from clinical areas, such as the emergency department, or by express overnight delivery to the laboratory. a technician in the laboratory scans the barcode of the specimen with an optical scanner, which is connected to the lims. if the laboratory has an automated analyzer for blood counts, the technician simply places the vial into the specimen carousel of the analyzer. the analyzer recognizes the bar code, communicates with the lims over an internal laboratory network to determine which tests were ordered for the spedmen, runs the tests, and transmits the results to the lims. other types of specimens may require preparation, such as centrifugation, before being placed into the carousel of an automatic analyzer, but the information processing and communication between the analyzer and the lims are otherwise identical. for tests that are done by hand, the lims provides user-interfaces into which medical technologists register specimens and enter intermediate and final results of tests. depending on the laboratory and the needs of its clinical customers, the lims may deliver the results as paper reports, via web-browser interfaces, or by e-mail. a lims typically offers all of these options. a lims invariably has an outbound computerto-computer interface that can transmit results to other clinical information and public health information systems. although our example is of a clinical test, the process is identical for environmental tests ordered by sanitarians, water quality technicians, or outbreak investigators. the vast majority of laboratory work in the united states is highly automated in the fashion just described. with the exception of tests done in the field or in office practices, limss track and manage the analytic results of most laboratory tests performed in the united states. limss are designed to make test results available to clinicians and other information systems soon after they are performed. limss are highly reliable and operate in real time. limss are developed within the laboratory by information technology staff, purchased from commercial vendors, or a combination of both. because of the importance of laboratory tests in biosurveillance, biosurveillance organizations are attempting to establish connections between limss and their own biosurveillance computers. at present, however, there are significant technical barriers to connecting a lims located in a laboratory with a computer located in a biosurveillance organization. the most difficult technical barrier is data incompatibility. most laboratories do not use standard coding systems to identify the names and results of laboratory tests. data standards exist, but few laboratories use them. most laboratories have evolved their own naming or coding systems for the tests that they perform and the results of those tests. they use these proprietary codes (or free text) to identify the laboratory test, specimen type, organism, or other results of a test. as a result, each lims-tobiosurveillance-computer interface requires significant effort to understand the data and to create means to translate the data into a standard format so that it can be integrated with data coming from other lims. we discuss standard data formats in detail in chapter . outbound communication standards, such as hl , also exist and we discuss them in chapter . although most lims support these standards, the specific implementations vary. even if both the biosurveillance computer and the lims use the hl standard, they will not be able to communicate without significant effort to understand the specifics of the messages and to create a means for extracting the data from the messages. importantly, a new version of hl (version . ) will solve this problem; but its penetration in the lims market is low at present. because of the customization required to connect even a single lims to a biosurveillance organization, there are only a few regions that have integrated data from most of the limss that serve their region into biosurveillance. ultimately, these barriers will be addressed by standardization, but as we discuss in chapter , it takes many years to achieve widespread standardization of any component in a biosurveillance system. the organization of laboratories into collaborative networks has been ongoing for more than a decade. the concept of laboratory networks arose from the need to ensure that critical laboratory services were available throughout the country (gilchrist, ) . the cdc, fda, usda, and state governmental laboratories formed many of the original partnerships that grew into the laboratory networks that exist today. early networks included the national laboratory system (nls) of clinical, public health and federal laboratories (mcdade and hughes, ) , and the public health laboratory information system (phlis). phlis was an early dos-based system that involved voluntary reporting of selected laboratory tests directly to the cdc by state and local public health laboratories and numerous military laboratories (see chapter ). phlis was one of the earliest laboratory-based surveillance systems that became an effective tool for the identification of outbreaks of salmonellosis (bean et al., ; hutwagner et al., ) . the cdc's lrn was established in in compliance with a presidential directive that outlined federal agencies' counterterrorism goals and responsibilities. the mission of the lrn is "to maintain an integrated national and international network of laboratories that can respond quickly to acts of chemical or biological terrorism, emerging infectious diseases and other public health threats and emergencies." the lrn was first tasked to address state and local public health laboratory preparedness and response for bioterrorism. since its inception, its mission has expanded to include chemical terrorism. the scope of laboratories in the lrn has expanded beyond state and local public health laboratories in order to meet national security needs (http://www.bt. cdc.gov/lrn/). the lrn and its partners maintain a network of laboratories that can respond quickly to acts of chemical or biological terrorism, emerging infectious diseases, or other public health threats and emergencies. the network included federal, state, and local public health; military; and international laboratories as of august , . figure . shows the distribution of lrn laboratories by type as of march , . the lrn employs tests that can detect biological threat agents in clinical specimens, environmental samples, food, animals, and water. the association of public health laboratories was a partner in the early development of the lrn and has played an important role in ensuring that the lrn provides the training, standardized methods, and equipment necessary for detecting biologic agents of terrorism and other threats to public health. the federal bureau of investigation (fbi) was also a key partner in establishing the network. the fbi brought its forensic expertise and evidence-gathering requirements to the program. public health and law enforcement have overlapping approaches to their investigations that required collaboration between cdc and law enforcement to both enhance and protect the integrity of their investigations. three levels of laboratories are recognized within the lrn for bioterrorism agent detection. lrn laboratories responsible for bioterrorism agent detection are designated as national, reference, or sentinel laboratories (figure . ). the national laboratories include laboratories at the cdc, usamriid, and the naval medical research center. they have unique resources to safely identify highly infectious agents (biological safety level agents) and the ability to provide definitive characterization of biologic agents. the national laboratories have developed standard tests and protocols, trained laboratory analysts, and established secure communications for the rapid sharing of laboratory results from reference laboratories. reference laboratories in the lrn perform tests to detect and confirm the presence of biological threat agents, such as those that cause anthrax, plague, tularemia, smallpox, or botulism. these laboratories ensure that state and local laboratories can have a timely response in the event of a bioterrorism incident or an emerging disease. rather than having to rely on confirmation testing from national laboratories, reference laboratories are capable of producing conclusive results needed by local authorities for rapidly responding to emergencies. specimens received by reference laboratories that contain threat agents are usually submitted to a national laboratory for definitive characterizations of the agent. state and local public health laboratories comprise most of the reference laboratories within the lrn. although sentinel laboratories are not counted among the lrn laboratories, they represent the thousands of clinical (human and veterinary) and environmental laboratories identified by the state lrn reference laboratory to serve as the front line of defense in detecting agents of terrorism. qualification of the sentinel laboratory is based on the experience and competency of the laboratory staff, appropriateness of facilities, and completion of training provided by the lrn. sentinel laboratories can often rule out potential bioterrorism agents based on a battery of simple tests. in a covert terrorist attack, a sentinel laboratory could be the first facility to identify a suspicious agent or an unusual cluster f i g u r e . laboratory response network (lrn) structure for bioterrorism response laboratories. of diseases. a sentinel laboratory's responsibility is to rule out other diseases and refer a suspicious sample to an appropriate reference laboratory. the lrn uses an array of presumptive and confirmatory assays to detect biological threat agents or chemical agents. presumptive assays generally include traditional microbiological assays, such as growth on special media, use of special stains, and the use of rapid molecular diagnostic assays, such as real-time pcr. confirmatory methods used by the national laboratories are considered the gold standard for detecting the target agent. methods, such as time-resolved fluorescence (trf) and molecular characterization, have replaced many of the more traditional confirmatory methods that were based on the growth and biochemical properties of the agent. reference laboratories have access to lrn protocols through a secure web site and are supplied standardized reagents needed to perform the necessary tests. uniform procedures for use by sentinel laboratories have also been developed and are used for training of sentinel laboratory staff. all laboratories that are part of the lrn must provide a safe and secure environment for performing tests and must participate in a recognized proficiency testing program. the chemical component of the lrn employs a more centralized structure, with only a few laboratories currently prepared to provide definitive analysis of specimens for chemical agents or their metabolites. lrn laboratories responsible for chemical agent detection are designated as level , , or laboratories. five laboratories located in california, michigan, new mexico, new york, and virginia participate in level activities. at this level, personnel are trained to detect exposure to an expanded number of chemicals in human blood or urine, including all level laboratory analyses, plus analyses for mustard agents, nerve agents, and other toxic chemicals. fortyone laboratories participate in the chemical lrn by providing level activities. at this level, laboratory personnel are trained to detect exposure to a limited number of toxic chemical agents in human blood or urine. analysis of cyanide and toxic metals in human samples are examples of level laboratory activities. each of the chemical network members participates in level activities. level laboratories are responsible for the following: working with hospitals in their jurisdiction knowing how to properly collect and ship clinical specimens ensuring that specimens used as evidence in a criminal investigation are handled properly and chain-of-custody procedures are followed being familiar with chemical agents and their health effects training on anticipated clinical sample flow and shipping regulations working to develop a coordinated response plan for their respective state and jurisdiction initial testing in a suspected chemical event will occur at cdc or i of level i chemical laboratories that have been established by cdc. by use of mass spectrometry, cdc laboratories perform tests on the first or more clinical specimens to measure human exposure. results of these tests would be reported to affected states, and if needed, appropriate lrn members may be asked to test additional samples. this approach is necessary because the analytical expertise and technology resources required to respond to a chemical event is expected to be high. the lrn supports secure communications on emerging and emergency issues, a secure mechanism for ordering reagents and testing protocols, and a system for electronically reporting test results. the lrn provided valuable testing after the release of anthrax spores in , the identification of monkey pox in , and the response to severe acute respiratory syndrome (sars) in . in , canada created a laboratory network, known as the canadian public health laboratory network (cphln), to strengthen the linkages between federal and provincial public health laboratories. this canadian network is modeled after the lrn in the united states. the cphln has been providing responses to naturally occurring infections and deliberate releases of biologic agents and toxins. the cphln coordinates pathogen detection and infectious disease prevention activities, as well as conducts laboratory-based surveillance and early warning systems for emerging pathogens and bioterrorism threats. the national animal health laboratory network (nahln) is part of a national strategy in the united states to coordinate the nation's federal, state, and academic animal health laboratories. the usda has taken the lead in the development of this network, which includes agriculture and animal health laboratories operated by state agricultural agencies and those associated with veterinary teaching facilities. the facilities and professional expertise of nahln members allows authorities to better respond to animal health emergencies that might include a bioterrorist event, the emergence of a new domestic animal disease, or the appearance of a foreign animal disease that could threaten the nation's food supply and public health. because many of the biologic agents that cause the greatest concern as terrorist agents infect both humans and animals, the role of veterinarians in the early detection of disease is very important. the nahln currently consists of laboratories in states. an effort is underway to deploy standardized testing methods in member laboratories and to improve the information technology system used by member laboratories to track test requests and report results. the u.s. animal health association (usaha) and the american association of veterinary laboratory diagnosticians (aavld) have members who participate in the nahlh and contribute expertise to protect animals and public health. the national plant diagnostic network (npdn) is an agricultural laboratory network that provides detection, identification, and reporting of pests and pathogens that have been deliberately or accidentally introduced into agricultural systems. the primary concern of this network is food security and the economic threats to the nation's food supplies. the npdn includes five regional centers located at cornell university, michigan state, kansas state, university of florida at gainesville, and the university of california at davis. the npdn recently implemented a new database that helps with required reporting to state and national agencies. a web-based plant diagnostic system using digital photography allows laboratories to share images with specialists in remote locations. the food emergency response network (fern) is a network of state and federal laboratories that are committed to analyzing food samples in the event of a biological, chemical, or radiological terrorist attack in the united states. the federal partners in the fern include the fda, usda, cdc, and epa. as of may , there are laboratories in fern, representing states and puerto rico. twenty-six federal laboratories, state laboratories, and five local laboratories are enrolled in fern. the mission of fern is to integrate the nation's food testing laboratories for the detection of threat agents in food while using standardized diagnostic protocols and procedures. of the laboratories in fern, there are that perform chemical tests on food, that perform biological tests on food, and that perform radiological tests on food. these laboratories strengthen preparedness and provide surge capacity. the fda and usda jointly share the leadership within fern and have been working to obtain federal funds that can be made available to support further development of the network. the data capture and information exchange system for fern is the elexnet, is an integrated, secure system designed for use by multiple governmental agencies involved in food safety activities. laboratories report test results and public health officials assess risks and analyze trends in foodborne diseases, elexnet has gis reporting functions and uses hl data exchanges between laboratories. similar to those in lrn, participants in fern receive training on the latest equipment and are required to participate in proficiency testing programs, elexnet provides the necessary infrastructure for an early warning system that can identify potentially hazardous foods and share laboratory reports in a timely manner. as of january , federal, state, and local laboratories in all states have joined the elexnet system. about laboratories actively exchange data by using elexnet. the radiological emergency analytical laboratory network (realnet) is a national network of radiological laboratories that are capable of responding to the needs for radiological testing after a terrorist attack. academic, commercial, military, federal, state, and local laboratories participate in realnet. these laboratories serve as a science and technology asset for the department of homeland security. realnet is modeled after the lrn and fern and includes a web-based database containing information on the capabilities, capacity, and competence of member laboratories. information on accreditation, certification, and performance testing is also maintained. standards, guidelines, and laboratory procedures are developed and distributed by realnet. gaps in the standards are being addressed by appropriate standards development organizations. internet-based tools, such as bulletin boards and list servers, are used to promote the exchange of information. the system provides links to other resources that would be useful during an emergency caused by the release of a radioactive material. the expansion of laboratory networks designed to produce test results in response to an act of terrorism or other public health emergency has led to increased sharing of laboratory results. coordination and integration of the various networks has not always been a priority. duplicate systems and overlapping missions suggest that an integrated consortium of laboratory networks could provide timely results for early detection and response to acts of terrorism. the networks need to agree on standardized tests and policies that would promote a timely response no matter which network is reporting results. an overall system to ensure that laboratory capacity will be available to test clinical (human and animal) specimens and environmental samples, including food and water, does not exist. laboratories that can perform screening, monitoring, and definitive testing are needed for each class of specimen. although laboratory information systems have been developed for capturing and sharing data, the diverse systems are not fully compatible with each other. failure to standardize nomenclatures and use recognized data transmission protocols make sharing of large quantities of data for surveillance purposes problematic. in an effort to improve coordination among laboratory networks, the department of homeland security is working to integrate these networks through the creation of the integrated consortium of laboratory networks (icln). the icln employs the lrn model for coordinating laboratory assets for terrorism among federal, state, local, and scientific partners. a memorandum of agreement was signed in by the usda, dod, doe, dhhs, epa, and the departments of homeland security, state, justice, and interior to form the icln. these federal agencies will collaborate to ensure that laboratory resources available within each agency can be used to respond to terrorist events and other national emergencies. clinical, commercial, and governmental laboratories are an important source of data for biosurveillance systems. test results obtained from the analysis of human and animal specimens may be early indicators of disease within the population. before the establishment of a definitive diagnosis, a sudden rise in the number of tests being requested by clinicians might be the first indication of an outbreak. the combination of laboratory data from environmental laboratories and the occurrence of illness in humans or animals might signal onset of an infectious disease or poisoning. the establishment of a lims that can rapidly capture and report laboratory data electronically will greatly contribute to the use of laboratory data in biosurveillance. challenges still exist for integrating , laboratories into a real-time network to support biosurveillance. the multitude of laboratory networks that are being formed will enhance the analytical capabilities of laboratories as well as the ability of laboratories to distribute peak loads during emergencies and quickly and efficiently share data electronically. enormous potential exists for the use of data that that is locked up in systems by the lack of standardization. although much recent emphasis has been focused on building laboratory networks in preparation for a biological, chemical, or nuclear attack, many of the enhanced laboratory capabilities will assist with the response to other public health emergencies. association of public health laboratories national plant diagnostic network (npdn) informatics for the clinical laboratory: a practical guide laboratory information management systems: development, and implementation for a quality assurance laboratory phlis: an electronic system for reporting public health data from remote sites detection and measurement of biological agents. in chemical and biological terrorism--research and development to improve civilian medical response validating the performance of biological detection equipment: the role of the federal government a national laboratory network for bioterrorism: evolution from a prototype network of laboratories performing routine surveillance evaluation of the prodesse hexaplex multiplex pcr assay for direct detection of seven respiratory viruses in clinical specimens using laboratory-based surveillance data for prevention: an algorithm for detecting salmonella outbreaks c gi ? cmd---r etriev e &db=pub med &dop t=citation high-throughput laboratories for homeland and national security the u.s. needs a national laboratory system microbial forensics: building a national capacity to investigate bioterrorism sentinel bioterrorism responders: are hospital labs ready key: cord- -c pbr i authors: hao, weiming; zhao, liping; yu, huiqian; li, huawei title: vestibular prognosis in idiopathic sudden sensorineural hearing loss with vestibular dysfunction treated with oral or intratympanic glucocorticoids: a protocol for randomized controlled trial date: - - journal: trials doi: . /s - - - sha: doc_id: cord_uid: c pbr i background: idiopathic sudden sensorineural hearing loss (issnhl) is a rapid-onset sensorineural hearing impairment with unclear etiology and unsatisfying treatment effects. vestibular dysfunction has been considered as a poor indicator in the clinical manifestations and prognosis of issnhl, which occurred in approximately – % cases. glucocorticoids, administered through oral or intratympanic way, are currently regularly and standardly applied for issnhl to improve the hearing outcome. however, the vestibular prognosis of issnhl after routine treatments remains seldom explored. this study aims to compare the effectiveness of oral and intratympanic glucocorticoids in issnhl with vestibular dysfunction in terms of the pattern and trajectory of possible process of vestibular function recovery. methods/design: a randomized, outcome-assessor- and analyst-blinded, controlled, clinical trial (rct) will be carried out. seventy-two patients with issnhl complaining of vestibular dysfunction appearing as vertigo or imbalance will be recruited and randomized into either oral or intratympanic glucocorticoid therapy group with a : allocation ratio. the primary outcomes will be vestibular function outcomes assessed by sensory organization test, caloric test, video head impulse test, cervical vestibular evoked myogenic potential, and ocular vestibular evoked myogenic potential; the secondary outcomes include self-reported vestibular dysfunction symptoms; dizziness-related handicap, visual analogue scale for vertigo and tinnitus; and pure tone audiometry. assessments of primary outcomes will be performed at baseline and at and weeks post-randomization, while assessments of secondary outcomes will be performed at baseline and , , , and weeks post-randomization. discussion: previous intervention studies of issnhl included only hearing outcomes, with little attention paid on the prognosis of vestibular dysfunction. this trial will be the first rct study focusing on the progress and prognosis of vestibular dysfunction in issnhl. the efficacy of two commonly used therapies of glucocorticoids will be compared in both auditory and vestibular function fields, rather than in the hearing outcome alone. trial registration: clinicaltrials.gov nct . registered on july discussion: previous intervention studies of issnhl included only hearing outcomes, with little attention paid on the prognosis of vestibular dysfunction. this trial will be the first rct study focusing on the progress and prognosis of vestibular dysfunction in issnhl. the efficacy of two commonly used therapies of glucocorticoids will be compared in both auditory and vestibular function fields, rather than in the hearing outcome alone. trial registration: clinicaltrials.gov nct . registered on july keywords: randomized controlled trial, vestibular function, sudden hearing loss, glucocorticoid background sudden sensorineural hearing loss (ssnhl) is a rapidonset inner ear disease. it is defined as a sensorineural hearing loss of at least db over at least three test frequencies occurring within h [ , ] . the reported incidence rate of ssnhl is about - / , people per year [ ] , which has been widely considered underestimated because of the unregistered cases with out-ofhospital spontaneous recoveries. the etiology in about to % of ssnhl cases remains uncertain, which is defined as idiopathic ssnhl (issnhl) [ , ] . various postulated etiological theories have been proposed including microvascular impairment, viral infections, inner ear electrolytic disorders, trauma, autoimmune diseases, and central nervous system (cns) diseases [ ] [ ] [ ] [ ] [ ] . based on the close anatomic relationship between cochlea and vestibule, approximately - % of issnhl patients have also reported of co-occurring symptoms of vertigo [ ] . there are two administration patterns of glucocorticoids for issnhl: systemic (oral or intravenous) and intratympanic therapies. compared with the traditional oral administration, intratympanic therapy is thought to be superior for its ( ) bypassing the blood-labyrinth barrier and achieving higher drug concentrates in the inner ear and ( ) avoiding most of the systemic side-effects of glucocorticoids. a well-designed randomized trial was conducted in by rauch and his colleagues, which supported the non-inferiority in hearing outcomes of intratympanic therapy compared with oral prednisone in issnhl. however, the study was failed to reject the inferiority based on the -db non-inferiority standards in the subgroup analysis of issnhl with dizziness [ ] . considering that few investigations have been carried out on progress and prognosis of issnhl-related vestibular dysfunctions after basic treatment, we designed this randomized, assessor-and analyst-blinded, controlled trial with two interventional arms, one is the oral glucocorticoid therapy group and the other one is the intratympanic glucocorticoid therapy group. our research hypothesis is that intratympanic methylprednisolone is superior to oral prednisone on vestibular function recovery of issnhl patients with vertigo. this protocol is reported in accordance with the standard protocol items: recommendations for interventional trials guidelines (spirit) (additional file ) [ ] . this study is designed as an -week, single-center, randomized, assessor-and analyst-blinded, controlled trial with two parallel interventional groups in a : allocation. patients will be recruited from outpatient clinics of the eye and ent hospital of fudan university in shanghai, qualified with well-trained doctors, staff, and required facilities for this clinical trial. patients who meet all of the following inclusion criteria will be considered eligible: patients who visit doctors from the outpatients and suspected of issnhl with vestibular dysfunction will be screened for eligibility. eligible patients who consent to participate will receive either oral prednisone or intratympanic methylprednisolone randomly in a : allocation. the randomization sequence will be generated through @random.org, an internet website (https:// www.random.org) producing true random sequence according to atmosphere noise. the concealed randomization sequence file will be constructed and kept in sequentially numbered, sealed, opaque envelopes by a staff member (zhao l.) in the eye and ent hospital of fudan university outside the study team. all the potential participants will be evaluated in strict chronological order of visiting time. when a patient is officially enrolled and numbered, the staff member will be contacted by telephone and open the corresponding envelope to find the randomized treatment for this patient. assessors in examination rooms and statistician analysts are not allowed to receive any information of the group allocation. the information of participants will be referred using research code among investigators, and their personal information (like name and contacts) will be kept confidential before, during, and after the trial. following randomization, baseline information of the participants in demographic and clinical characteristics will be collected, such as age, gender, nationality, occupation, date of onset, predisposition, initial symptoms, time of diagnosis, any treatments before enrolments, body mass index (bmi), and comorbidities. the objective vestibular function evaluated by sot, videonystagmography (vng), vhit, cvemp, and ovemp and the hearing outcome assessed by pta will be performed at baseline and at and weeks after randomization, while the subjective vestibular dysfunction feelings reflexed by dizziness handicap inventory (dhi) and visual analogue scale for vertigo (vas-v) and the tinnitus condition assessed by vas in tinnitus (vas-t, visual analogue scale for tinnitus) will be performed at baseline and at , , , and weeks after randomization. caloric test is routinely included in vng. acoustic impedance and magnetic resonance imaging of the internal auditory canal (mri-iac) will be performed only once at the baseline examination to exclude the potential misdiagnosed ssnhl. once a participant is randomized, the treatment procedure starts immediately ( table ). the participants in group will receive oral prednisone mg/kg/day (maximum daily dosage is no more than mg) for days, followed by a -day taper ( table ). the patients are advised to take the medicine in min before every breakfast, and not to divide the doses. the participants in group will receive intratympanic mg/ml methylprednisolone injections in days, one injection every other day. the otolaryngologists in charge of the injection work are asked to inject at the posterior superior quadrant and fulfill the tympanic cavity using operating microscopes, after lidocaine spray anesthesia. patients will be asked to keep supine position with the affected ear slightly up to °and avoid swallow during injection and in min after the injection. the drug for injection is methylprednisolone sodium succinate for injection by pfizer manufacturing belgium nv. of all the participants, the length of treatment would be extended for another week if the change in hearing threshold (average db in pta) is less than db, or average of pta is worse than db in the patient's affected ear, under the participant's agreement. the salvage treatment regimen is injections of mg/ml methylprednisolone every other day. records and effects of the salvage treatments will be reported in the study results and evaluated according to both intention-totreat (itt) and per-protocol analyses. for those with severe vertigo attacks, drugs for symptom control like mannitol or diazepam can be used temporarily. in table , criteria are listed in detail to distinguish the central vestibular system (cvs) compensation and peripheral vestibular system (pvs) restoration according to the following evidence: ) sot is a measurement for dynamic and static posturography, which may figure out the different roles of the somatosensory, visual, and vestibular systems. the vestibular scores in sot will help us to distinguish peripheral function self-restoration from cvs compensation. ) the caloric test has been used to evaluate the lateral semicircular canal function with a good sensitivity [ ] . in the caloric test, unilateral weakness (uw), directional preponderance (dp), and spontaneous nystagmus (spn) are three parameters to judge the different phases of central vestibular compensation. uw presents at all three phases of acute injury, static compensation, and dynamic compensation phase and dp presents at the acute injury phase and static compensation phase, while spn only presents at the acute injury phase [ ] . meanwhile, the caloric test results of complete function restoration in pvs should be the same as those in normal individuals: absence of uw, dp, or spn. ) vhit can be employed for evaluating horizontal and vertical semicircular canals and has been taken as a specific indicator of peripheral vestibular function [ , ] . the decreased gains and corrective saccades are signs of the corresponding semicircular canal dysfunction. ) cvemp is a widely used measurement for assessing the saccular and inferior vestibular pathway functions, while ovemp for evaluating the utricular and superior vestibular pathway functions [ ] . based on the integrity of neural pathways, we may reasonably assume that if the dysfunction of otolith organ and its afferent pathway has not recovered in our participants, the compensation effects of cvs will not bring a normal vemp result [ , ] . here come two possible patterns in vestibular dysfunction recovery of issnhl. the first pattern (pattern a) is that the patients undergo well central vestibular compensations with no recovery of pvs function. in this pattern, patients may show a quite normal ability of balance evaluated by subjective complaints, dhi or vas-v; however, since the peripheral vestibular organs remain dysfunctional, vestibular test battery (i.e., sot, caloric tests, vhit, and vemps) will come out with abnormal results. the second possible pattern (pattern b) is that the pvs injuries are completely or partially restored in the patients. in this condition, not only the subjective complaints will disappear, but also the objective vestibular test results will get back to normal, or at least less abnormal. the methodology details of the following tests have been reported before [ ] . if the patient's weight is less than kg, the administration will be stopped after the day with < mg prednisone administered, for example, a patient weighs kg will stop receiving glucocorticoids at the th day b one day early or late of injection is allowed for practicality . six sensory test modes are performed with changing supports and visual conditions. the results are analyzed comprehensively to give a score for each sensory system (somatosensory, visual, and vestibular systems) and a composite score. results are considered abnormal when the score is lower than the age-specific normative data. caloric test we deliver the caloric test using the air caloric irrigator system of ics aircal (gn otometrics, taastrup, denmark) and record eye movements using videonystagmography (vng) of synapsys vng ulmer (synapsys, inc. marseille, france). patients are placed in a supine position in a darkroom, with the head flexed at °. the temperature of the warm and cool air is °c and °c, respectively. the unilateral weakness (uw) and directional preponderance (dp) are used to quantify the difference between the caloric responses of the two ears. the abnormal caloric result is defined as an absolute value of uw% greater than % and/or an absolute value of dp greater than %. vhit ics impulse system (gn otometrics, taastrup, denmark) will be used for vhit in this study. the examiner performs head impulses ( to °/s peak head velocity) randomly in unpredictable timing and direction in the plane of each canal (the horizontal, anterior, and posterior semicircular canal), and at least impulses for each side are acquired. the software analysis algorithm calculates the vestibular-ocular gain. normal gain is defined as > . for the lateral canals and > . for the vertical canals. the pathological saccade is defined as refixation saccades categorized as either covert saccades (occurring during a head movement) or overt saccades (occurring after a head movement) [ ] . the result of a semicircular canal will be considered abnormal when there are pathological saccades and the gain is out of normal range. vemp the recording device of both cvemp and ovemp is the bio-logic navigator pro (natus medical inc., san carlos, usa). cvemp patients are asked to lie in supine position on a bed, with head raised to to °away from the bed during recording to ensure good muscle tone. electrodes are placed as operation manual. air-conducted sound with -hz short tone bursts ( ms rise/fall time and ms plateau time) are presented through insert headphones as stimuli. the starting stimulus intensity is db nhl and decreases by db nhl each time until the meaningful wave is undetectable. the lowest intensity with a characteristic waveform is defined as threshold. the result will be considered abnormal if one of the following conditions is met: ( ) the amplitude asymmetry ratio (ar) is more than %; ( ) the cvemp meaningful waveform (where the waveforms with positive-negative-positive peak, p -n -p , could be recognized and well repeatable) is absent at -db nhl stimulus or the threshold is out of range compared with age-specific normative data; ( ) delayed response: the cvemp threshold shift is out of the range: p range . ± . ; n range . ± . (the mean of normal range ± × sd) [ ] [ ] [ ] [ ] . ovemp the recording device, software, and stimuli are the same as those in cvemp. the patients remain lying supine and are asked to look upward (approximately °a bove the horizontal plane) during recording. electrodes are placed as reported in previous studies [ ] . the recording procedure is the same as that in cvemp, and the lowest intensity with a characteristic waveform is defined as threshold. we define the abnormal result of ovemp as ( ) absence of meaningful waveform (where the waveforms with negative-positive peak, n -p , could be recognized and well repeatable); ( ) the threshold out of range compared with age-specific normative data; and ( ) amplitude asymmetry ratio (ar) ≥ % [ , ] . all examinations will be performed by trained physicians skilled at neuro-otological tests. is a self-assessment questionnaire with items, and the reliability of the chinese version has been verified [ ] [ ] [ ] [ ] . the items can be divided into subscales: physical, emotional, and functional aspects, and the total scores range from to . the higher the score, the more severe the dizziness is in the patients. visual analogue scale is a universal psychometric scale evaluating subjective attitudes [ , ] . when applied in vertigo or tinnitus (vas-v or vas-t), respondents specify their level of vertigoes or tinnitus by indicating a position along a continuous line between two endpoints without marked scale. a score from to will be made based on the length of the line. the higher the score, the more severe the symptom is. to evaluate the recovery of vestibular function, we set the recovery rates of the whole battery of vestibular function tests (sot/caloric test/vhit/vemps) as the primary outcome, which is the proportion of patients whose abnormal results of vestibular function tests at baseline recover to normal at -/ -week follow-up: in this study, we define a -db pta criterion as clinically significant difference based on a previous rct [ ] . ) safety: rates of study-related adverse events (aes), such as short-term systemic use of glucocorticoids related saes and aes, and intratympanic injectionrelated aes. the study included follow-up visits in total: a baseline visit to sign the consent and to record the baseline information, visits during treatment interval to record subjective vestibular questionnaires (dhi, vas-v, and vas-t) and hearing outcomes (pta) and to monitor treatment safety outcomes, and follow-up visits at weeks and weeks to assess hearing and vestibular functions and monitor safety outcomes. to optimize examination resources and reduce burden of examiners, among all five vestibular function tests (sot, caloric test, vhit, cvemp, and ovemp), only those with previous abnormal results will be repeated at follow-up visits. the study flow diagram is shown in fig. , and the spirit figure of enrolment, interventions, and assessments is presented in table . any untoward medical occurrences with unfavorable symptoms in the participants are defined as adverse events (aes). ae is not necessarily to have a causal relationship with the treatment. if the aes are lifethreatening, result in death, persistent, and significant disability or incapacity, or make the participants' hospitalization, we define them as serious adverse events (saes). the investigators will routinely ask the patients if there have been any unexpected symptoms. study- related and non-study-related aes will be recorded in the patient's clinical history by doctors in clinics and then reported to a trial investigator (yu h.) . participants experiencing aes will be followed up until the end of the events or the end of the trial. any saes during this trial will be reported to the trial steering committee table the spirit figure of enrolment, interventions, and assessments vng videonystagmography which includes the caloric test, mri-iac magnetic resonance of the internal auditory canal *a follow-up test is only repeated when the previous test results in abnormal findings (tsc) and adverse drug reaction administration (adra) of the eye & ent hospital of fudan university within h at learning of the event. we list some possible study-related aes here: ) short-term systemic use of glucocorticoids related saes: fracture, sepsis, and venous thromboembolism [ ] ; ) short-term systemic use of glucocorticoids related aes: blood glucose problem, appetite change, sleep change, weight change; and ) intratympanic injection-related aes: ear pain, ear infection, tympanic membrane perforation, and worse vertigo after injection. the participants will be informed of the right to withdraw from the study at any time after consent. the enrolled participants who are found ineligible later, lost to follow-up, or withdraw consent for any reason will be regarded as withdrawal. as for those who decided not to receive the protocol intervention, we will ask them if they would like to continue with the follow-up visits and if they agreed, their results will be regarded as variation other than withdrawals in itt analysis. we provide an online wechat and telephone contacts to all the participants for timely communication and health education, which will promote the participants' retention and adherence to the intervention protocols. furthermore, we optimized the follow-up process by setting a specialty clinic for ssnhl, minimizing the waiting time, and waiving extra examination and treatment fees. we decide not to set blindness of the interventions to patients and doctors, because that setting blindness to patients and doctors will need placebo injections to some of the participants, which may bring unnecessary pain and tympanic membrane perforation risk to the patients. the specialists in test rooms and statistical analysts will be kept blinded during the trial until the statistical analyses are done. a data monitoring committee (dmc) has been established to store, monitor, and check the authenticity, security, and integrity of the database. all members in the dmc are independent of the study sponsors and declared no competing interests. the dmc will periodically review the accumulated data and communicate the problems of its deliberations to the study team if necessary. the frequency of the interim analyses will be judged by the chair of the dmc, based on the consultation with the tmc. we anticipate that there might be - interim analyses before the final analysis. in our previous studies, we reported the poor indicator of the vestibular system lesion patterns in ssnhl and put forward that the incidence of vestibular dysfunction [ , ] . however, we only found the existence of vestibular recovery in clinical case reports [ ] . due to lack of previous reported data on changes of vestibular function test results, this study sample size was calculated based on data from preliminary clinical practice in our hospital. among patients who were diagnosed as issn hl and treated with oral prednisone, the recovery proportion of the vestibular function tests (measured by sot, caloric test, or vemps) was . , while the recovery proportion among those treated with intratympanic glucocorticoids was approximate . . using the program of g*power . for fisher's exact test, we calculated a sample size of per arm with % power at a two-tailed % level of significance [ ] . to allow for % dropout, participants per arm will be needed. for the outcomes, categoric variables will be expressed as rates, while numerical variables as the mean ± sd. baseline data will be compared between two groups with a chi-squared test for dichotomous samples and student's t test or mann-whitney u test for two independent samples where appropriate. for comparisons of recovery in and weeks from baseline, the recovery rates of vestibular function tests will be calculated by chi-squared tests, and logistic regression adjusts for potential confounders like age, initial pta, the number of involved vestibular organs, mri-iac results, and other characteristics, while the numerical variables like uw of the caloric test, pta, and scores in dhi, vas-v, and vas-t will be calculated by mixed-model with repeated measures analyses of variance (anova), with group and time as fixed effects and subject as a random effect, controlling for the potential confounders. between two intervention groups, the chi-squared test will be used to analyze the difference for dichotomous outcomes (e.g., recovery rates) and student's t test for two independent samples or mann-whitney u test where appropriate. a value of p < . of two-sided is considered statistically significant. we will calculate relative risk (rr) with corresponding % confidence intervals to compare dichotomous variables, and mean difference (md) for continuous variables. an itt analysis and a per-protocol analysis will be both performed at each outcome. for the missing data in itt analyses, if there is any, multiple imputation methods will be used. up-to-date versions of spss (spss, chicago, il, usa) will be used to conduct analyses. a statistician from the medical college of fudan university will perform the analyses. not until the statistician complete the analysis, will he be unblinded to the group allocations and the study hypotheses. all data sent to the analyst will be anonymized, and the study groups will be coded as groups a and b. this protocol and the template informed consent forms have been reviewed and approved by the institutional review board (irb) and the ethical committee of eye & ent hospital of fudan university (reference number: ). the tmc will make safety and progress reports to the irb at least annually and within months of study completion. patients and the public were not involved in the design of this study. however, the study was initially discussed with issnhl patients' representative on how best to involve patients throughout the proposed project. finally, the study results will be informed to the public via peer-reviewed journals or academic conferences. vestibular dysfunction, commonly complained by patients as vertigo, dizziness, or lateropulsion, has been considered as a risk factor of profound hearing loss and poor prognosis [ ] [ ] [ ] [ ] [ ] . recently, researchers made their efforts to specify the lesion patterns of the vestibular system in issnhl and proposed that the utricle and superior vestibular pathway is the most vulnerable vestibular site in issnhl, followed by the lateral semicircular canal and superior vestibular pathway [ ] . severe vertigo and static imbalance markedly improve over a couple of days or weeks in most of patients, while some may suffer from long-term residual dizziness. recovery of peripheral vestibular function and central vestibular compensation might be involved in this process. vestibular function tests, such as sot, caloric test, vhit, and vemp, are effective and objective methods to distinguish restoration of peripheral vestibular function and compensation of the central vestibular. it has been reported that in a few cases of ssnhl, function of otolith organs reflexed by vemps was absent at onset and recovered or improved after weeks to months [ ] . these cases suggested the role of peripheral vestibular function restorations. when peripheral vestibular injury is failed to recover by itself, the central compensation will take place. however, due to few previous researches in this field, the roles and proportions of central compensation versus peripheral recovery remain uncertain. we assume that appropriate treatments for issnhl may have favorable effects promoting the vestibular recovery process, as those in hearing outcomes. glucocorticoid therapy is currently a regular and standard treatment for issnhl according to guidelines [ , ] . the plausible mechanisms include anti-inflammatory, immune-suppressive, and inner-ear-homeostasis-related gene regulative effects [ ] . regrettably, with numerous studies of different evidence levels delivered in the past six decades, the effectiveness of glucocorticoids in treating issnhl remains uncertain. most of the rcts and meta-analyses on this topic claimed of disappointing results with little measurable improvements in glucocorticoids over placebo arms [ ] [ ] [ ] . it is worth noting that many confounding factors like various regimens and administration of drugs, different time points of starting treatments, and different probable causes existed in these studies. few studies have focused on the effects of glucocorticoids in vestibular recovery of issnhl. taking the previous researches in acute unilateral vestibulopathy for reference, improvements have been found evaluated by vestibular function tests, the symptom loads, and dhi scores [ , ] . hereby, we may speculate that glucocorticoids could possibly accelerate vestibular function recovery via restoration of the peripheral vestibular system. to assess the vestibular functions, we intend to perform a battery of vestibular function tests including ( ) the sot for assessing static and dynamic posture control ability of somatosensory, visual, and vestibular systems distinguishingly and comprehensively; ( ) the caloric test for evaluating horizontal semicircular canal functions and superior vestibular integrity; ( ) vhit for evaluating functions of horizontal and vertical semicircular canals; and ( ) cvemp for investigating the saccular function and the inferior vestibular pathway and ovemp for assessing utricular function and the superior vestibular pathway [ , , , , ] . moreover, we plan to perform dhi and vas-v, two qualified and widely used subjective measurements, to assess the severity of symptoms and negative influence on patients' daily lives [ , ] . in conclusion, our study will be the first to assess and follow the vestibular function conditions of issnhl up using a whole battery of vestibular function tests. based on our clinical practice experience, we hypothesize that the effects of intratympanic glucocorticoids will be superior to those of oral therapy in terms of the outcome measurements mentioned above. moreover, we expect that participants in the intratympanic group will experience more significantly reduced dhi scores, lessened vas-v scores, and better enhanced recovery of pta. the planned date of the first enrolment is sep . the estimated time required for recruitment is months. the total duration of this study is expected to be months, including statistical analysis and article writing. this protocol version number is ver. . clinical practice guideline: sudden hearing loss (update) national institute on deafness and other communication disorders. nidcd fact sheet: sudden deafness accessed systematic review of the evidence for the etiology of adult sudden sensorineural hearing loss pathology of vascular sensorineural hearing impairment autoimmune sensorineural hearing loss the pathology of sudden deafness sudden sensorineural hearing loss: is there a connection with inner ear electrolytic disorders? a literature review idiopathic sudden sensorineural hearing loss oral vs intratympanic corticosteroid therapy for idiopathic sudden sensorineural hearing loss: a randomized trial spirit statement: defining standard protocol items for clinical trials the caloric irrigation test vestibular function examination technique. xi'an: air force medical university press the video head impulse test plasticity during vestibular compensation: the role of saccades vestibular-evoked myogenic potentials recovery of ocular and cervical vestibular evoked myogenic potentials after treatment of inner ear diseases contrasting results of tests of peripheral vestibular function in patients with bilateral large vestibular aqueduct syndrome vestibular migraine screening in a migraine-diagnosed patient population, and assessment of vestibulocochlear function assessment of balance and vestibular functions in patients with idiopathic sudden sensorineural hearing loss the potential dysfunction of otolith organs in patients after mumps infection normal values of cervical vestibular evoked myogenic potential and its influence factors prognostic factors in sudden sensorineural hearing loss the development of the dizziness handicap inventory discussion of the dizziness handicap inventory uni-and multivariate models for investigating potential prognostic factors in idiopathic sudden sensorineural hearing loss analysis of reliability and validity of the chinese version of dizziness handicap inventory (dhi) visual vertigo analogue scale: an assessment questionnaire for visual vertigo measuring pain. visual analog scale versus numeric pain scale: what is the difference? short term use of oral corticosteroids and related harms among adults in the united states: population based cohort study association of vertigo with hearing outcomes in patients with sudden sensorineural hearing loss: a systematic review and meta-analysis vestibular dysfunctions in sudden sensorineural hearing loss: a systematic review and meta-analysis gpower: a general power analysis program vertigo as a prognostic sign in sudden sensorineural hearing loss the relationship between hearing loss and vestibular dysfunction in patients with sudden sensorineural hearing loss society of otorhinolaryngology head and neck surgery, chinese medical association. guideline of diagnosis and treatment of sudden deafness ( ) corticosteroid therapy for hearing and balance disorders treatment of sudden sensorineural hearing loss: ii. a meta-analysis steroids for treatment of sudden sensorineural hearing loss: a meta-analysis of randomized controlled trials corticosteroid treatment of idiopathic sudden sensorineural hearing loss: randomized triple-blind placebocontrolled trial glucocorticoids improve acute dizziness symptoms following acute unilateral vestibulopathy methylprednisolone, valacyclovir, or the combination for vestibular neuritis characteristics and clinical applications of ocular vestibular evoked myogenic potentials learning effects of repetitive administrations of the sensory organization test in healthy young adults efficacy and safety of acupuncture for dizziness and vertigo in emergency department: a pilot cohort study publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations we would like to thank the patients for participating in the trial and our colleagues for supporting the study. supplementary information accompanies this paper at https://doi.org/ . /s - - - .additional file . spirit checklist.additional file . case report forms template.additional file . adverse event forms template. this study was supported by the science and technology commission of shanghai municipality (grant number ), contact at + - - . this funding source played no part in the study design and will not have any role in its collection, management, analysis, and interpretation of data; writing of the report; or the decision to submit the report for publication. during the study, the datasets used in the current study are available from the corresponding author on reasonable request. after the study, the results of this trial will be published in peer-reviewed journals and presented at national and/or international conferences. the study has been approved by the ethical committee of eye & ent hospital of fudan university (reference number - ), and informed consent will be obtained from all participants of this trial before participating; the model consent form is attached in crf in additional file . not applicable. key: cord- -d ty etr authors: horta, bernardo l; silveira, mariângela f; barros, aluísio j d; barros, fernando c; hartwig, fernando p; dias, mariane s; menezes, ana m b; hallal, pedro c; victora, cesar g title: prevalence of antibodies against sars-cov- according to socioeconomic and ethnic status in a nationwide brazilian survey date: - - journal: rev panam salud publica doi: . /rpsp. . sha: doc_id: cord_uid: d ty etr objectives. to investigate socioeconomic and ethnic group inequalities in prevalence of antibodies against sars-cov- in the federative units of brazil. methods. in this cross-sectional study, three household surveys were carried out on may - , june - , and june - , in brazilian urban areas. multi-stage sampling was used to select individuals in each city to undergo a rapid antibody test. subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard brazilian classification in five categories: white, black, brown, asian or indigenous. principal component analyses of assets was used to classify socioeconomic position into five wealth quintiles. poisson regression was used for the analyses. results. subjects were tested in the first, in the second, and in the third wave of the survey, with prevalence of positive results equal to . %, . %, and . % respectively. individuals in the poorest quintile were . times ( % confidence interval . ; . ) more likely to test positive than those in the wealthiest quintile, and those with or more years of schooling had lower prevalence than subjects with less education. indigenous individuals had . ( . ; . ) times higher prevalence than whites, as did those with black or brown skin color. adjustment for region of the country reduced the prevalence ratios according to wealth, education and ethnicity, but results remained statistically significant. conclusions. the prevalence of antibodies against sars-cov- in brazil shows steep class and ethnic gradients, with lowest risks among white, educated and wealthy individuals. in brazil, prominent covid- cases, including state governors and more recently president jair bolsonaro (https://www. bbc.com/news/world-latin-america- ), led to a disseminated impression that the epidemic affects brazilian society as a whole, without distinction of class or ethnic group. if true, this finding would be in sharp contrast with data from high-income countries, where the pandemic is disproportionally affecting ethnic minorities and poor populations ( ) . in the united states (https://www.nytimes.com/interactive/ / / / us/coronavirus-latinos-african-americans-cdc-data.html), african-americans and latinos are suffering from higher disease incidence and mortality than whites, according to reported cases. a study carried out in the oxford royal college of general practitioners research and surveillance centre network observed that black people and those living in the more deprived areas were more likely to test positive for sars-cov- ( ) . another study in the united kingdom ( ) reported that non-white ethnicity and higher deprivation scores were strongly associated with increased covid- mortality. in contrast, the large national surveys carried out in spain did not find either nationality or education as risk factors for the presence of antibodies against sars-cov- ( ). we were only able to locate a single study of ethnic or social inequalities in covid- in low-or middle-income countries. baqui et al ( ) described that in brazil, covid- hospital case-fatality was higher among individuals classified with black or with mixed ancestry, compared to whites ( ) . a commentary on this publication argued, without providing new data, that living conditions of brazil's poor would make them more vulnerable to covid- morbidity and mortality ( ) . their study did not include a sufficient number of indigenous individuals for analyses. we were unable to locate any population-based study from low or middle-income countries on social and ethnic inequalities in covid- morbidity or mortality. the present analyses were aimed at assessing socioeconomic and ethnic group inequalities in prevalence of antibodies against sars-cov- in sentinel cities throughout brazil, as part of the epicovid- study (www.epicovid brasil.org). in this cross-sectional study, three population-based repeated serological surveys were carried out in brazilian sentinel cities in brazil's federative units. the cities included brasilia, state capitals and the largest cities in each of the country's intermediate regions, as defined by the brazilian institute of geography and statistics (ibge). in each city, urban census tracts were selected with probability proportionate to size, and households were randomly sampled in each tract. in each sampled household, all residents were listed, and one was randomly selected to be tested. if the selected individual refused to provide a blood sample, a second household member was randomly selected. if this person also refused, the interviewers moved on to the next household to the right of the one that had been originally selected. the next household to the right was also selected in case of absent residents. in the present manuscript, we pooled the data from the three survey waves that took place on may - , june - , and june - , . with individuals per city, the margins of error (approximately two standard errors) for estimating prevalence figures of %, % and % are respectively . , . , and . percent points, and at national level, with total sample size of , the corresponding margins of error are . , . and . . the wondfo sars-cov- antibody test (wondfo biotech co., guangzhou, china) was used to evaluate the presence of antibodies for sars-cov- , using finger prick blood samples. at the time of the first survey, this was the only test available in the country in large numbers, and over tests were provided to the study by the ministry of health. the test detects immunoglobulins of both igg and igm isotypes specific to sars-cov- antigens in a lateral flow assay. the assay reagent consists of colloidal gold particles coated with recombinant sars-cov- antigens. following the introduction of the blood sample, reactive antibody:antigen:colloidal gold complexes, if present, are captured by antibodies against human igm and igg present on the "test" (t) line in the kit's window, leading to the appearance of a dark-colored line. valid tests are identified by a positive control line (c) in the same window. if this control line is not visible, the test is deemed non-conclusive, which is uncommon. the rapid test underwent independent validation studies that used rt-pcr as the gold standard. according to the manufacturer, it has a sensitivity of . % and specificity of . % (https://en.wondfo.com.cn/product/wondfo-sars-cov- -antibody-test-lateral-flow-method- /). a validation study carried out by the national institute for quality control in health (incqs, oswaldo cruz foundation, rj, brazil) showed a sensitivity of % and specificity of . %. whitman et al evaluated different lateral flow assays ( ) and reported that the wondfo test had a sensitivity of . % and specificity of . %. a validation study carried out by our research group observed a sensitivity of . % and specificity of . % ( ) . by pooling the results from the four validation studies, weighted by sample sizes, sensitivity is estimated at . % ( % ci . %; . %) and specificity at . % ( % ci . %; . %) ( ) . participants answered short questionnaires including sociodemographic information (sex, age, schooling, skin color, household size and household assets), covid- -related symptoms, use of health services, compliance with social distancing measures and use of masks. due to the presence of widespread multiethnic population, the official brazilian classification of ethnicity recognizes five groups, based on the question: "how do you classify yourself in terms of color or race?" the five response options are "white", "brown" ("pardo" in portuguese), "black", "yellow (asian)" and "indigenous". interviewers were instructed to check the "yellow" option when the respondent mentions being of asian descent, and "indigenous" when any of the multiple first nations are mentioned. the "brown" category reflects mixed ancestry including european, african and/or indigenous backgrounds. this system is endorsed by the afro-descendants movement, which advocates for disaggregation of all national statistics to raise their visibility ( ) . socioeconomic position was assessed using a wealth index derived through principal component analyses of household assets ( ). the first component was divided into quintiles. achieved schooling was recorded as the highest grade completed successfully. field workers used tablets to record the full interviews, register all answers, and photograph the test results. the questionnaire was applied before the test result was disclosed to each participant. inconclusive tests were repeated, and subjects presented a non-conclusive result in the second test, which were treated as missing values. all positive or inconclusive tests were read by a second observer, as well as % of the negative tests. five regions of the country. in these analyses, the prevalences of seropositivity were still lower in the richest quintile, but the magnitude of the prevalence ratio decreased. indigenous individuals still showed higher prevalence than whites (prevalence ratio: . ; % ci . ; . ), as did individuals classified as black or brown. table shows that in the northern region, in spite of the decrease in the magnitudes of the associations compared to the national analyses (table ) , the inverse associations with wealth remained significant, and the higher prevalence among indigenous and brown subjects compared to whites also persisted. in the northeastern region, seroprevalence was also inversely associated with wealth, but not with ethnicity. prevalence for indigenous subjects were . times higher than for whites. in the remaining regions, where prevalence was low at the time of the surveys, we did not observe any clear pattern of association with wealth, but black and brown subjects had significantly higher risks than whites. consistent results were observed for education in all regions, with lower risk for subjects with or more years of schooling than for the other groups. table shows that the even after controlling for region and socioeconomic status, the seroprevalence remained significantly higher among indigenous, brown and black subjects. interviewers were tested and found to be negative for the virus and were provided with individual protection equipment that was discarded after visiting each home. we used stata for the analyses. proportions of positive tests according to region, sex, wealth quintiles, achieved schooling and skin color were compared using the chi-squared test. for ordinal variables, both in bivariate and multivariate analyses, we estimated the p-value for linear trend and for heterogeneity, and presented the one with the lower p-value. we also stratified the analyses of seroprevalence according to socioeconomic variables by region of the country (north; northeast; southeast; south and center-west), using poisson regression with robust variance to estimate prevalence ratios. all analyses controlled for the cluster-sampling design using svy prefix. ethical approval was obtained from the brazilian's national ethics committee (process number caae . . . ), with written informed consent from all adult participants; for minors, written consent was provided by parents or caregivers, and assent forms were also signed by the child or adolescent (provided that they were literate). the dataset is stored in anonymous form. positive cases were reported to the municipal covid- surveillance systems. in the three waves of the seroprevalence survey, subjects were tested and individuals with inconclusive test results in the test and retest were excluded from the analyses. therefore, in the present study we evaluated subjects. the response rates were . %, . % and . % in the three waves, mainly due to the fact that the whole family was away from home when the visit took place. the prevalence of positive results was . %, . %, and . % in the first, second and third surveys, respectively. table shows that the proportion of males and young subjects in the studied population was below what was expected on the basis of the national population. concerning skin color, most of the studied subjects reported being mixed (brown) or white and only . % self-identified as indigenous. the proportion of subjects who reported being white was lower than the national estimates. in the three phases of the study, there were positive tests ( . %) among the subjects with valid test results. table shows that the proportion of positive tests was higher in the north region ( . %), whereas in the southern region only . % of the studied subjects had a positive test. results for unadjusted analyses, and analyses with adjustment for age and sex, were very similar. antibody prevalence was inversely associated with wealth quintiles; compared to the wealthiest, the poorest were about twice as likely to present antibodies against sars-cov- . for schooling, the association was not linear, but subjects with or more years of schooling were less likely to present positive tests than any of the other groups. the largest prevalence ratio were observed in the comparison between indigenous and white individuals, with a near five-fold ratio. whites were less likely to test positive than any ethnic group, followed by asians. because the proportion of individuals with antibodies against sars-cov- was higher in the northern (amazon) region, where indigenous and poor populations are concentrated, we carried out additional analyses with further adjustment for the our study is the largest population-based serological survey for antibodies against sars-cov- in low-and middleincome countries, and only comparable to the national surveys carried out in spain ( ). our findings show that the covid- pandemic is hitting harder at the poorest and disadvantaged groups in brazil. the proportions of individuals with positive tests was higher among indigenous, black and brown subjects compared to whites, as well as being inversely associated with socioeconomic position. concerning ethnic inequalities in health and nutrition in brazil, several studies have reported that indigenous children and adolescents show higher mortality than other ethnic with respect to the study limitations, the use of rapid serological tests for clinical decision-making and for defining individuals as immune to covid- has been criticized. but the use of such tests to estimate the seroprevalence is much less controversial, provided the test has been validated ( , ) . the rapid test used in our study (wondfo sars-cov- antibody test) underwent different validation studies using rt-pcr as the gold standard, including one carried out by our own team. these studies estimated the test's sensitivity and specificity at . % and . %, respectively. it has been suggested that using capillary blood to estimate seroprevalence tends to increase the rate of false negative results ( ) ; however, this finding has not been replicated by other studies ( ) . furthermore, our validation study ( ) used capillary blood and the observed sensitivity was similar to that reported in another studies. therefore, this should not be considered as a main study limitation as all population subgroups should be affected. recent evidence suggests that antibody levels against sars-cov- fall rapidly over a few weeks, regardless of the type of test used ( ) ; therefore, our results correspond to relatively recent infections rather than cumulative prevalence. again, all population subgroups are likely to be similarly affected. the restriction of the sample to sentinel sites that are the larger and more developed cities should not be considered as a major limitation, as we are not trying to estimate the prevalence of the infection in the whole country, but its association with socioeconomic and demographic characteristics. due to logistic difficulties including a massive fake news campaign through social media, it was not possible to complete the first round of the study in cities, so that the sample size was instead of the planned tests. these difficulties were overcome in the next two rounds, when the intended sample size was nearly achieved. concerning selection bias, the response rates of around % are similar to that reported in the spanish survey ( . %) and higher than achieved in national surveys in iceland and austria, both of which had response rates of about one third of the intended sample ( ) . the higher proportion of female in the studied sample could be due to the fact that males were less like to comply with the stay at home recommendations. the most frequent reason for non-response was the fact that the whole family was away from home when the visit took place, which may be associated with temporary moves to smaller towns or to rural area, as larger cities were more strongly hit by the pandemic in the early phases. regarding indigenous populations, it should be noted that our sample was restricted to those living in urban areas. lastly, our sample had fewer children than expected, which was probably due to their reluctance to undergo a finger prick when randomly selected within the household; in these cases, a second person was randomly selected and if that person also refused the household was replaced. in summary, the analyses of the three waves of national serological surveys in brazil showed important inequalities in the prevalence of antibodies against sars-cov- according to family wealth, education and ethnic groups. contrary to the initial impressions that covid- would strike all groups in brazilian society with similar intensity, our analyses show that individuals from poor families and with little schooling were at higher risk of having been infected. in terms of ethnicity or skin color, whites had the lowest risk, whereas indigenous subjects and those with black or brown skin color were most affected ( ) . groups ( ) , and that similar gaps are also observed for adult mortality ( ) . indeed, there is overwhelming evidence that indigenous populations have been left behind when health conditions improved in brazil in the recent past ( ) . it would be surprising if covid- turned out to be different from other existing health conditions. it has been reported that covid- is hitting hard at rural indigenous villages in reservations ( ) , but there are no comparisons with other ethnic groups. as mentioned in the introduction, baqui et al ( ) found that covid- hospital case-fatality was higher among individuals classified with black and with mixed ancestry, compared to whites. this study was based on a public dataset on hospitalizations and only a few subjects were identified as indigenous, and for this reason the case fatality among them was not estimated ( ) . because the magnitude of the association of seroprevalence for covid- and skin color decreased after controlling for region of the country, the five-fold difference observed in antibody prevalence between indigenous and white subjects had been partly inflated by place of residence. yet, even after adjustment for region, indigenous individuals were about twice as likely as whites to present antibodies against sars-cov- , and in the national analyses including adjustment for region of the country and socioeconomic status, the prevalence ratio remained at around two. the interpretation of these analyses suggests that indigenous subjects were at substantially higher risk than other ethnic groups. this was partly due to the fact that they were concentrated in the amazon region, where prevalence was the highest in the country at the time of the surveys, and also because their living standards were the lowest when compared to other groups. nevertheless, their increased risk persisted in the stratified and adjusted analyses for socioeconomic status. future studies will need to investigate the mechanisms behind this association. in terms of ethnicity, the "brown" or "pardo" category had the second highest prevalence among the five groups. this category includes individuals who self-report has having mixed ancestry. genomic ancestry studies ( ) show that in the northern city of belém self-classified brown individuals had, on average, % european ancestry, followed by % amerindian ancestry and % african ancestry, while in the south they had on average % european, % amerindian and % african ancestries. therefore, the evidence suggests that brown subjects in the north -among whom seroprevalence was . %-were genetically closer to amerindians than was the case for the same group in other parts of the country. sponsors did not influence in any way the design, the data collection, the analysis, the writing, and the decision to publish these results. prevalencia de anticuerpos contra el sars-cov- según el estatus socioeconómico y étnico en una encuesta nacional de brasil resumen objetivos. investigar las desigualdades socioeconómicas y entre distintos grupos étnicos en la prevalencia de anticuerpos contra el sars-cov- en las unidades federativas del brasil. métodos. en este estudio transversal, se realizaron tres encuestas de hogares los días - de mayo, - de junio y - de junio, en áreas urbanas brasileñas. se utilizó un muestreo de etapas múltiples para seleccionar individuos en cada ciudad a fin de someterlos a una prueba rápida de anticuerpos. los sujetos respondieron un cuestionario sobre los bienes del hogar, la escolaridad y el color de la piel/etnia (autodeclarado utilizando la clasificación brasileña estándar de cinco categorías: blanco, negro, pardo, asiático o indígena). se utilizó el análisis de los componentes principales de los bienes para clasificar la posición socioeconómica en cinco quintiles de riqueza. se empleó la regresión de poisson para los análisis. resultados. se analizaron sujetos en la primera encuesta, en la segunda y en la tercera, que mostraron una prevalencia de resultados positivos de , %, , % y , % respectivamente. los individuos del quintil más pobre tuvieron , veces más probabilidades de presentar un resultado positivo (intervalo de confianza del % , ; , ) que los del quintil más rico, y los que tenían o más años de escolaridad tuvieron una prevalencia menor que los sujetos con menos educación. las personas indígenas presentaron una prevalencia , ( , ; , ) veces mayor que las blancas, al igual que las de piel negra o parda. el ajuste por región del país redujo los índices de prevalencia según la riqueza, la educación y el origen étnico, pero los resultados siguieron siendo estadísticamente significativos. conclusiones. la prevalencia de anticuerpos contra el sars-cov- en el brasil muestra gradientes relacionados con la posición socioeconómica y la etnia muy pronunciados, con menor riesgo en las personas blancas, educadas y ricas. epidemiología; infecciones por coronavirus; encuestas y cuestionarios; inequidad social; brasil. objetivos. investigar as desigualdades socioeconômicas e étnicas na prevalência de anticorpos contra sars-cov- nas unidades federativas do brasil. métodos. neste estudo transversal, três pesquisas domiciliares foram realizadas de a de maio, a de junho, e - de junho, em áreas urbanas brasileiras. amostragem em várias etapas foi utilizada para selecionar indivíduos em cada cidade para se submeter a um teste rápido de anticorpos. os sujeitos responderam a um questionário sobre bens domésticos, escolaridade e cor da pele/etnicidade (auto-relatada utilizando a classificação padrão brasileira de cinco categorias: branco, preto, pardo, asiático ou indígena). a análise dos componentes principais dos ativos foi utilizada para classificar a posição socioeconómica em cinco quintis de riqueza. a regressão de poisson foi utilizada para as análises. resultados. indivíduos foram testados na primeira pesquisa, na segunda, e na terceira, com prevalência de resultados positivos de , %, , % e , %, respectivamente. indivíduos no quintil mais pobre tinham , vezes (intervalo de confiança de % , ; , ) mais probabilidade de ter um resultado positivo do que aqueles do quintil mais rico, e aqueles com ou mais anos de escolaridade tinham uma prevalência menor do que aqueles com menos educação. os indivíduos indígenas tinham , ( , ; , ) vezes mais prevalência do que os brancos, assim como aqueles com cor da pele preta ou parda. o ajuste regional reduziu as taxas de prevalência de acordo com a riqueza, educação e etnia, mas os resultados permaneceram estatisticamente significativos. conclusões. a prevalência de anticorpos contra a sars-cov- no brasil mostra gradientes relacionados com a posição socioeconómica e a etnia muito acentuados, com os menores riscos entre os indivíduos brancos, educados e ricos. society and the slow burn of inequality risk factors for sars-cov- among patients in the oxford royal college of general practitioners research and surveillance centre primary care network: a cross-sectional study opensafely: factors associated with covid- death in million patients prevalence of sars-cov- in spain (ene-covid): a nationwide, population-based seroepidemiological study ethnic and regional variations in hospital mortality from covid- in brazil: a cross-sectional observational study in the covid- pandemic in brazil, do brown lives matter? lancet glob health test performance evaluation of sars-cov- serological assays sensitivity and specificity of a rapid test for assessment of exposure to sars-cov- in a community-based setting in brazil características étnico-raciais da população: classificação e identidades a nationwide wealth score based on the brazilian demographic census differences in mortality between indigenous and non-indigenous persons in brazil based on the population census indigenous children and adolescent mortality inequity in brazil: what can we learn from the national demographic census? emerging health needs and epidemiological research in indigenous peoples in brazil covid- experience among brasil s indigenous people the genomic ancestry of individuals from different geographical regions of brazil is more uniform than expected serology for sars-cov- : apprehensions, opportunities, and the path forward the role of antibody testing for sars-cov- : is there one? sensitivity of the wondfo one step covid- test using serum samples analytical performance of lateral flow immunoassay for sars-cov- exposure screening on venous and capillary blood samples rapid decay of anti-sars-cov- antibodies in persons with mild covid- spread of sars-cov- in the icelandic population health conditions and health-policy innovations in brazil: the way forward disclaimer. authors hold sole responsibility for the views expressed in the manuscript, which may not necessarily reflect the opinion or policy of the rpsp/pajph and/or paho.authors´ contributions. blh, mfs, pch, cgv conceived the study, analyzed the data, wrote/reviewed the manuscript. ajdb, fcb, fph, msd, ambm contributed with data analysis, interpreted the results, and reviewed the manuscript. all authors reviewed and approved the final version.funding. the study was funded by the brazilian ministry of health, instituto serrapilheira, brazilian collective health association and the jbs sa initiative fazer o bem faz bem. the key: cord- -ntgt hy authors: ginocchio, christine c. title: strengths and weaknesses of fda-approved/cleared diagnostic devices for the molecular detection of respiratory pathogens date: - - journal: clin infect dis doi: . /cid/cir sha: doc_id: cord_uid: ntgt hy the rapid, sensitive, and specific identification of the microbial etiological characteristics of respiratory tract infections enhances the appropriate use of both antibiotics and antiviral agents and reduces the risk of nosocomial transmission. this article reviews the current nucleic acid amplification tests approved by the u.s. food and drug administration (fda) for the detection of respiratory pathogens. in addition, emergency use authorization tests for the detection of influenza a h n are discussed. the advantages and limitations of the current fda-approved/cleared tests are reviewed. the identification of the causative agent(s) of respiratory tract infections is essential to provide an accurate diagnosis, appropriately manage patient care, and reduce the risk of nosocomial transmission within health care facilities. with the steady rise of antibiotic resistance and limited or no options available for the treatment of multidrug or panresistant bacterial infections, pathogen identification is a key component in restricting antibiotic use to those circumstances in which antibiotic therapy is clearly indicated [ ] . initial empiric therapeutic choices may be standardized and initiated on the basis of patient clinical status, underlying disease, and/or risk for infection with a multidrug-resistant pathogen. however, subsequent bacterial pathogen identification and accurate susceptibility data should assist in promoting switches to targeted specific therapies and reduce the use of broad-spectrum antibiotics when not indicated, thereby promoting good antibiotic stewardship [ ] . viral infections probably cause between % and % of respiratory tract diseases. nonetheless, it is estimated that . million ( %) of million antibiotic prescriptions for respiratory tract infections, including both lower and upper respiratory infections, were for causes unlikely to have a bacterial etiology [ ] . although in many cases of otitis and sinusitis and probably %- % of cases of community-acquired pneumonia a bacterial superinfection may occur, respiratory infections due to a virus(es) alone are common in the adult and pediatric outpatient populations. in addition, the vast majority of respiratory tract infections in nonimmunocompromised hospitalized children (especially those , years of age) are due to or more viruses, without a secondary bacterial infection. the overuse of antibiotics for the treatment of outpatients is primarily due to the fact that in adults respiratory virus testing is either not performed or generally limited to rapid antigen direct tests (radts) for influenza. testing for the elderly, for persons with chronic obstructive pulmonary disease, and for pediatric patients is limited to radts for influenza and respiratory syncytial virus (rsv). radts have highly variable sensitivities ( %- %) and specificities ( %- %) depending on the viral target, age of the patient, sample collection, and duration of symptoms prior to testing [ ] [ ] [ ] . in general, radts perform better when testing pediatric samples, because children shed higher titers of virus and for longer time periods than adults [ , [ ] [ ] [ ] . in addition to radts, there are u.s. food and drug administration (fda)-approved/cleared nonmolecular-based viral diagnostic methods with a more rapid time to result, compared with traditional viral tube culture, eg, direct fluorescent antibody (dfa) testing and rapid cell culture. both methods can readily detect of the common respiratory viruses (adenovirus, influenza a, influenza b, parainfluenza , , and [piv- , piv- , piv- ], and rsv). in addition, dfa testing can detect human metapneumovirus (hmpv) [ ] . the specificity of dfa testing and rapid cell culture are high, but the sensitivities of the tests can vary from a low of % (rsv culture) to a high of . % (influenza a), when compared with nucleic acid amplification tests (naats) [ , , ] . dfa testing can be performed in as little as - min, and shell vial and r-mix rapid cell cultures (quidel/diagnostic hybrids) generally identify respiratory viruses in - h [ ] . if these tests are performed on site, the time to virus detection can be within a time frame that could affect patient management. however, these tests are not widely available outside larger hospitals and reference laboratories. although these viruses are responsible for a large number of respiratory tract infections, bocavirus, selected coronaviruses ( e, oc , nl , and hku- ), parainfluenza , and rhinovirus are also important causes of respiratory disease and are generally only detected using naats. because antiviral therapies are currently limited to the treatment of influenza a, influenza b, cytomegalovirus pneumonia, and varicella zoster virus pneumonia, it is often argued that the specific identification of other viruses is not relevant, because the information would not change patient management. from a treatment standpoint, this may currently be true; however, the respiratory viruses cause similar illnesses, and diagnosis based on clinical symptoms alone can be highly inaccurate [ ] . for example, a study by poehling et al revealed that physicians who used only clinical symptoms recognized influenza in only % of hospitalized children and % of nonhospitalized children with laboratory-confirmed influenza [ ] . therefore, establishing the viral etiological characteristics of the illness is often highly dependent on accurate diagnostic testing. in addition, new therapeutic agents for respiratory viruses are in development, and clinical trials for these agents will need rapid diagnostics that detect a broad range of viral pathogens. once these new drugs are approved, clinical laboratories will need the tools to identify each virus so that appropriate antiviral therapy can be rapidly initiated. in addition, during the first weeks of the influenza a h n outbreak in the spring of , multiple influenza viruses were cocirculating [ ] . it was necessary to subtype influenza a strains to differentiate seasonal influenza a/h , seasonal influenza a/h , and influenza a h n . subtyping is necessary to provide relevant information needed for appropriate selection of antiviral therapy, in particular for acutely ill patients. antiviral resistance testing of influenza isolates from (www.cdc.gov/flu) revealed that the circulating seasonal influenza a/h strains were resistant to oseltamivir ( . %), and seasonal influenza a/h and influenza a h n were resistant to the adamantanes ( %). in addition, several patients with influenza a h n infections developed oseltamivir resistance [ , ] . other clinical factors, such as the potential for the development of more severe disease on the basis of the virus etiology, may need to be considered in the management of certain patients. for example, studies from our laboratory have revealed that children with hmpv infections have a higher incidence of admission to an intensive care unit and more often require mechanical ventilation than children with rsv infections [ , ] . especially in the treatment of inpatients, the costs of rapid viral diagnostics can be offset by the improvement in patient care and financial outcomes [ ] [ ] [ ] [ ] . hendrickson et al showed that rapid respiratory virus diagnosis can lead to benefits in several areas, including up to a % reduction in hospital days, % reduction in antibiotic use, and % reduction in unnecessary diagnostic tests and procedures [ ] . the burden of nosocomial influenza can be high, incurring additional costs for diagnostic tests, increased morbidity, and extended hospitalization [ , ] . therefore, rapid diagnostic tests are needed to identify patients with influenza at admission, in order to prevent nosocomial transmission by facilitating isolation and cohorting decisions [ ] . studies have documented substantial nosocomial transmission of hmpv in pediatric units [ ] , as well as in chronic care facilities [ ] , similar to what is seen with rsv. during the height of rsv season, many institutions must cohort rsv-positive children because of a lack of private rooms. however, dual infections with rsv and hmpv do occur. limiting diagnostics to rsv alone in a cohorting scenario could put other seriously ill children at risk for acquisition of a second viral infection with hmpv. the meaning of mixed viral infections can be defined only if testing is comprehensive. broad test panels also allow for monitoring the epidemiologic patterns of respiratory disease and for identifying new or reemerging pathogens. finally, the identification of the exact respiratory virus is essential for the accurate assessment of the efficacy of vaccines. the costs for testing using fda-approved/cleared naats are highly variable and can range from approximately $ to .$ per test. factors that determine test cost include test volume, the price of the test kits, the number of tests per kit, size of the testing run, the number of controls required per testing run, and the type and amount of ancillary supplies. often fda-approved/ cleared kits do not contain nucleic acid extraction reagents, so additional equipment and reagents are necessary and can add $ -$ per test. batch testing of samples may reduce the cost per test; however, often batching is not practical if the time to result is delayed beyond a period that would affect either clinical management or infection control practices. instrumentation costs for molecular tests can be substantial, with real-time instrumentation costing on average $ , -$ , per instrument, and higher volume laboratories may require multiple instruments. laboratories must also calculate the cost for technical time, which is again highly variable depending on the test complexity and run size. finally, the costs for quality control, proficiency testing, and competency assessment all affect the overall cost per test. in deciding which tests are appropriate and at what cost for the patient population at a particular health care facility, all of the above factors need to be considered in light of the clinical impact of the test result. the use of naats is an intrinsic part of infectious disease diagnostics. the ability of naats to rapidly and accurately detect a novel pathogen was best exemplified during the influenza a h n pandemic [ , [ ] [ ] [ ] . naats are especially suited for the identification of respiratory pathogens that are not routinely or easily cultured (eg, hmpv, bocavirus, parainfluenza , and chlamydophila pneumoniae), pathogens that are dangerous to culture (eg, severe acute respiratory syndrome coronavirus), pathogens for which the time to detection by traditional means is often too delayed to affect patient care (eg, tube cell culture for influenza), and pathogens for which serologic testing is difficult to interpret (eg, c. pneumoniae). in most cases, naats offer enhanced sensitivity over culture methods, radts, and dfa testing [ , , ] . the specificity of naats varies with target and assay design but is generally very high. in addition, laboratorydeveloped naats validated in accordance with the clinical laboratory improvement amendments (clia) requirements can be used to identify new pathogens until fda-approved/ cleared in vitro diagnostic (ivd) devices become available. with clinical integration of real-time polymerase chain reaction (pcr) and fda-approved/cleared simple cartridge-based naats, laboratories of all sizes are now able to perform molecular diagnostic tests. the detection of mycobacterium tuberculosis directly in a clinical sample from a patient not yet identified as m. tuberculosis positive is always clinically relevant. detection of such bacterial pathogens as bordetella pertussis, bordetella parapertussis, legionella pneumophila, mycoplasma pneumoniae, or c. pneumoniae usually indicates active infection. in contrast, the detection of other bacteria, such as streptococcus pneumoniae, may indicate infection or simply colonization. therefore, interpretation of the molecular detection of many bacterial pathogens must be viewed in light of the clinical specimen (sterile vs nonsterile body site) and determination of the quantity of organisms present. in addition, molecular methods must include all potential pathogens, even though culture is still required for antimicrobial susceptibility testing. for these reasons, there is currently a scarcity of fda-approved/cleared assays for nonviral respiratory pathogens (table ). for such targets as the atypical pneumonia pathogens, the interpretation of naat results is generally not an issue, quantitative tests are not necessarily indicated, and naats could replace traditional test methods. however, the lack of fda-approved/cleared naats for these pathogens most probably relates to the ivd device manufacturers' reluctance to perform costly clinical trials for targets with a relatively low prevalence rate and for which the potential volume of testing may be minimal. in light of the rise in m. tuberculosis drug resistance worldwide, the rapid identification of patients with pulmonary tuberculosis is essential and allows for improved patient outcomes, the appropriate use of isolation facilities, the initiation of appropriate treatment, and the identification of possible infected contacts [ ] [ ] [ ] . in addition, studies have shown that the estimated costs associated with an inaccurate diagnosis of m. tuberculosis infection are substantial ($ , per patient) because of institutional isolation procedures [ ] . direct sample testing can detect m. tuberculosis within - h of sample collection, compared with - weeks for liquid and traditional solid media culture methods. although acid-fast bacilli (afb) smear microscopy is inexpensive and rapid to perform, the sensitivity of the test can be poor ( %- % with culture-confirmed pulmonary m. tuberculosis colonization or infection) and cannot differentiate m. tuberculosis from mycobacteria other than m. tuberculosis [ ] . the centers for disease control and prevention (cdc) guidelines recommend that naats should be performed on at least respiratory sample from patients with signs and symptoms of pulmonary m. tuberculosis colonization or infection for whom a diagnosis of m. tuberculosis colonization or infection has not been established or when the results would alter case management or infection control procedures [ ] . mycobacterial culture is still required, because the m. tuberculosis isolate is needed for drug susceptibility testing. currently, there are fda-approved naats available for the detection of m. tuberculosis complex from respiratory samples, the amplified mycobacterium tuberculosis direct test (amtd, gen-probe) [ , [ ] [ ] [ ] and the amplicor mycobacterium tuberculosis test (amplicor, roche diagnostics) [ ] [ ] [ ] [ ] . recently, a new assay called the xpert mtb/rif (cepheid) was developed to detect the presence of m. tuberculosis and rifampin resistance directly from processed clinical samples [reviewed in ] . the assay uses a heminested real-time pcr with molecular beacon detection and is performed on the genexpert instrument (cepheid). benefits of this assay include low technical complexity, allowing for potential point-of-care testing; minimal hands-on time ( - min); test turnaround time of , h; and containment of the sample, extracted nucleic acids, and amplicons in the test cartridge. when compared with culture, the sensitivity of the assay for the detection of m. tuberculosis ranged from . % ( sample tested per patient) to . % ( samples tested per patient) for afb smear-positive samples and from . % ( sample tested per patient) to . % ( samples tested per patient) for afb smear-negative samples. the specificity of the assay ranged from . % to . %. the assay is currently available for diagnostic testing only in europe. amplified mycobacterium tuberculosis direct test (amtd, gen-probe) the amtd is a target-amplified nucleic acid probe test for the direct detection of m. tuberculosis complex (mycobacterium bovis, m. bovis bcg, mycobacterium africanum, mycobacterium microti, and m. tuberculosis) ribosomal rna (rrna) [ , [ ] [ ] [ ] . amtd is approved for testing both afb smear-positive and smear-negative respiratory specimens collected from patients suspected of having m. tuberculosis colonization or infection. the amtd test is based on isothermal ( o c) transcription-mediated amplification that uses enzymes, reverse transcriptase (rt) and t rna polymerase, and targetspecific primers. a hybridization protection detection assay that uses a chemiluminescent-labeled, single-stranded dna probe complementary to the m. tuberculosis complex-specific sequences detects the amplified rrna using the gen-probe leader luminometer. numerous studies have evaluated amtd and have revealed an average sensitivity and specificity of . % and . %, respectively, for the detection of m. tuberculosis complex in smear-positive respiratory samples and a sensitivity and specificity of . % and . %, respectively, for smear-negative respiratory samples [ ] [ ] [ ] . additional studies have evaluated the use of the test for several types of nonrespiratory samples, such as cerebrospinal fluid and lymph nodes [ ] [ ] [ ] . amplicor mycobacterium tuberculosis test (amplicor, roche diagnostics) the amplicor mycobacterium tuberculosis test is fda approved for use with afb smear-positive respiratory specimens from patients suspected of having m. tuberculosis infection or colonization [ ] [ ] [ ] [ ] . the amplicor mycobacterium tuberculosis test uses traditional pcr to amplify a region of the gene encoding the s rrna of all mycobacteria. members of the m. tuberculosis complex are identified after hybridization with a dna target-specific probe, followed by substrate addition and colorimetric detection [ ] . when testing afb smear-positive samples, the amplicor mycobacterium tuberculosis test demonstrated sensitivities and specificities for the detection of m. tuberculosis complex ranging from . % to % and from . % to %, respectively [ , ] . the sensitivities and specificities of amplicor mycobacterium tuberculosis for afb smear-negative specimens ranged from . % to . % and % to . %, respectively [ , ] . the amplicor mycobacterium tuberculosis test has also been evaluated for detection of m. tuberculosis meningitis [ ] and for use with nonrespiratory sample types [ ] . viral respiratory pathogens are particularly suited for detection using naat, since the number of targets is relatively limited, compared with the numerous potential bacterial pathogens that can cause respiratory disease (table ) . although there is much to learn regarding the clinical relevance of mixed viral respiratory infections, the detection of a respiratory virus is generally considered diagnostic at this time. today, most laboratories do not have the facilities for comprehensive tissue culture based viral diagnostics and therefore are limited to testing with less sensitive and less specific radts for only influenza a, influenza b, and rsv. naats offer an excellent alternative to greatly expand the test menu of clinical laboratories, thereby providing rapid, accurate comprehensive diagnostics. the first multiplex naat to receive clearance by the fda was the xtag respiratory virus panel (rvp) assay in january . the fda-approved version of rvp detects adenovirus, influenza a (with subtyping of seasonal influenza a/h and seasonal influenza a/h ), influenza b, piv- , piv- , piv- , hmpv, rhinovirus, rsv a, and rsv b [ , ] . the us/canadian research use-only version of the assay also detects coronaviruses (oc , e, nl , and hku- ), parainfluenza type , and enterovirus. the test is approved for use with nasopharyngeal swab samples collected from persons symptomatic for a respiratory virus infection and placed in viral transport media. the xtag rvp is a multistep test that takes approximately - h to complete, depending on the number of samples to be tested (figure ). viral nucleic acid and an internal control (e. coli ms phage) are coextracted from clinical samples using the qiaamp minielute (qiagen), the easymag (biomérieux), or the minimag (biomérieux) extraction platforms. a multiplex reverse transcription polymerase chain reaction (rt-pcr), using primer sets specific for the test targets, amplifies the viral nucleic acid and internal control nucleic acid. pcr products are treated with exonuclease i to degrade any remaining primers and with shrimp alkaline phosphatase to degrade any remaining nucleotides. the next step consists of target-specific primer extension (tspe). when a viral target(s) is present, the target-specific primer (containing a unique tag sequence) is extended and biotin-deoxycytidine triphosphate is incorporated into the extending chain. on completion of the tspe, the detection of amplified products is performed using luminex's universal tag sorting system. the tspe reaction is added directly to microwells containing spectrally distinguishable beads with antitags, which are complementary to the sequence tags on the primers. each tagged primer will hybridize only to its unique antitag complement associated with a specific colored bead. a fluorescent reporter molecule (streptavidin-phycoerythrin) will bind to the biotin on the extended primers. the beads are then analyzed with the luminex xmap / instruments. two lasers read each bead; the first identifies the virus-specific color-coded bead, and the second determines whether an amplicon is hybridized to the bead on the basis of the detection of fluorescence (mean fluorescence intensities [mfis]) above a background threshold. the clinical performance characteristics of the xtag rvp assay were established by the manufacturer through prospectively collected nasopharyngeal swab samples (n ) tested during the - influenza season at north american clinical laboratories [ ] . all specimens were tested by means of viral culture and/or dfa testing for the following targets: influenza a, influenza b, rsv, piv- , piv- , piv- , and adenovirus. the comparator methods for influenza a subtyping, rsv subtyping, and hmpv and rhinovirus detection were wellcharacterized rt-pcr assays followed by bidirectional sequencing. xtag rvp sensitivity for each target was determined as follows: the benefits of the xtag rvp assay include the broad spectrum of viruses detected by a single test, with a cost per test comparable to real-time assays that only target up to analytes. the subtyping of influenza a viruses as seasonal influenza a/h or seasonal influenza a/h or the identification of an ''unsubtypeable'' virus has proven to be an important aid in identifying novel influenza a strains. a limitation of the assay is the decreased sensitivity for the detection of certain adenovirus strains. in-house validation studies by our laboratory have found that by reducing the positive cutoff mfi level from to for adenovirus, improved sensitivity for the detection of adenovirus was obtained without loss of specificity (unpublished data). additional limitations of the assay include the time to final results, number of required steps, technical handson time, and a potential for amplicon contamination. there is a second-generation assay called rvp fast (luminex) available in europe that addresses several of these issues by reducing the number of steps and the time to results by - h, making it possible to provide comprehensive results within a single shift. gen-probe/prodesse proflu, proflu-st, pro hmpv , and proparaflu assays (gen-probe/prodesse) currently, there are gen-probe/prodesse fda-cleared multiplex real-time rt-pcr assays for the qualitative detection and discrimination of respiratory viruses. the proflu assay targets the matrix gene for influenza a, nonstructural genes ns- and ns- for influenza b, and the polymerase gene for rsv a and rsv b. the pro hmpv assay targets highly conserved regions of the nucleocapsid (n) gene for hmpv and a transcript derived from escherichia coli bacteriophage ms a-protein gene (internal control). the proparaflu assay targets conserved regions of the hemagglutinin-neuraminidase gene for piv- , piv- , and piv- and a transcript derived from e. coli bacteriophage ms a-protein gene (internal control). all assays are approved for testing nasopharyngeal swab specimens obtained from symptomatic persons. viral nucleic acids from patient samples are coextracted with an internal control that monitors assay performance and the presence of amplification inhibitors that could lead to false-negative results. nucleic acids are extracted using a magna pure lc instrument (roche diagnostics corp) and the magna pure total nucleic acid isolation kit (roche) or a nuclisens easymag system and the automated magnetic extraction reagents (bio-mérieux). the purified nucleic acids are amplified by means of rt-pcr using target-specific oligonucleotide primers and taqman probes complementary to highly conserved regions of the target gene. the taqman probes are labeled with a quencher dye attached to the '-end and a reporter dye at the '-end. when amplified target is present, the probes bind and the '- ' exonuclease activity of taq polymerase cleaves the probe, thus separating the reporter dye from the quencher. because the quencher and reporter dye are now physically separated, there is an increase in fluorescent signal upon excitation from a light source. the fluorescent signal increases with each cycle as additional reporter dye molecules are cleaved from their respective probes. during each pcr cycle, the fluorescent intensity is monitored by the realtime instrument, the smartcycler ii (time to results, including extraction, is approximately - . hr for each test run). the performance characteristics of the assays were established by the manufacturer through prospective and retrospective clinical studies used for fda clearance of the tests. proflu assay results obtained by testing nasopharyngeal samples were compared with results of rapid shell vial culture. proflu sensitivities and specificities for the detection of influenza a were % and . %, respectively; for influenza b were . % and . %, respectively; and for rsv were . % and . %, respectively [ ]. a study by liao et al compared the prodesse proflu- assay, a previous version of the proflu assay, with viral culture and radts for rsv (now rsv, binax, inverness medical) and for influenza a and b (directogen a b, bd diagnostics) [ ] . the specificities of all methods were found to be . %. the sensitivities for detection of influenza were % for directogen a b, % for viral culture, and % for proflu- ; the sensitivities for the detection of rsv were % for rsv now, % for viral culture, and % for proflu- . in another study, legoff et al evaluated the performance of proflu- in pediatric nasopharyngeal specimens [ ] . results were compared with dfa testing and viral culture. the sensitivities and specificities of proflu- ranged from % to %, and proflu- detected viruses in % of the samples that had negative results by conventional methods. in response to the influenza a h n outbreak, an influenza a subtyping assay (proflu-st) was developed by prodesse and received emergency use authorization (eua) from the fda in july (see eua section). proflu-st is a qualitative multiplex real-time rt-pcr assay that targets the nucleoprotein gene of influenza a h n , the specific hemagglutinin genes of seasonal influenza a/h and seasonal influenza a/h , and an internal control (ms phage). the identification of influenza a h n is aided by an algorithm that relies on seasonal influenza a/h virus and seasonal influenza a/h virus results in nasopharyngeal swab specimens from patients who receive a diagnosis of influenza a by a currently available fda-cleared or authorized device. this assay is intended for use in only clia high-complexity laboratories. the performance of the assay was evaluated retrospectively using nasopharyngeal swab specimens that were previously tested with either the cdc rrt-pcr flu panel (ivd device) to detect seasonal influenza a/h and influenza a/h or the cdc rrt-pcr swine flu panel (eua). the positive and negative agreements for the detection of seasonal influenza a/h were . % and %, respectively; for seasonal influenza a/h were % and %, respectively; and for influenza a h n were . % and %, respectively [ ] . the pro hmpv assay clinical trial study for fda clearance evaluated the assay's clinical performance using nasopharyngeal swab specimens tested by clinical laboratories across the united states. using the luminex rvp assay as the predicate device, the sensitivity of pro hmpv was . % and the specificity was . % [ ]. the performance of the proparaflu assay was evaluated during the clinical trials for fda clearance. using nasopharyngeal swab specimens tested by clinical laboratories across the united states [ ], the sensitivities and specificities of the assay for the detection of piv- were . % and . %, respectively; for the detection of piv- were . % and . %, respectively, and for the detection of piv- were . % and . %, respectively [ ] . at this time, no additional independent performance data are available. the benefits of the gen-probe/prodesse assays include ease of use, with approximately . h of hands-on time for nucleic acid extraction preparation and a -step rt-pcr setup. the overall time to results is . - . h. multiple smartcycler instruments can be run simultaneously, with as many units per cycler used as needed, giving flexibility to run sizes. because tubes containing amplicons are never opened, the risk of amplicon contamination is minimal. one limitation of the assays is a maximum of targets plus an internal control that can be detected in a single reaction. therefore, a comprehensive viral diagnostic panel requires multiple pcrs. multiple pcrs are costly to the laboratory in both technical time and reagent cost. however, the limited panel size could provide a mix-and-match test menu, allowing clinicians the option of selecting or several panels. the first-generation verigene respiratory virus nucleic acid test (vrnat) was cleared by the fda in may . this test has been replaced by the automated verigene vrnat sp , a clia moderately complex test that is intended for the identification of influenza a, influenza b, and rsv (types a and b inclusive) from nasopharyngeal swab specimens placed in viral transport media. the verigene system consists of instruments (the fully automated verigene processor and the verigene reader) and single-use test cartridges (figure ). the entire test process only requires user pipetting step, less than min of technical handson time, and a sample-to-result turnaround time of about . h. the basis of vrnatsp is nanosphere's proprietary gold nanoparticle hybridization technology [ ] . the gold nanoparticles contain a high density ( ) of sequence-specific oligonucleotides with a high affinity for complementary dna, which allows for very efficient hybridization kinetics. the clinical sample is pipetted into a single-use extraction tray, which is loaded into the verigene processing unit. chaotropic agents are added to the sample to lyse cells, viral particles, and an internal control (ms phage) that is added prior to the extraction step. the released nucleic acids are then captured on magnetic microparticles (mmps). the mmp-bound nucleic acids are washed, and the purified nucleic acids are eluted from the mmps and transferred to the amplification tray. a -step rt-pcr is performed using primers that target the influenza a matrix gene, the influenza b matrix gene and nonstructural gene, and the rsv l gene and f gene. the rt-pcr reaction is followed by the primary hybridization step. during primary hybridization, target dna is simultaneously hybridized to target-specific capture dna oligonucleotides arrayed in replicate on a solid substrate (a microarray) and to target-specific mediator dna oligonucleotides. after removal of uncaptured target nucleic acids and unhybridized mediator oligonucleotides, the process continues with the secondary hybridization. each microarray spot, where an appropriate target is hybridized to capture both an oligonucleotide and a mediator oligonucleotide, is saturated with silver-coated gold nanoparticle probes. after hybridization, the cartridge is removed from the processor unit and the glass slide (microarray) is separated from the cartridge and inserted into the verigene reader. a light-scattering technique, in which the slide is illuminated internally with light parallel to the slide surface, is used to analyze the results. spots where silverenhanced gold nanoparticle probes are present scatter this light, and the light scatter is detected optically and translated into a measurable signal. the performance characteristics of the first-generation vrnat assay were established during the clinical trials for ivd device clearance. vrnat was compared with viral culture/dfa testing with bidirectional sequencing to resolve discordant results. test sensitivities and specificities for the detection of influenza a were % and . %, respectively; for influenza b were % and . %, respectively; and for rsv were . % and . %, respectively [ ] . comparison of vrnat with vrnatsp revealed an overall positive agreement of . % and a negative agreement value of % [ ] . the benefits of the vrnatsp system include the scalability of the system (addition of multiple processors and readers), individual sample processing with random access format, minimal hands-on time, and minimal technical expertise required to perform the test. because this test is clia moderate complexity, trained laboratory technicians could perform the testing. this test would be well suited for small-to medium-sized laboratories, in particular for laboratories with little or no molecular testing experience. limitations of the assay include the single test format that requires a dedicated processor for each sample for - . h. multiple processor units would be needed for larger volume laboratories, and the additional instrumentation would increase costs for the lab, compared with using an instrument that can run multiple tests at a time. table were rescinded as of june . as of july , only of these tests have received fda approval for use as an ivd device for the diagnosis of pandemic influenza a h n . the first test approved was a new optimized cdc h n assay that is available in cdc-qualified laboratories. the second test is the focus diagnostics simplexa influenza a h n ( ), which is performed using the m integrated cycler ( m). the use of fda-approved/cleared naats, in contrast to laboratory-developed tests, has substantial benefits for the laboratory. approved tests have undergone extensive analytical and clinical validations during the course of the fda evaluations. therefore, performance parameters are well characterized, and the fda monitors postapproval performance. most laboratories do not have the expertise and resources to perform extensive (table ) , thereby saving the laboratory considerable cost and technical time. the regulatory requirements for ongoing quality assurance monitoring are also fewer for fda-approved/cleared naats than for laboratory-developed tests [ ] . in addition, for regulatory reasons, some health care institutions will only allow the use of fda-approved/cleared naats. because the clinical relevance of the assays has been established, the use of fda-approved/cleared naats has a higher chance of reimbursement from both federal and private insurance payors. however, fda approval/clearance does not guarantee that these tests will be reimbursed, and, if reimbursed, the actual amount of the reimbursement can vary from state to state and by payor. finally, the simple-to-use fully automated molecular platforms, such as the genexpert and genestat, which incorporate all steps of the test process in a single test cartridge and have random-access sample-in result-out reporting, enable laboratories of all sizes to perform rapid, accurate, and sensitive molecular diagnostic testing. the most important limitation of the current fda-approved/ cleared naats is the lack of tests for the detection of nonviral targets. in particular, naats are needed for the detection of the atypical pneumonia pathogens. however, the costs of clinical trials for ivd device clearance can sometimes be quite prohibitive (.$ million, not including the costs of developing and manufacturing the ivd device) and depend on the complexity and clinical relevance of the test and what is required for fda approval (eg, number of trial sites, number of patients enrolled, clinical indications sought, need for long-term patient follow-up, associated diagnostic procedures [such as biopsy], device evaluations, predicate device comparisons, legal and regulatory components, and so forth). manufacturers must consider the potential number of tests that will be purchased and the difficulty of the trials for low-prevalence pathogens before committing the finances and resources to bring such tests through the approval process. these factors will continue to limit the scope of fda-approved/cleared naats until the approval process can be modified to encourage the submission of naats for low-prevalence targets. the current formats of the naats require laboratories to choose between real-time, easier to perform, more rapid assays that have limited targets (generally up to ) and more highly multiplex tests (. ) that require more hands-on time and technical steps and more time to result reporting. naats with limited targets would require laboratories to run multiple tests if a broader range of target detection is indicated. multiple tests would increase both the required technical time and the cost per patient diagnosis. conversely, the use of multiple, lower multiplex tests allows for the selection of the most appropriate panels as related to age of the patient, clinical status, underlying disease, state of immune competence, and the suspected virus(es). currently in development are modified faster versions of the highly multiplex assays that have been designed to reduce technical hands-on time and the time to results. some of the fda-approved/cleared real-time naats do not allow the user to see and evaluate the actual amplification curves. the inability to see the curves makes it difficult to troubleshoot when problems occur. although the user should not be able to alter cutoff values established during the fda trials, access to all or part of the raw data is desirable. one caveat for most qualitative naats is that they cannot distinguish between live and dead organisms and therefore, depending on the time for nucleic acid clearance, can be limited in monitoring response to therapy. in addition, with multiple viral infections, determining the relevance of each virus present in the sample is difficult, because residual virus detected may have been from a previous infection and may not be contributing to the current illness. the development of quantitative assays and evidence of declining viral load may clarify or resolve both of these issues. finally, issues relating to billing and reimbursement are substantial. the lack of specific current procedural terminology (cpt) codes for each of the individual targets requires laboratories to bill for multiple targets using the same generic amplified probe cpt code ( ). although it is appropriate to bill for each target present in a multiplex assay, the use of the same cpt code multiple times for a single test can be problematic. for example, many laboratory or hospital billing systems do not recognize multiple similar cpts for a single test and will only drop cpt code charge. some insurance payors will cover only the charge of the first cpt code, and there are also limitations on how many times per day a similar cpt code can be billed. as a result, reimbursement for a highly multiplexed assay could be limited to charge, thereby significantly increasing the costs to the laboratory and decreasing test profitability. under these circumstances and with pressure to reduce medical costs, many administrators will not approve the implementation of this testing if reimbursement is questionable. laboratories need analyte-specific cpt codes, and payors should reimburse for medically relevant naats. the north shore-long island jewish health system (ns-lijhs) infectious diseases molecular diagnostics laboratory opened years ago. we performed tests: human immunodeficiency virus type viral load, amtd, and chlamydia trachomatis/ neisseria gonorrhoeae naats, with a total testing volume of tests per year. today, the laboratory performs naats for different pathogens (including bacterial, mycobacterial, fungal, parasitic, and viral targets), with a volume of more than , tests per year, and in space that has tripled in size. molecular diagnostics for infectious diseases, along with molecular pathology, are of the fastest growing laboratory departments in the ns-lijhs. in addition, as best exemplified by the anthrax bioterrorism event and the influenza a h n pandemic, laboratories must be able to respond immediately by rapidly expanding testing capabilities, including sensitive and specific molecular diagnostics [ ] . at the onset of the queens, new york, area influenza a h n outbreak, the ns-lijhs laboratories' respiratory virus testing volume increased from a baseline of tests per day to more than tests per day, within days. it was clear from the first week of the outbreak that the laboratory urgently needed to switch all influenza testing to molecular methods to obtain sufficient diagnostic sensitivity and to subtype the influenza strains. fortunately, an fda-approved test, the luminex xtag rvp test, was available and met our diagnostic requirements [ , , ] . laboratories must continue to plan for future pandemic outbreaks and biothreat events. therefore, laboratories are constantly under pressure to expand testing and meet the demands of their clinical staff and their diverse patient populations. to do this, laboratories must provide clinically relevant, high-quality, cost-effective naats that are preferably fda approved/cleared. as we move forward, we request that the fda work closely with such organizations as the infectious diseases society of america and the american society for microbiology, with laboratory directors, and with ivd device manufacturers so that this goal can be met. the labor-intensive, complex methods and platforms of yesterday have evolved into simpler, user friendly versions that can be applicable to all health care settings. we encourage the fda to allow the submission process to evolve in a similar manner. no longer are the old ''gold standards'' of culture applicable, and new ways to evaluate these tests must be considered [ ] so that accurate performance characteristics can be determined in a cost-effective manner. the latter is especially true for low-volume but highly relevant assays, such as quantitative naats for transplantation monitoring. in a reasonable and clear regulatory environment, the ivd device manufacturers will succeed in bringing their naats through the approval process. the role of antimicrobial management programs in optimizing antibiotic prescribing within hospitals antimicrobial stewardship programs in health care systems excessive antibiotic use for acute respiratory infections in the united states lack of sensitivity of 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(h n ) virus infections in a school likelihood that an unsubtypeable influenza a result in the luminex xtag respiratory virus panel is indicative of novel a/h n (swine-like) influenza comprehensive evaluation of performance, laboratory application, and clinical usefulness of two direct amplification technologies for the detection of mycobacterium tuberculosis complex use of the amplified mycobacterium tuberculosis direct test in a public health laboratory: test performance and impact on clinical care evaluation and follow up of infectious tuberculosis at the university of ottawa updated guidelines for the use of nucleic acid amplification tests in the diagnosis of tuberculosis comparative evaluation of initial and new versions of the gen-probe amplified mycobacterium tuberculosis direct test for direct detection of mycobacterium tuberculosis in respiratory and nonrespiratory specimens comparison of the real-time pcr method and the gen-probe amplified mycobacterium tuberculosis direct test for detection of mycobacterium tuberculosis in pulmonary and nonpulmonary specimens evaluation of gen-probe amplified mycobacterium tuberculosis direct test by using respiratory and nonrespiratory specimens in a tertiary care center laboratory detection of mycobacterum tuberculosis by pcr amplification with pan-mycobacterium primers and hybridization to an m. tuberculosis-specific probe rapid diagnosis of pulmonary tuberculosis by using the roche amplicor mycobacterium tuberculosis pcr test use of roche amplicor mycobacterum tuberculosis pcr in early diagnosis of tuberculous meningitis application of the roche amplicor mycobacterum tuberculosis (pcr) test to specimens other than respiratory secretions xpert m. tuberculosis/ rif for point-of-care diagnosis of tb in high-hiv burden, resourcelimited countries: hype or hope? development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex pcr and a fluid microbead-based assay principles of the xtag respiratory viral panel assay (rvp assay) xtag respiratory virus panel luminex molecular diagnostics enhanced viral etiological diagnosis of respiratory system infection outbreaks by use of a multitarget nucleic acid amplification assay wi: gen-probe/prodesse evaluation of the one-step multiplex real-time reverse transcription-pcr proflu- assay for detection of influenza a and influenza b viruses and respiratory syncytial viruses in children wi: gen-probe/prodesse wi: gen-probe/prodesse wi: gen-probe/prodesse verigene respiratory virus nucleic acid test il: nanosphere il: nanosphere homogeneous detection of unamplified genomic dna sequences based on colorimetric scatter of gold nanoparticle probes quality assurance in clinical virology laboratory surge response to pandemic (h n ) outbreak discrepant analysis: how can we test a test? i sincerely thank the fda and the infectious diseases society of america for providing a forum for discussion and exchange of ideas relating to this timely and clinically relevant topic.financial support. this work was supported by us department of defense award w xwh- - - . potential conflicts of interest. c. c. g. is a member of the scientific advisory boards of gen-probe/prodesse and luminex molecular diagnostics. c. c. g. has received research grants and honoraria from gen-probe/prodesse, luminex molecular diagnostics, and diagnostic hybrids and research grants from m molecular diagnostics and has been a consultant for nanosphere. key: cord- -neqsup authors: grzegorzewski, przemyslaw title: two-sample dispersion problem for fuzzy data date: - - journal: information processing and management of uncertainty in knowledge-based systems doi: . / - - - - _ sha: doc_id: cord_uid: neqsup the problem of comparing variability of two populations with fuzzy data is considered. a new permutation two-sample test for dispersion based on fuzzy random variables is proposed. a case-study illustrating the applicability of the suggested testing procedure is also presented. various two-sample statistical tests are designed to determine whether given two populations differ significantly. in such case we assume that the universe of discourse consists of two populations, say x and y , with cumulative distribution functions f and g, respectively. then, having a random sample of size n drawn from the x population and another random sample of size m drawn from the y population, we consider the null hypothesis that these two samples are actually drawn from the same population, i.e. h : f = g. one may verify h against the general alternative hypothesis that the populations just differ in some way. the kolmogorov-smirnov test or the wald-wolfowitz run test are often used in this context (see e.g. [ ] ). however, they are really useful in preliminary studies only since affected by any type of difference between distributions, they are not very efficient in detecting any specific type of the difference like difference in location or difference in variablity. other tests, like the mann-whitney-wilcoxon test, the median test, etc. (see e.g. [ ] ) are particularly sensitive to differences in location when the populations are identical otherwise and hence cannot be expected to perform extremely well against other alternatives. however, sometimes we need statistical procedures designed to detect differences in variability or dispersion instead of location. indeed, comparison of variability might be of interest in many areas including social sciences, biology, clinical trials, engineering, manufacturing and quality control, etc. moreover, tests for the equality of variances are often required as a preliminary tool for the analysis of variance (anova), dose-response modeling, discriminant analysis, etc. it is important to emphasize that comparing variability is much harder than comparing measures of location. the famous f test assumes that both underlying populations are normally distributed and is not robust to departures from normality even asymptotically. thus many nonparametric two-sample tests based on the ranks have been proposed for the scale problem. the best-known tests are the ansari-bradley test, the mood test, the siegel-tukey test, the klotz normal-scores test, the sukhatme test, etc. designing tests for the dispersion problem turns out to be much more difficult in the case of imprecise or vague data which appear quite often in the real-life problems. in particular, human ratings based on opinions or associated with perceptions often lead to data that cannot be expressed in a numerical scale because they consist of intrinsically imprecise or fuzzy elements. since they are also realizations of some random experiment, we are faced with random fuzzy structures that cannot be analyzed with classical statistical methods. obviously, one may try to neglect, hide or remove imprecision but the most recommended approach is to consider it as a challenge for modeling and developing new inferential tools. a general framework for such modeling is given by fuzzy random variables. however, besides mathematical elegence they also bring some fundamental difficulties. for instance, random fuzzy numbers are not linearly ordered so the aforementioned tests based on ranks cannot be directly applied in fuzzy environment. depending on the context various test constructions have been proposed in the literature (for the overview we refer the reader e.g. to [ , , [ ] [ ] [ ] [ ] , , , , ] ). however, the dispersion problem with imprecise data has not beed considered very often. ramos-guajardo and lubiano [ ] proposed the bootstrap generalization of the levene test for random fuzzy sets to examine homoscedasticity of k populations. grzegorzewski [ ] introduced two generalizations of the sukhatme test for interval-valued data. in this paper we suggest a permutation test for fuzzy data to compare variability of two populations. for motivations we turned back to the classical inference showing that permutation tests, like the bootstrap, require extremly limited assumptions. indeed, permutation tests are totally distribution-free and require only exchangeability (i.e., under the null hypothesis we can exchange the labels on the observations without affecting the results). classical permutation test are often more powerful than their bootstrap counterparts (see [ ] ). permutation test are exact if all permutation are considered, while bootstrap tests are exact only for very large samples. moreover, asymptotically permutation tests are usually as powerful as the most powerful parametric tests (see [ ] ). keeping this in mind we combine the pan test [ ] and the marozzi test [ ] and then generalize them into the permutation testing procedure that handle fuzzy data. the paper is organized as follows: in sect. we recall basic concepts related to fuzzy data modeling and operations on fuzzy numbers. section is devoted to fuzzy random variables. in sect. we introduce the two-sample test for the dispersion dedicated to fuzzy data. next, in sect. we present some results of the simulation study and the case study with the proposed test. finally, conclusions and some indications for the futher research are given in sect. . a fuzzy number is an imprecise value characterized by a mapping a : r → [ , ], called a membership function), such that its α-cut defined by is a nonempty compact interval for each α ∈ [ , ]. operator cl in ( ) denotes for the closure. thus every fuzzy number is completely characterized both by its memberschip function a(x) or by a family of its α-cuts {a α } α∈ [ , ] . two α-cuts are of special interest: a = core(a) known as the core, which contains all values which are fully compatible with the concept described by the fuzzy number a and a = supp(a) called the support, which are compatible to some extent with the concept modeled by a. the most often used fuzzy numbers are trapezoidal fuzzy numbers (sometimes called fuzzy intervals) with membership functions of the form where a , a , a , a ∈ r such that a a a a . a trapezoidal fuzzy number ( ) is often denoted as tra(a , a , a , a ). obviously, a = inf supp(a), a = inf core(a), a = sup core(a) and a = sup supp(a), which means that each trapezoidal fuzzy numbers is completely described by its support and core. a fuzzy number a is said to be a triangular fuzzy number if a = a , while if a = a and a = a we have the so-called interval (or rectangular) fuzzy number. the families of all fuzzy numbers, trapezoidal fuzzy numbers, triangular fuzzy number and interval fuzzy numbers will be denoted by f(r), basic arithmetic operations in f(r) are defined through natural α-cut-wise operations on intervals. in particular, the sum of two fuzzy numbers a and b is given by the minkowski addition of corresponding α-cuts, i.e. for all α ∈ [ , ]. similarly, the product of a fuzzy number a by a scalar θ ∈ r is defined by the minkowski scalar product for intervals, i.e. for all α ∈ [ , ] it is worth noting that a sum of trapezoidal fuzzy numbers is also a trapezoidal fuzzy number: if a = tra(a , a , a , a ) and b = tra moreover, the product of a trapezoidal fuzzy number a = tra(a , a , a , a ) by a scalar θ is a trapezoidal fuzzy number unfortuntely, f(r), +, · has not linear but semilinear structure since in general a + (− · a) = { } . consequently, the minkowski-based difference does not satisfy, in general, the addition/subtraction property that (a+(− ·b))+b = a. to overcome this problem the so-called hukuhara difference was defined as follows: hold but the hukuhara difference does not always exist. therefore, one should be aware that subtraction in f(r) generally leads to critical problems and should be avoided, if possible. at least some of the problems associated with the lack of a satisfying difference in constructing statistical tools for reasoning based on fuzzy observations could be overcome by using adequate metrics defined in f(r) -for the general overview see [ ] . obviously, one can define various metrics in f(r) but perhaps the most often used in statistical context is the one proposed by gil et al. [ ] and by trutschnig et al. [ ] . let λ be a normalized measure associated with a continuous distribution having support in [ , ] and let θ > . then for any a, b ∈ f(r) we define a metric d λ θ as follows denote the mid-point and the radius of the α-cut a α , respectively. both λ and θ correspond to some weighting: λ allows to weight the influence of each α-cut, while by a particular choice of θ one may weight the impact of the distance between the mid-points of the α-cuts (i.e. the deviation in location) in contrast to the distance between their spreads (i.e. the deviation in vagueness). in practice, the most common choice of λ is the lebesgue measure on [ , ]), while the most popular choice is θ = or θ = . it is worth noting that assuming θ = we obtain i.e. the metric which weights uniformly the two squared euclidean distances and is equivalent to the distance considered in [ , ] . one may also notice that assuming θ = we obtain where a aggregates uniformly the squared euclidean distances between the convex combination of points in α-cuts representing a and b. it should be stressed that whatever (λ, θ) is chosen d λ θ is an l -type metric in f(r) having some important and useful properties. is a separable metric space and for each fixed λ all d λ θ are topologically equivalent. suppose that the result of an experiment consists of random samples of imprecise data described by fuzzy numbers. to cope with such problem we need a model which grasps both aspects of uncertainty that appear in data, i.e. randomness (associated with data generation mechanism) and fuzziness (connected with data nature, i.e. their imprecision). to handle such data puri and ralescu [ ] introduced the notion of a fuzzy random variable (also called a random fuzzy number). in other words, x is a random fuzzy variable if and only if x is a borel measurable function w.r.t. the borel σ-field generated by the topology induced by d λ θ . puri and ralescu [ ] defined also the aumann-type mean of a fuzzy random variable x as the fuzzy number e(x) ∈ f(r) such that for each α ∈ [ , ] the α-cut e(x) α is equal to the aumann integral of x α . it is seen that to characterize dispersion of a fuzzy random variable x we can also define (see [ ] ) the d λ θ -fréchet-type variance v(x), which is a nonnegative real number such that given a sample of random fuzzy numbers x = (x , . . . , x n ) a natural estimator of e(x) is the average x ∈ f(r) such that for each α ∈ [ , ] while the estimator of v(x) is the d λ θ -type sample variance s ∈ r given by although aforementioned constructions preserve many properties known from the real-valued inference, one should be aware of the problems typical of statistical reasoning with fuzzy data. as it was noted in sect. , there are problems with subtraction of fuzzy numbers. similar problems appear in the case of division of fuzzy numbers. hence, it is advisable to avoid both operations wherever it is possible. moreover, some difficulties in fuzzy data analysis is caused by the lack of universally accepted total ranking between fuzzy numbers. another source of possible problems that appear in conjunction of randomness and fuzziness is the absence of suitable models for the distribution of fuzzy random variables. even worse, there are not yet central limit theorems for fuzzy random variables which can be applied directly in statistical inference. the disadvantages mentioned above make the straightforward generalization of the classical statistical methodology into the fuzzy context either difficult or, sometimes, even impossible. for instance, in most cases we are not able to find the null distribution of a test statistic based on fuzzy data and, consequently, to find either the critical value or to compute the p-value required for rejection or acceptance of the hypothesis under study. to break through that problem some researchers propose to use the bootstrap [ , , , , , , ] . in this paper we suggest another methodology based on permutations. for motivations we turn back to the classical inference which shows that permutation tests, like the bootstrap, require extremly limited assumptions. bootstrap tests usually rely on assumption that successive observations are independent, while permutation tests require only exchangeability, i.e. under the null hypothesis we can exchange the labels on the observations without affecting the results (obviously, if the observations in a sample are independent and identically distributed then they are exchangeable). in the real-valued framework one can also indicate two advantages of the permutation tests over the bootstrap tests. firstly, permutation test are often more powerful than their bootstrap counterparts (see [ ] ). secondly, permutation test are exact if all permutation are considered, while bootstrap tests are exact only for very large samples. moreover, asymptotically permutation tests are usually as powerful as the most powerful parametric tests (see [ ] ). for more information on classical permutation tests we refer the reader to [ , ] . all these reasons indicate that the permutation test applied to fuzzy random variables might be also a competitive tool useful in statistical inference for imprecise data. suppose, we observe independently two fuzzy random samples x = (x , . . . , x n ) and y = (y , . . . , y m ) drawn from populations with unknown distributions function f and g, respectively. we want to verify the null hypothesis that both samples come from the same distribution, i.e. against the alternative hypothesis that the dispersion of the distributions f and g differ (or against the one-sided alternative that the indicated distribution is more dispersed that the other one). most of the tests for scale assume that the distributions under study do not differ in location since possible location differences may mask differences in dispersion. otherwise, the sample observations should be adjusted by subtrating the respective location parameters, like means or medians. if the true characteristics of location are not known we usually subtract their estimators. following remarks of marozzi [ ] on the resampling version of the pan test [ ] and the resampling framework for scale testing described by boos and brownie [ ] , we'll try to eliminate the location effects with sample means. however, keeping in mind problems with subtratiion in fuzzy environment described in sect. , contrary to the crisp case, we do not consider the differences but the distances between sample observations and corresponding sample means calculated as in ( ) . therefeore, further on instead of x = (x , . . . , x n ) and y = (y , . . . , y m ) we consider the adjusted samples v = (v , . . . , v n ) and w = (w , . . . , w m ), respectively, where . . , m. now let us consider the following test statistics where s v and s w denote sample variances of v and w, respectively, calculated by ( ) . obviously, too big or too small values of ( ) indicate that the null hypothesis should be rejected since the considered distributions differ in dispersion. in the original pan test [ ] the decision whether to reject the null hypothesis is based on the test statistic valued with respect to some quantile from the t-student distribution. however, marozzi [ ] showed that the resampling version of the pan test should be rather preferred to the original one. in the case of fuzzy data any assumptions on the type of the underlying distribution of the samples are much more dubious than in the crisp case. for this reason we also consider here the permutation version of the pan test. to carry out such a test we adapt the general idea of permutation tests to our fuzzy context. the crucial idea of the proposed test construction is that the null hypothesis implies total exchangeability of observed data with respect to groups. indeed, if h holds then all available observations may be viewed as if they were randomly assigned to two groups but they come from the same population. let z = x y, where stands for the vector concatenation, so that the two samples are pooled into one, i.e. now, let z * denote a permutation of the initial dataset z. more formally, if ν = { , , . . . , n} and π ν is a permutation of the integers ν, then z * i = z πν (i) for i = , . . . , n. then the first n elements of z * is assigned to the first sample z * and the remaining m elements to z * . in other words, it works like a random assignment of elements into two samples of the size n and m, respectively. each permutation corresponds to some relabeling of the combined dataset z. please, note that if h holds then we are completely free to exchange the labels x or y attributed to particular observations. as a consequence of elements' exchangeability in z * under h we can estimate the distribution of the test statistic t by considering all permutations of the initial dataset z and computing a value of t (z * ) corresponding to each permutation. namely, given z = z, where z = x y, we take its permutation z * and determine its adjustment with respect to sample means, i.e. we create two samples v * = (v * , . . . , v * n ) and w * = (w * , . . . , w * m ) as follows next, following ( ) we compute its actual value corresponding to given permutation z * , i.e. finally, assuming k denotes a fixed number of drawings (usually not smaller than ), we calculate the p-value of our test. in the case on the one-sided upperer-tail test, i.e. when verifying h : f = g vs. h stating that f is more disperded than g, we obtain where each z * k ∈ p(z), z * k = x * k y * k , and t = t (x, y) stands for the test statistic value obtained for the original fuzzy samples x and y. for the one-sided lower-tail test, i.e. when verifying h : f = g vs. h : f is less disperded than g, we have while for the two-sided test, i.e. when verifying h : f = g vs. h : f and g differ in dispersion, we obtain we conducted some simulations to illustrate the behavior of the proposed test. to generate fuzzy samples from a trapezoidal-valued fuzzy random variable x = tra(ξ , ξ , ξ , ξ ), where ξ , ξ , ξ , ξ are real-valued random variables such that ξ ξ ξ ξ , the following characterization appears to be useful (see [ ] ): c = (ξ + ξ ) = mid x, s = (ξ − ξ ) = spr x, l = ξ − ξ and r = ξ − ξ . conversely, we have tra c, s, l, r = tra(c − s − l, c − s, c + s, c + s + r). in our study we generated fuzzy observations x = (x , . . . , x n ) and y = (y , . . . , y m ) by simulating the four real-valued random variables x i = c xi , s xi , l xi , r xi and y i = c y j , s y j , l y j , r y j , respectively, with the last three ones random variables in each quartet being nonnegative. in particular, we generated trapezoidal-valued fuzzy random variables using the following real-valued random variables: c xi , c y j from the normal distribution and s xi , s y j , l xi , l y j , r xi and r y j from the uniform or chi-square distribution. an illustration how the test works, is shown in fig. and fig. . figure shows a histogram made for the test statistic ( ) null distribution obtained for two fuzzy samples of sizes n = and m = . both samples were generated as follows: c x and c y came from the standard normal distribution n( , ) and s x , s y , l x , l y and r x , r y from the uniform distribution u( . . ). in this case we have obtained t = . , which is illustrated by a vertical line, while p-value = . . a decision suggested by our test is: do not reject h . on the other hand, in fig. we have a histogram made for the test statistic ( ) null distribution obtained for two fuzzy samples of the same samle sizes as before but which differ in dispersion. namely, c x was generated from the standard normal distribution n( , ), but c y from n( , ), while s x , s y , l x , l y and r x , r y were, as befor, uniformly distributed from u( . . ). in this case we have obtained t = − . , illustrated by a vertical line, and p-value = . , leading to the decision: reject h . we also examined the proposed permutation test with respect to its size. therefore, simulations of the test performed on independent fuzzy samples comming from the same distribution were generated at the significance level . . in each test k = permutations were drawn. then empirical percentages of rejections under h were determined. the results both for equal and nonequal sample sizes are gathered in table . it is seen that our test is conservative. moreover, this tendency deepens significantly as the imbalance of the sample sizes increases. these interesting results of the preliminary study of the proposed test properties indicate that further and more extensive study is highly recommended. some statistical analyses of fuzzy data related to the gamonedo cheese quality inspection was performed by ramos-guajardo and lubiano [ ] and ramos-guajardo et al. [ ] . the gamonedo cheese is a kind of a blue cheese produced asturias, spain. it experiences a smoked process and later on is let settle in natural caves or a dry place. to keep the quality of a cheese the experts (or tasters) usually express their subjective perceptions about different characteristics of the cheese, like visual parameters (shape, rind and appearance), texture parameters (hardness and crumbliness), olfactory-gustatory parameters (smell intensity, smell quality, flavour intensity, flavour quality and aftertaste) and their overall impression of the cheese. recently some of the tasters were proposed to express their subjective perceptions about the quality of the gamonedo cheese by using trapezoidal fuzzy numbers. these fuzzy sets were determined in the following way: the set of values considered by the expert to be fully compatible with his/her opinion led to α = -cut, while the set of values that he/she considered to be compatible with his/her opinion at some extent (i.e., the taster thought that it was not possible that the quality was out of this set) led to α = -cut of a fuzzy number. then these two α-cuts were linearly interpolated to get the trapezoidal fuzzy set representing exppert's personal valuation. for more details on the data aquisition and analysis we refer the reader to ramos-guajardo et al. [ ] . here we utilize some data given in [ ] to compare the opinions of the two experts about the overall impression of the gamonedo cheese (the trapezoidal fuzzy sets corresponding to their opinions are gathered in table ). thus we have two independent fuzzy samples of sizes n = and m = comming from the unknown distributions f and g, respectively. our problem is to check whether there is a general agreement between these two experts. to reach the goal we verify the following null hypothesis h : f = g, stating there is no significant difference between experts' opinions, against h : ¬h that their opinions on the cheese quality differ. substituting data from table into formula ( ) we obtain t = . . then, after combining samples and generating k = random permutations we have obtained the p-value of . . hence, assuming the typical % significant level we may conclude that there is no significant difference between the dispersion of experts' opinion on the overal impression of the gamonedo cheese. in fig. one can find the empirical null distribution of the permutation test with red vertical line indicating the value t of the test statistic. hypothesis testing with samples which consist of random fuzzy numbers is neither easy nor straightforward. most of statistical tests developed in this area are based on the bootstrap. in this paper another approach for constructing tests for fuzzy data is proposed. namely, the two-sample permutation test for dispersion is suggested. some simulations to illustrate its behavior and to examine its properties are given. moreover, the case study dedicated to fuzzy rating problem is performed. the results obtained seem to be promissing, but further research including power studies and a comparison with other tests are still intended in the nearest future. in particular, the behavior of the test under strong imbalance in the sample sizes is worth of further examination. next, we would like to perform an extensive simulation study to compare the performance of our permuatation test and the bootstrap test for the dispersion. moreover, some other topics related to the dispersion problem with fuzzy data seem to be of interest. firstly, we plan to design other two-sample tests for scale, like the permutation test for fuzzy data based on the classical o'brien test, as well as a permutation test for the homogeneity of more than two fuzzy samples. secondly, a permutation test for fuzzy data to compare jointly the central tendency and variability of two populations would be of desirable. asymptotic expansion for the power of distributionfree tests in the two-sample problem a distance-based statistic analysis of fuzzy numbervalued data (with rejoinder) comparing variances and other measures of dispersion metric spaces of fuzzy sets nonparametric statistical inference least squares fitting of an affine function and strength of association for interval-valued data bootstrap techniques and fuzzy random variables: synergy in hypothesis testing with fuzzy data. fuzzy sets syst fuzzy data treated as functional data. a one-way anova test approach permutation, parametric and bootstrap tests of hypotheses metrics and orders in space of fuzzy numbers statical inference about the median from vague data testing statistical hypotheses with vague data. fuzzy sets syst fuzzy tests -defuzzification and randomization. fuzzy sets syst k-sample median test for vague data two-sample dispersion tests for interval-valued data goodness-of-fit tests for fuzzy data the λ-mean squared dispersion associated with a fuzzy random variable hypothesis testing for means in connection with fuzzy rating scale-based data: algorithms and applications hypothesis testing-based comparative analysis between rating scales for intrinsically imprecise data levene type tests for the ratio of two scales asymptotic and bootstrap techniques for testing the expected value of a fuzzy random variable on a levene type test for equality of two variances multivariate permutation tests fuzzy random variables applying statistical methods with imprecise data to quality control in cheese manufacturing k-sample tests for equality of variances of random fuzzy sets a new family of metrics for compact, convex (fuzzy) sets based on a generalized concept of mid and spread key: cord- -yvj pqh authors: bergman, christian; stall, nathan m.; haimowitz, daniel; aronson, louise; lynn, joanne; steinberg, karl; wasserman, michael title: recommendations for welcoming back nursing home visitors during the covid- pandemic: results of a delphi panel date: - - journal: j am med dir assoc doi: . /j.jamda. . . sha: doc_id: cord_uid: yvj pqh objectives nursing homes became epicenters of covid- in the spring of . due to the substantial case fatality rates within congregate settings, federal agencies recommended restrictions to family visits. six months into the covid- pandemic, these largely remain in place. the objective of this study was to generate consensus guidance statements focusing on essential family caregivers and visitors. design a modified two-step delphi process was used to generate consensus statements. setting and participants the delphi panel consisted of us and canadian post-acute and long-term care experts in clinical medicine, administration, and patient care advocacy. methods state and federal reopening statements were collected in june and the panel voted on these using a three-point likert scale with consensus defined as ≥ % of panel members voting “agree.” the consensus statements then informed development of the visitor guidance statements. results the delphi process yielded consensus statements. regarding visitor guidance, the panel made five strong recommendations: ) maintain strong infection prevention and control precautions, ) facilitate indoor and outdoor visits, ) allow limited physical contact with appropriate precautions, ) assess individual residents' care preferences and level of risk tolerance, and ) dedicate an essential caregiver and extend the definition of compassionate care visits to include care that promotes psychosocial wellbeing of residents. conclusions and implications the covid- pandemic has seen substantial regulatory changes without strong consideration of the impact on residents. in the absence of timely and rigorous research, the involvement of clinicians and patient care advocates is important to help create the balance between individual resident preferences and the health of the collective. the results of this evidence-based delphi process will help guide policy decisions as well as inform future research. visitor guidance for america's nursing homes regarding the abrogation of self-determination and clinical concerns that ongoing restrictions have begun to outweigh any potential benefits. , - cms released phased reopening guidelines on may , , instructing nursing homes to reopen only when the facility had no new covid- cases for a day period and no shortages in ppe, staffing, or testing capacity. , three months after release of these guidelines, many facilities are still far from meeting these criteria. residents, families, clinicians, and advocates are calling for a more immediately actionable, sustainable, balanced, nuanced, and resident-centered approach to reopening nursing homes that respects residents' rights to autonomy, informed risk taking, access to essential family caregivers, and other face-to-face interactions. a group of experts convened to develop a set of evidence-informed guidance statements to welcome back visitors and essential family caregivers to america's nursing homes. in round one, participants voted on the statements, using a three-point likert scale ("agree," "neutral," or "disagree") with an option to offer "absent" due to a lack of perceived expertise. consensus was defined as ≥ % of participants voting "agree" (green statements). we grouped non-consensus statements into ≤ % (red statements) and - % (yellow statements) for purposes of facilitating discussion after each round. the whole panel discussed statements not reaching consensus in a videoconference, starting with statements that had the highest degree of uncertainty (red statements). in preparation for round two of voting, participants also suggested additional statements for consideration. following the second round of voting, a final videoconference discussion collected comments on the non-consensus statements to help inform the final document. we report the final count of consensus and non- consensus statements. descriptive statistics and tables illuminated differences in responses among the expert panel. although the present reopening statements cover a wide range of topics, we focused on the statements specific to visitors in order to communicate immediately actionable recommendations to policymakers. those statements reaching consensus shaped our visitor guidance document. we edited the final guidance statements for clarity, aiming to capture the consensus of the delphi aspects of the following topics (see table ): testing of asymptomatic staff and residents, surveillance testing, visitor guidance, immunity from prior covid- infection and associated risk of infecting others. the panel generally agreed on the need for testing of asymptomatic staff ( %); but the panel discussion reflected the importance of understanding community prevalence as a key factor in deciding to test asymptomatic individuals. while the panel mostly agreed j o u r n a l p r e -p r o o f visitor guidance for america's nursing homes ( %) that residents should be allowed to opt out of testing for sole purposes of surveillance, fewer agreed that testing of asymptomatic residents should not be done ( %). most members agreed that an asymptomatic resident who has recovered from the disease need not be tested within weeks from the onset of symptoms ( %) but fewer agreed to extend that to days ( %) or to never test again ( %). this general uncertainty about the time was again reflected when the panel commented on whether an asymptomatic covid- resident who has recovered could be contagious weeks after recovery ( % agreement that they are not contagious), or after days ( % agreement that they are not contagious). a minority of the panel members ( %) agreed that a recovered covid- who remains asymptomatic is not contagious. the delphi process reached consensus on of statements related to visitors. these statements were then merged and expanded into guidance statements (see table guidance that begins to balance the well-being and self-determination of residents and their families with the very real public health concern of preventing nursing home outbreaks. our panel was able to review guideline statements and develop consensus around general statements to help inform a set of suggested visitor guidance statements. the panel strongly agreed on some preconditions that would be essential prior to welcoming back visitors, such as universal masking for staff, sufficient disinfecting supplies, ppe, and written plans around isolation, cohorting, screening, testing, and outbreak investigations. furthermore, our panel had wide consensus on testing of symptomatic residents and staff, the importance of contact tracing, and barring communal and group activities for symptomatic residents. a key finding reinforced by the panel was the future need to assess individual residents' care preferences and level of risk tolerance, something that has been missing in many of the existing reopening guidelines, in part due to cohorting challenges. this was envisioned by the panel as allowing some residents to participate in a risk-accepting group that could be cohorted together for increased social interactions and dining. however, as illustrated in table j o u r n a l p r e -p r o o f agreed that limited physical contact between visitors and residents should be allowed with meticulous hand hygiene before and after resident contact, and the use of masks, gowns and gloves. a lack of visitor access to ppe should not preclude a visit, so nursing homes must be able to provide masks, gloves and gowns when required. the panel had less accord, however, regarding infection prevention strategies during a visit encounter. for example, universal masking for staff was supported but the group did not reach consensus on which type of mask (e.g. surgical vs. cloth) or whether all visitors had to wear a mask all of the time during a visit. similarly, it was agreed that physical distancing be required in public, common spaces such as the lobby, hallways, or nursing stations, but perhaps not applicable during a visit encounter with an asymptomatic resident. regarding visitor guidance logistics, the panel strongly recommended the use of an electronic process to schedule visits and a sign-in log with contact information to aid in potential contact tracing. additionally, the panel recommended allowing the designation of one or two essential family caregivers by the resident or surrogate decision maker. the essential family caregiver(s) and the surrogate decision maker would have priority to visit the resident. these visitors, for example, might provide complex care, such as assistance with feeding or support for responsive behaviors commonly encountered in residents with dementia. all visitors and essential family caregivers must be provided entry during serious illness, including at the end-of- life, irrespective of covid- status of the resident, provided that the visitor dons appropriate lastly, regarding visitor guidance and risk tolerance, the panel acknowledged that essential family caregivers may wish to visit a resident who may be contagious such as ) a symptomatic resident with a positive covid- test, ) a symptomatic resident with an j o u r n a l p r e -p r o o f unknown or pending covid- test, or ) an asymptomatic resident who has tested positive for covid- . after discussion, the authors recommend three steps be followed. first, a shared informed consent discussion between essential caregivers and nursing leadership that would regarding immunity and cohorting, our panel agreed ( %) that cohorting asymptomatic residents who have all recovered for covid- can be safely done and that a resident who has recovered from covid- , remains asymptomatic, and is at least weeks post onset of symptoms is likely not infectious ( % consensus). regarding the role of antibody testing, a modest majority agreed ( %) that antibody testing could be a surrogate marker of individual immunity; but all agreed that a positive immunity test does not currently inform clinical practice and instead one has to rely upon recovery from prior infection. it should be noted that the delphi process occurred before the cdc guidance that recovered covid- residents do not require re- testing or precautions for days had been released . the areas of congruence leading to the suggested visitor guidance statements stem from thoughtful resident-centered debates among a panel of delphi experts. the fact that there are many areas with substantial variation certainly arises from the state of the science but might also be a result of the interaction of certain statements with each other, difficulties with precise wording or statements, or the persistent inability of guidelines to accommodate the wealth of variations in clinical situations. one limitation of this study was that a rapid two-step modified j o u r n a l p r e -p r o o f delphi process may not have allowed enough time for the panel to develop consensus around some of the challenging language or the more controversial topics, but the panel felt the urgency to produce high-quality guidance statements promptly. the use of a modified delphi process to standardize the process, provide iterative feedback, and consensus-gathering strengthens the findings of this study. the delphi process itself limits bias but could be influenced by how panelists were selected . there was some degree of self-selection in the organization of this panel as the group shared a common concern regarding the health and wellbeing of the vulnerable older adults living in nursing homes during the covid- pandemic. additionally, the panel had substantial diversity but did not include all important stakeholders, such as nurse leaders, direct care workers, or residents. nevertheless, the panelists were chosen for their expertise in the field of geriatrics and long-term care medicine, and have all been listed in the acknowledgement section. the objective of this study was to develop a set of visitor guidance statements that could be used to welcome back visitors and essential family caregivers to us nursing homes. even after a structured delphi process, experts in nursing home care still had substantial discord on important elements. however, through rigorous and evidence-informed discussions, a concise and practical set of guidance statements was developed (table ) in order for a nursing home to proceed with phased reopening, there should be no new nh-onset cases for days. ( ) testing a proportion of randomly selected asymptomatic hcp (staff) who have not previously tested positive should be done for surveillance efforts. the frequency and sample size of staff should be guided by size of the nursing home and level of local community spread. in facilities without any positive covid- cases, test % of asymptomatic hcp (staff) who have previously not tested positive weekly for weeks; if no new positives may test % of asymptomatic hcp (staff) every days such that % of the nursing home staff are tested each month. ( ) testing a proportion of randomly selected asymptomatic residents who have not previously tested positive should not be done for surveillance efforts. instead, residents who are asymptomatic should only be tested during outbreak investigations of close contacts of a known covid- positive resident or staff member. residents who are asymptomatic should be allowed to opt out of testing for sole purposes of surveillance. this statement would not be applicable for contact tracing with a known exposure to a covid- resident or staff member. an asymptomatic resident who has previously tested positive for covid- and recovered does not need to be ( ) tested again within an week window of prior onset of symptoms. an asymptomatic resident who has previously tested positive for covid- and recovered does not need to be tested again within a day window of prior onset of symptoms. an asymptomatic resident who has previously tested positive for covid- and recovered does not need to be tested again. a new or returning asymptomatic nursing home resident without a prior diagnosis of covid- and who has remained under isolation in a private room for days since admission tests positive during nursing home testing of asymptomatic residents. not during an outbreak investigation and there has been no exposure to a covid- positive resident or staff. in this situation, re-test the resident only. if subsequently negative and no further suspicion of covid- in the building, this scenario would not warrant nursing home-wide testing or phase regression. ( ) a negative covid- test is not a requirement prior to visiting a nursing home. ( ) visitors who wish to visit a nursing home resident who is actively symptomatic but for whom covid- testing is pending or unknown should have an informed consent discussion with nursing leadership, demonstrate appropriate donning/doffing of ppe and agree to wear appropriate ppe during the visit. allow entry of all essential and non-essential healthcare personnel, contractors, and vendors with appropriate screening, physical distancing, hand hygiene, and face coverings. they would be subject to the same testing and surveillance requirements as the rest of the hcp (staff) cohort. visitors including non-employed caregivers and surrogate-decision makers would be subject to the visitor the nursing home should consider a designated care giver (or dedicated support person, surrogate decision-maker) an essential member of the healthcare team who would not be subject to visitor guidelines if resources (ppe, training, monitoring) are available at the time and the person is directly engaged in compassionate care to alleviate a residents psycho-social stress as a result of isolation. ( ) a resident who engages in a visit with family or friends beyond the nursing home grounds, remains outside, and the visit does not involve close contact with covid+ individuals or symptomatic individuals would not be subject to isolation upon re-entry to the nursing home. after a resident returns from an outside trip beyond the nursing home grounds and prior to the resident resuming activities within a shared space, the resident should be bathed according to accepted practice with soap and have the clothes they were wearing laundered in a standard fashion. immunity a currently asymptomatic individual who has recovered from covid- and is post weeks from onset of symptoms is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the resident is not contagious. a currently asymptomatic individual who has recovered from covid- and is post days from onset of symptoms is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the resident is not contagious. a currently asymptomatic individual who has recovered from covid- is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the resident is not contagious. antibody testing can be a surrogate marker of individual immunity but does not currently inform clinical practice; recovery from prior infection does. color scheme represents level of consensus among panel. yellow represents statements in which - % of members voted "agree" and red represents statements in which < % of members voted "agree." j o u r n a l p r e -p r o o f all staff, residents, and visitors engage in basic hand hygiene and physical distancing in public, shared spaces. all staff wear a medical-grade mask while in the nursing home. all residents and visitors wear a face covering when in shared, public spaces. if a resident or visitor does not own a face covering, one must be provided by the nursing home. the facility has sufficient disinfecting supplies (hand sanitizers, soap, detergent, etc.) and adequate personal protective equipment (gloves, gowns, masks, face shields/goggles). a written isolation and cohorting plan is in place. a written screening and testing plan with adequate capacity for implementation is in place. a written contact tracing and outbreak investigation plan is in place. all persons entering the nursing home (staff, visitors, volunteers, and vendors) undergo the same entrance screening process, including a temperature check and answering an exposure and symptom questionnaire by a trained entrance screener. visitors that do not comply with the screening procedure are not allowed to enter. visitors and volunteers can sign up to visit a resident for a defined time period using an electronic process. the nursing home maintains a sign-in log that includes contact information (name, phone number, email address) of visitors and volunteers to help with contact tracing in the event of an exposure. a nursing home may need to limit the number of indoor visitors to no more than visitors at one time to allow physical distancing between visitor groups. visit frequency and the number of visitors a nursing home is able to accommodate would depend on the physical space, availability to visit outdoors, and ppe availability. visitors must be guided to the designated visit area to limit interactions with patient-care areas, staff, or other residents. gloves and a gown with associated hand hygiene are required if visitors wish to engage in limited physical contact with a resident, such as hugging, hand holding, or direct resident care such as assistance with meals. the nursing home must provide gloves and gowns for this purpose. the nursing home should designate areas for indoor and outdoor visits. ideally the visits would occur outside, conditions permitting. indoor areas should be accessible without walking through a resident care area, must be disinfected between scheduled visits, and should be large enough to facilitate physical distancing between visit groups. a nursing home should allow each resident or surrogate decision maker to choose essential family caregivers who, along with the surrogate decision maker, would have priority to frequently visit a resident, e.g. to provide complex care, aid in feeding, or redirect and reassure those residents living with dementia who have responsive behaviors. visiting a resident with or without symptoms who has a positive, unknown, or pending covid- test result requires the following steps: . the visitor must participate in an informed consent discussion with leadership regarding the risks of potential exposure to covid- and whether they outweigh the benefits of a visit. additionally, visitors should be counseled to understand the covid- test status and encouraged to wait for a pending test result to return prior to a scheduled visit. . the nursing home must provide education and training so that the visitor can demonstrate appropriate donning/doffing of ppe, including a mask, gowns, gloves, and possibly a face shield. . the visitor must agree to wear the recommended ppe during the visit and follow all infection prevention and control procedures within the nursing home. the nursing home should make every attempt possible to work with visitors of residents who are seriously ill, receiving care focused on comfort, and approaching end-of-life. specifically, facilities may waive the visitor limits, offer extended hours, and offer an in-person room visit to help facilitate the psycho-social well-being of the resident and family members. j o u r n a l p r e -p r o o f  social distancing, hand washing, and disinfection practices need to continue in directpatient care areas.  residents, visitors, and volunteers wear cloth face coverings or a facemask when in a shared-space.  all persons entering the facility (including staff, visitors, volunteers, and vendors) should undergo screening to include: temperature check, exposure questionnaire, and symptom questionnaire.  entry screening is performed by a screener who has received training in basic infection control, appropriate education on questionnaires and hands-on practice with thermometer.  all persons attempting to enter the facility who have either recorded a temperature > . f or report having taken a medication to treat fever (anti-pyretic such as acetaminophen) should not be permitted to enter.  all residents should undergo a daily symptom screening and have temperature monitored.  symptomatic residents/staff o test all symptomatic residents and staff but allow individual residents autonomy with an appropriate plan on how to isolate and cohort a resident who is symptomatic but does not wish to be tested. o a symptomatic staff member who does not wish to be tested would be excluded from work until they meet the return to work criteria of a presumed positive individual. o treat a symptomatic resident who does not wish to be tested as a presumed positive. isolate and cohort accordingly. o  asymptomatic residents/staff o all residents, staff should have undergone baseline testing as part of phase and phase . o have a plan for ongoing surveillance testing of asymptomatic staff and residents.  testing a proportion of randomly selected asymptomatic hcp (staff) who have not previously tested positive should be done for surveillance efforts. the frequency and sample size of staff should be guided by size of facility and level of local community spread. - % agreement  in facilities without any positive covid- cases, test % of asymptomatic hcp (staff) who have previously not tested positive weekly for weeks; if no new positives may test % of asymptomatic hcp (staff) every days such that % of facility staff are tested each month. % agreement  testing a proportion of randomly selected asymptomatic resident who have not previously tested positive should not be done for surveillance efforts. instead, residents who are asymptomatic should only be tested during outbreak investigations of close contacts of a known covid- positive resident or staff member. % agreement  residents who are asymptomatic should be allowed to opt out of testing for sole purposes of surveillance. this statement would not be applicable for contact tracing with a known exposure to a covid- patient or staff member. - % agreement o triggers to increase testing:  a trigger to increase testing of asymptomatic individuals would be based on response to an outbreak investigation and contact tracing results.  one covid- + case in staff or residents should trigger the execution of a comprehensive plan addressing contact tracing, isolation/cohorting, and testing within hours of positive test result.  during an outbreak investigation, there should be a low threshold to extend testing of all staff and residents to entire units, floors, buildings if the situation deems it necessary.  asymptomatic residents and staff who have previously tested positive would not be subject to repeat testing.  once one nh-onset case (case definition from cdc) has been identified within a facility, facilities should resume testing of asymptomatic hcp (staff) who have not previously tested positive o the facility should make every effort possible to secure a collection method that is least invasive and uncomfortable if testing residents and staff with a low pretest probability of covid- disease (asymptomatic without known exposure), such as saliva testing or nasal/oral swabs instead of a nasopharyngeal swab. o asymptomatic covid- recovered resident  an asymptomatic resident who has previously tested positive for covid- and recovered does not need to be tested again within an week window of prior onset of symptoms. % agreement  an asymptomatic resident who has previously tested positive for covid- and recovered does not need to be tested again within a day window of prior onset of symptoms. % agreement  an asymptomatic resident who has previously tested positive for covid- and recovered does not need to be tested again. % agreement  a process should be identified for how facilities will actively track staff/ resident and visitor interactions to help facilitate appropriate contact tracing in the event of an outbreak investigation.  in the event of a pui or covid- positive staff or resident, a list of individuals with possible exposures should be able to be generated for the prior days (preferably days) within hours.  facilities should be aware and document individual resident and/or surrogate decisionmakers' care preferences regarding testing, cohorting, and isolation. it may be possible to cohort a certain group of individuals (ie recovered covid- positive patients who are asymptomatic) as long as the risks for other residents is not substantially increased.  new admissions should be placed in a dedicated area of the facility where appropriate isolation and contact precautions are maintained.  there should be a written cohorting and isolation plan for the facility. group activities  do not allow symptomatic residents with an unknown covid- status to participate in group activities in which proper infection control practices cannot be maintained.  make every effort possible to maintain social distancing, practice hand hygiene, and wear a mask during group activities.  try to facilitate indoor group activities in a well-ventilated space that allows for appropriate social distancing.  make an effort to offer residents the ability to join a risk-accepting group that could be cohorted together for activities, provided that the facility can manage them separately. non-medically necessary trips outside facility  residents must adhere to face coverings, hand hygiene, and social distancing during trips outside of the facility.  isolation o a resident who engages in a supervised outside visit with family or friends within the nursing home grounds, remains outside, and the visit does not involve close contact with covid+ individuals or symptomatic individuals would not be subject to isolation upon re-entry to the facility. o a resident that makes a trip outside the facility and is exposed to a covid+ individual, symptomatic individual or otherwise fails the screening questionnaire upon re-entry to the building would be subject to days of isolation. o a resident who engages in a visit with family or friends beyond the nursing home grounds, remains outside, and the visit does not involve close contact with covid+ individuals or symptomatic individuals would not be subject to isolation upon re-entry to the facility. % agreement  infection control o after a resident returns from an outside trip beyond the nursing facility grounds and prior to the resident resuming activities within a shared space, the resident should practice hand hygiene and have their wheelchair and belongings disinfected. o after a resident returns from an outside trip beyond the nursing facility grounds and prior to the resident resuming activities within a shared space, the resident should be bathed according to accepted practice with soap and have the clothes they were wearing laundered in a standard fashion. % agreement  leave of absence o the facility should have a discussion regarding risks/benefits with every resident and family who requests a leave of absence with a bed hold. this would include a discussion on hand hygiene, social distancing, and mask covering as well as subsequent isolation upon return to the facility if deemed necessary at the time of the visit based on level of community spread.  phase regression and facility wide restrictions should not be imposed after one isolated covid- case. rather, a prompt outbreak investigation should occur with further results triggering appropriate restrictions.  response to positive resident o once one nursing home resident tests positive for covid- , an outbreak investigation should include baseline testing of close contacts (to include roommate, neighboring rooms, and staff) o once one nh-onset case (case definition from cdc) has been identified within a facility, facilities should resume testing of asymptomatic hcp (staff) who have not previously tested positive. o during an outbreak investigation of a single case it is determined that there is nh-onset case on an isolated wing with isolated staff. this scenario would warrant testing of the entire wing staff and residents but not warrant facility wide testing or phase regression. o a new snf admission who has remained under isolation in a private room becomes symptomatic within days of admission and tests positive. in this situation, i would re-test and extend testing to close contacts. if no further positive cases, this situation would not warrant facility wide testing or phase regression. o a new or returning asymptomatic nursing home resident without a prior diagnosis of covid- and who has remained under isolation in a private room for days since admission tests positive during facility testing of asymptomatic residents. not during an outbreak investigation and there has been no exposure to a covid- positive patient or staff. in this situation, i would re-test the resident only. if subsequently negative and no further suspicion of covid- in the building, this scenario would not warrant facility-wide testing or phase regression. % agreement  response to positive hcp o an asymptomatic hcp tests positive on routine surveillance testing and is appropriately following work-restrictions. this scenario should prompt an outbreak investigation of close contacts but should not automatically warrant a phase regression as long as the outbreak investigation does not identify new cases among staff or residents who have not previously tested positive. o a symptomatic hcp tests positive. this would warrant testing of close contacts (staff and residents) of the immediate patient care area. o once one nursing home staff member tests positive for covid- , an outbreak investigation should include baseline testing of close contacts (to include roomate, neighboring rooms, and staff)  phase regression o during an outbreak investigation, it is determined that there is > nhonset cases in a building within a short time period (< days). there is concern for wide spread disease in the building. this scenario would warrant testing of the entire facility and phase regression with subsequent restrictions on visitors, communal dining, and group activities. immunity  a patient who has recovered from covid- disease and is weeks post onset of symptoms is likely not infectious to another individual as long as they have not developed new symptoms.  a cohort of asymptomatic individuals who have all recovered from covid- can safely be cohorted together.  antibody testing can be a surrogate marker of individual immunity but does not currently inform clinical practice; recovery from prior infection does. % agreement  covid- recovered individual o a currently asymptomatic individual who has recovered from covid- and is post weeks from onset of symptoms is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the patient is not contagious. % agreement o a currently asymptomatic individual who has recovered from covid- and is post days from onset of symptoms is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the patient is not contagious. % agreement o a currently asymptomatic individual who has recovered from covid- is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the patient is not contagious. % agreement  hairdressers, beauticians, hospice staff and other staff members who work within a nursing home should be included in the cdc definition of healthcare personnel (hcp) and follow the same guidelines regarding screening and testing.  hairdressers and stylists should be considered direct patient care staff and be subject to the same screening and work restrictions as other healthcare facility staff.  patients that are unable to adhere to social distancing or face coverings should be allowed to visit with family in a private isolated area as long as visitors were full ppe.  dialysis patients who leave the facility regularly for hemodialysis will remain under appropriate isolation and contact precautions and not mix with covid-, asymptomatic individuals. j o u r n a l p r e -p r o o f definitions i agree with the following modification of the formal cdc definition of healthcare personnel (hcp). "hcp include, but are not limited to, emergency medical service personnel, nurses, nursing assistants, physicians, technicians, therapists, phlebotomists, pharmacists, feeding assistants, students and trainees, contractual hcp not employed by the healthcare facility, and persons not directly involved in patient care but who could be exposed to infectious agents that can be transmitted in the healthcare setting (e.g., clerical, dietary, environmental services, laundry, security, beauticians and hairdressers, engineering and facilities management, administrative, billing, and volunteer personnel)". (added beauticians to cdc definition of hcp) nursing homes are ground zero for covid- covid- nursing home data covid- in nursing homes: calming the perfect storm coronavirus disease in geriatrics and long-term care: the abcds of covid- presymptomatic sars-cov- infections and transmission in a skilled nursing facility asymptomatic sars-cov- infection in belgian long-term care facilities presymptomatic transmission of sars-cov- amongst residents and staff at a skilled nursing facility: results of real-time pcr and serologic testing epidemiology of covid- in a long-term care facility in king county, washington cms announces new measures to protect nursing home residents from covid- centers for disease control and prevention. preparing for covid- in nursing homes html?cdc_aa_refval=https% a% f% fwww.cdc.gov% fcoronavirus% f -ncov% fhealthcare-facilities% fprevent-spread-in-long-term-care-facilities continued bans on nursing home visitors are unhealthy and unethical. the washington post amid the covid- pandemic, meaningful communication between family caregivers and residents of long-term care facilities is imperative families caring for an aging america essential family caregivers in long-term care during the covid- pandemic detrimental effects of confinement and isolation on the cognitive and psychological health of people living with dementia during covid- : emerging evidence. ltccovid, international long-term care policy network: care policy and evaluation centre (cpec) finding the right balance: an evidence-informed guidance document to support the re-opening of canadian nursing homes to family caregivers and visitors during the covid- pandemic we gratefully acknowledge the time and dedication of our delphi panel experts and other experts who have participated in this process, provided guidance, or critically appraised our manuscript. their names are listed below in alphabetical order. none received compensation, financial or otherwise, for their contributions. j o u r n a l p r e -p r o o f the facility should make every effort possible to secure a collection method that is least invasive and uncomfortbale if testing residents and staff with a low pretest probability of covid- disease (asymptomatic without known exposure), such as saliva testing or nasal/oral swabs instead of a nasopharyngeal swab. immunity q a currently asymptomatic individual who has recovered from covid- and is post weeks from onset of symptoms is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the patient is not contagious. immunity a currently asymptomatic individual who has recovered from covid- and is post days from onset of symptoms is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the patient is not contagious. % immunity a currently asymptomatic individual who has recovered from covid- is not considered infectious and should not be tested. if tested and the test returns positive, as long as the resident remains asymptomatic, it would not be considered a re-infection and the patient is not contagious. immunity q antibody testing can be a surrogate marker of individual immunity but does not currently inform clinical practice; recovery from prior infection does. key: cord- -wfuzk dp authors: meza, diana k.; broos, alice; becker, daniel j.; behdenna, abdelkader; willett, brian j.; viana, mafalda; streicker, daniel g. title: predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date: - - journal: biorxiv doi: . / . . . sha: doc_id: cord_uid: wfuzk dp serology is a core component of the surveillance and management of viral zoonoses. virus neutralization tests are a gold standard serological diagnostic, but requirements for large volumes of serum and high biosafety containment can limit widespread use. here, focusing on rabies lyssavirus, a globally important zoonosis, we developed a pseudotype micro-neutralization rapid fluorescent focus inhibition test (pmrffit) that overcomes these limitations. specifically, we adapted an existing micro-neutralization test to use a green fluorescent protein–tagged murine leukemia virus pseudotype in lieu of pathogenic rabies virus, reducing the need for specialized reagents for antigen detection and enabling use in low-containment laboratories. we further used statistical analysis to generate rapid, quantitative predictions of the probability and titer of rabies virus neutralizing antibodies from microscopic imaging of neutralization outcomes. using serum samples from domestic dogs with neutralizing antibody titers estimated using the fluorescent antibody virus neutralization test (favn), pmrffit showed moderate sensitivity ( . %) and high specificity ( . %). despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = . ), and for a second dataset of sera from wild common vampire bats (r = . , n = ), indicating repeatability. our test uses a starting volume of . μl of serum, estimates titers from a single dilution of serum rather than requiring multiple dilutions and end point titration, and may be adapted to target neutralizing antibodies against alternative lyssavirus species. the pmrffit enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. serology is a core component of the surveillance and management of viral zoonoses. virus neutralization tests are a gold standard serological diagnostic, but requirements for large volumes of serum and high biosafety containment can limit widespread use. here, focusing on rabies lyssavirus, a globally important zoonosis, we developed a pseudotype micro-neutralization rapid fluorescent focus inhibition test (pmrffit) that overcomes these limitations. specifically, we adapted an existing micro-neutralization test to use a green fluorescent protein-tagged murine leukemia virus pseudotype in lieu of pathogenic rabies virus, reducing the need for specialized reagents for antigen detection and enabling use in low-containment laboratories. we further used statistical analysis to generate rapid, quantitative predictions of the probability and titer of rabies virus neutralizing antibodies from microscopic imaging of neutralization outcomes. using serum samples from domestic dogs with neutralizing antibody titers estimated using the fluorescent antibody virus neutralization test (favn), pmrffit showed moderate sensitivity ( . %) and high specificity ( . %). despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = . ), and for a second dataset of sera from wild common vampire bats (r = . , n = ), indicating repeatability. our test uses a starting volume of . µl of serum, estimates titers from a single dilution of serum rather than requiring multiple dilutions and end point titration, and may be adapted to target neutralizing antibodies against alternative lyssavirus species. the pmrffit enables high-throughput detection of rabies virus neutralizing antibodies in low- biocontainment settings and is suited to studies in wild or captive animals where large serum volumes the last few decades have seen a surge in newly emerging human viruses that originate from wildlife ( of gfp fluorescence. next, the command "analyze particles" was used to count the total number of fluorescent cells per field (i.e. infected cells). this command grouped and counted the white neighboring pixels with a predetermined size area and circularity to be a single cell (size area: - circularity: . - . ), so counts corresponded to the number of infected cells. cell count outputs were converted into a standardized spreadsheet using a python version . . script (python core team, ) (script available in supplementary materials). at the end of the image processing step, each serum sample was described by data points consisting of the number of the fluorescent cells in each of fields (photographs) in the : and : dilutions (figure b) . all statistical analyses were executed in r (r core team, (scaled to improve model convergence) and ) the serum dilution level (two factors: : and : dilution). random slope and intercept terms were also considered for the date the test was run ("test date") to account for observed variation in the relationships between srig titers and infected cell counts across dates (figure ) and for the field number ( to ) within each microscope well ("field") to account for variation in cell counts between fields (the middle field, field , had more agglomerated cells in particular). to evaluate whether a simpler, single dilution test produced comparable results, the full dataset was then subset to the : dilution only. the binomial and log-normal models fit to this data subset included only the fixed effect of the virus-infected n a cell counts, but the random effects were identical to those explained above (i.e. test date and field). models were fit using the 'lme ' package (bates et al., ) . the 'predict' function was used to generate the predicted probability that a srig concentration or serum sample was seropositive (binomial model) and its corresponding rvna titer (log-normal model). predictions per field were averaged to obtain results per sample (figure c) with a threshold of > . iu/ml (positives) were used as the benchmark reference. to understand the variability of the pmrffit, replicate srig titer concentration curves were produced on different dates between / / and / / (hereafter "test " through "test "). as expected, the number of infected cells declined at higher srig titers in all replicates; however, the shape of the antibody decay curve varied across test dates (figure ) . at the . iu/ml srig concentration, infected cell counts were more dispersed in the : dilution than in the : dilution, as indicated by higher interquartile range (iqr) within each of the test dates. across all the srig concentrations in all test dates (n = ), . % of the count comparisons were less dispersed in the : dilution suggesting this dilution could be more precise for downstream statistical analysis (si ). binomial glmms accurately predicted seropositive and seronegative srig concentrations (figure ) . the best random effects for the binomial model included a random slope and intercept for test date ( table ) . the models built with the : dilution data only ("one-dilution model") and from both the : and : dilution data ("two-dilution model") had equivalent specificity ( %), but the one- dilution model was more sensitive ( % versus . %, figure a, b) . furthermore, the two-dilution binomial model failed to correctly predict the seropositive controls on out of the test dates, confirming improved performance of the one-dilution model (figure b) . the log-normal glmms gave repeatable predictions of rvna titers from the datasets generated through our protocol across test dates (figure c) . the best log-normal model included a random intercept and slope for test date. although the most complex model had the lowest aicc, the simpler model (without the random intercept of field) had a Δaicc < ( table ) . observed and predicted srig titers were highly correlated for both the one and two-dilution models (r = . , figure c). when comparing test dates (i.e. one-to-one comparison between correlations of the one-dilution and the two-dilution model from the same test dates), the correlation coefficients were similar, suggesting the simpler one-dilution model is sufficient for titer prediction (figure d) . the most commonly applied serological tests to detect rvna titers challenge a range of serial dilutions of serum with infectious rv. this process is labor-intensive and requires laboratory capacity to grow large quantities of pathogenic rv. here, we provide an alternative serological framework that uses a combination of digital image analysis and statistical analysis to estimate the presence and titer of rvna from a single dilution using only . µl of serum. the pmrffit differs from other lyssavirus neutralization tests in several key aspects. it uses an mlv(rg) pseudotype rather than pathogenic rv, allowing the pmrffit to be performed in any low- containment laboratory with appropriate cell culture and microscopy facilities. the addition of gfp expression is significant, since it removes the need for fitc-conjugated antibody (reducing reagent costs) and the fixation and staining steps used in traditional rffit or favn. one potential drawback of using gfp expression to measure infectivity is the prolonged neutralization period ( h versus h rffit and h favn) required to gain sufficient fluorescence for image processing (aubert, ; smith et al., ) . longer neutralization requirements ( h) were also required in a favn modification using a gfp expressing recombinant cvs- -egfp but did not alter results relative to the test run with cvs- (xue et al., ) . fortunately, extended incubations are unlikely to alter neutralization outcomes since mlv(rg) pseudotype is replication incompetent, preventing infection of additional cells during the incubation (temperton et al., ) . the pmrffit also uses an imaging pipeline that combines systematic photography of microscope fields with automated digital image processing to count infected cells. microscopy in neutralization tests is time consuming and presents challenges for interlaboratory comparisons due to multiple sources of variation, especially those that affect the manual readout (e.g. laboratory user, manual pipetting, uneven cell monolayer) ( the pmrffit standardized approach minimizes these sources of error while potentially reducing microscope operator time. moreover, the imaging process generates traceable and permanent electronic records of the raw data, eliminating the need to manually digitize records of field counts. several investigators have previously incorporated image processing into rv neutralization tests. to count pixels using a microrffit but did not make full use of the quantitative nature of imaging data to obtain rvna titers and used pathogenic rv rather than a viral pseudotype. a final distinction is that instead of scoring microscope field or wells as virus positive or negative, the pmrffit predicts serological status and rvna titer from infected cell counts in a single serum dilution using statistical modelling. the efficacy of this approach highlights the value of historically underutilized quantitative data on cellular infectivity for lyssavirus serology. model selection indicated substantial day-to-day variation in the srig dilution series. this was unsurprising, since virus neutralization tests are biologically dynamic systems that can be influenced by many factors (e.g. variability in the humidity of the incubator, technical manipulation, light condition of the microscope, variability in gfp expression in the cells) (briggs et al., ; hammami et al., ; kostense et al., ) . since our statistical approach handles this variability through the random effect of test date, the pmrffit is best suited for large numbers of serum samples that require testing to be carried out across multiple batches. however, performance is only marginally reduced when running single models for each test date, implying the pmrffit may still be useful when fewer samples are available for testing (see si , ). surprisingly, fitting the glmms to data from a single : dilution of srig predicted both seropositivity and rvna titer more accurately than models fit to both the : and : dilutions. the reduced performance of the two-dilution model reflected higher variability in the : dilution compared to the : dilution, as evidenced by greater iqr values (si ). ultimately, this variability likely reflects both higher stochasticity in infected cell counts at lower serum concentrations and pipetting error. regardless, the ability to detect low titers (< . the authors declare no conflict of interest. perform the cell count of the fluorescent cells to construct a database to fit the statistical models. c) construction of the statistical models with two different types of prediction. srig data to fit models~ hrs fields/well antibodies to rabies virus in terrestrial wild mammals in native rainforest on the north coast of são paulo state, brazil practical significance of rabies antibodies in cats and dogs rabies virus exposure of brazilian free-ranging wildlife from municipalities without clinical cases in humans or in terrestrial wildlife mumin: multi-model inference measurement of rabies-specific antibodies in carnivores by an enzyme-linked immunosorbent assay fitting linear mixed- effects models using lme temporal and spatial limitations in global surveillance for bat filoviruses and henipaviruses the use of pseudotypes to study viruses, virus sero-epidemiology and vaccination resolving the roles of immunity , pathogenesis and immigration for rabies persistence in vampire bats supporting online material contents : s seroprevalence data s estimation of seasonal birth rate s methods for parameter estimation use of a transient assay for studying the genetic determinants of fv restriction estimating time of infection using prior serological and individual information can greatly improve incidence estimation of human and wildlife infections a comparison of two serological methods for detecting the immune response after rabies vaccination in dogs and cats being exported to rabies-free areas rabies surveillance in wild mammals in south of brazil. transboundary and emerging diseases development 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rabies: updates and call for data who expert consultation on rabies, third report. world health organization technical report series virus neutralising activity of african fruit bat (eidolon helvum) sera against emerging lyssaviruses a robust lentiviral pseudotype neutralisation assay for in-field serosurveillance of rabies and lyssaviruses in africa investigating antibody neutralization of lyssaviruses using lentiviral pseudotypes: a cross- species comparison generation of recombinant rabies virus cvs- expressing egfp applied to the rapid virus neutralization test a pneumonia outbreak associated with a new coronavirus of probable bat origin mixed effects models and extensions in ecology with r tables table . random key: cord- -qwe ne q authors: poritz, mark a.; lingenfelter, beth title: multiplex pcr for detection and identification of microbial pathogens date: - - journal: advanced techniques in diagnostic microbiology doi: . / - - - - _ sha: doc_id: cord_uid: qwe ne q multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. these tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. the technology underlying these different systems is reviewed here with a special focus on the biofire filmarray® platform. the literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. finally, some improvements to this technology that should appear in the next few years are discussed. these include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests. over the last decade, a number of manufacturers have developed multiplexed in vitro diagnostic (ivd) platforms that can detect the nucleic acid signatures of many of the organisms responsible for infectious disease. some of these testing platforms offer limited test menus (i.e., influenza a, influenza b, and rsv), while others are designed to detect a more comprehensive set of potential pathogens that can cause a particular infectious disease syndrome (e.g., respiratory, gastrointestinal, sepsis, meningitis) [ ] [ ] [ ] . this chapter will describe fda-cleared and/or ce-marked multiplex assays that are designed to detect a comprehensive set of pathogens associated with a particular infectious disease syndrome (≥ assays/ test). these include the biofire (salt lake city, ut) filmarray ® system [ ] , the genmark (carlsbad, ca) esensor xt- ® [ ] and eplex® [ ] , and the luminex (austin, tx) xtag® [ ] , nxtag ® [ ] , and verigene® systems [ ] . in addition to being comprehensive with respect to pathogens responsible for a particular syndrome, these multiplex panels offer the advantage of superior test sensitivity and specificity. many of these panels have been designed to be easy-to-use, allowing molecular testing to be performed in moderate or low complexity settings and eliminating barriers that prevented many laboratories from being able to perform molecular assays on-site. another important benefit of multiplex panel is the fast time to result. molecular multiplex tests require hours to perform instead of the days required for culture-based methods. these systems differ in particular details (the exact turnaround time, sample throughput, cost per sample, and number of target pathogens detected). these differences are due to the underlying technologies used for the detection of the pathogen nucleic acid. however, all these systems share the common attribute that the incremental cost of each additional assay in the test cartridge (in materials, labor, and quality control (qc) testing) is small compared to the total manufacturing costs for the disposable. this has enabled ivd manufacturers to develop broad test panels that include organisms which have not been a part of standard testing protocols because of the technical limitations of existing methods. nonetheless the availability of syndromic infectious disease panels poses hard questions for clinicians and the healthcare system overall: does the wealth of information in a comprehensive test improve the treatment of an individual patient, and how can the economic value of this improved treatment be measured? commercially available fda-cleared multiplex nucleic acid-based tests for infectious agents include systems from luminex, genmark, and biofire (now a subsidiary of biomérieux) ( table ) . at present, all such systems combine the sequential steps of: . nucleic acid purification from the appropriate human sample matrix (e.g., nasal swab, blood or blood culture, stool) . cdna synthesis (reverse transcription) to convert viral rna to dna, if necessary . multiplex pcr to amplify molecules of the pathogen nucleic acid . specific detection of the expected amplicons to confirm that the correct target nucleic acids have been identified the different systems vary mainly in whether the nucleic acid purification steps are integrated into the same cartridge that is used for amplification (verigene, eplex, and filmarray) and in how the specific detection of amplicon is achieved. the luminex xtag and nxtag systems use a fluorescent signal generated after hybridization of the amplicon to fluorescently encoded bead arrays to detect a specific amplicon [ , ] . the verigene system uses hybrid capture of the amplicons on a microarray with detection by gold nanoparticle probes [ ] . the genmark esensor xt- and the eplex systems use electrochemical detection of the target amplicon hybridized to a specific gold microelectrode [ ] . the filmarray system is described in more detail below. the filmarray pouch and chemistry the filmarray system performs sample-to-answer multiplex nucleic acid testing for infectious disease. to accomplish this, the filmarray pouch ( fig. ) integrates all of the steps of nucleic acid purification, nested multiplex pcr amplification, and automated data analysis into a closed system [ ] . the pouch is created by welding two sheets of plastic film together with heat in such a fashion that fluid can move between the working areas of the pouch via channels left in the plastic. a hard plastic fitment attached to the film (indicated in fig. b) provides the enzymes and buffers needed to perform the biochemical reactions in the pouch. other reagents (# , # , and # in fig. a ) are inserted between the film layers during manufacture of the pouch. the filmarray reagents are lyophilized in the pouch, and the pouch is stored under vacuum before use. this benefits the end user in two ways. first the freezedrying process stabilizes the pcr reagents so that the pouch has a shelf life, at ambient temperature, in excess of year -which simplifies the logistics of acquiring and storing the pouches. second vacuum storage ensures that the wells of the fitment are also under vacuum. thus the user does not need to control the volume of hydration fluid or sample that is injected into the pouch -which simplifies the steps needed to load a pouch. lysis and homogenization of bacteria, spores, and viruses occur in the filmarray pouch by means of vigorous agitation in the presence of zirconium beads (# in fig. a ) and a denaturing buffer. dna and rna in the sample are purified by binding to silica magnetic beads (# in fig. a) , the beads are washed to remove proteins and other pcr inhibitors, and the nucleic acids are eluted into a buffer compatible with reverse transcription and pcr [ ] . the eluted material hydrates a pill (# in fig. a ) that contains all of the primers needed for reverse transcription (for rna targets) and first stage pcr. the primers in this pill are specific to each pathogen target (assay) contained in the pouch. the filmarray system performs nested, multiplex pcr in two stages (fig. ) . reverse transcription and first stage pcr (pcr ) are performed in the same reaction volume and in a multiplex format, combining primer sets for all assays for a filmarray panel in one mix. following pcr amplification, the reaction is diluted approximately -fold to reduce the concentrations of the outer primers, nonspecific products, and first-stage pcr chemistry. the diluted reaction is then combined with a fresh pcr master mix and flooded over a -well array, where a second stage pcr occurs (pcr ). each well of the array contains assay-specific primers that anneal within the first-stage outer amplicon. at the end of pcr , a dna melt curve analysis of the amplicons is performed using a nonspecific dna-binding dye, lcgreen® plus [ ] , that fluoresces in the presence of double-stranded dna. the presence of a specific melt curve with tm (melting temperature) in the range predicted for that specific amplicon confirms the presence and identity of the products made in each well. the mechanics and chemistry of the filmarray pouch have been described in greater detail elsewhere [ ] . here we highlight some of the features of the system that have contributed to the robustness of the test. the combination of a denaturing lysis buffer and "bead beating" with zirconium beads has been shown to lyse organisms and release intact total nucleic acid (dna and rna) from spores [ ] as well as from the cerebral spinal fluid (csf), stool, blood culture media, and whole blood. the nested pcr of the multiplex chemistry makes the filmarray test remarkably resistant to pcr inhibitors that may remain after nucleic acid purification. even modest levels of amplification in first-stage pcr can still be detected as an amplicon in the inner, nested product of pcr . the dilution step following the firststage amplification reduces the complexity of the input material to the second-stage reaction enough that, in most cases, the dna-binding dye detects the presence of a single amplicon in the reaction (the melt curve analysis serves as an additional filter for the correct product). the filmarray pouch and instrument contribute to the sensitivity of the overall system in several important ways. first the nucleic acid sample purification starts with a relatively large volume of the sample ( μl for the rp and gi panels, μl for the bcid), and, nominally, all of the nucleic acid purified from this volume is delivered to the combined reverse transcription -first-stage pcr reaction. unlike some benchtop protocols, there is no dilution from the purified nucleic acid into an rt step and a second dilution into a pcr. secondly the pouch is controlled by pneumatic actuators (described below) that can move liquid between blisters of the pouch in seconds. this minimizes the time during which nucleic acid could be degraded or pcr primers could bind to an incorrect dna or rna target and thus generate specific "nonspecific" amplicons. to the same end, the filmarray pouch achieves a true mechanical hot start. in both the first stage and second stage pcrs, the primers do not come in contact with the dna polymerase/mg, dntp mixture until both components are at or above the temperature at which polymerization will take place. this minimizes the formation of primer dimers, and higher-order multiplex primer structures in the first-stage pcr, which compete with the correct amplicons for pcr reagents. this enhances the specificity of the amplification reactions and thus increases the sensitivity of the individual pcr assays. all filmarray pouches have at least two internal controls that demonstrate the proper functioning of the pouch. one is a small amount of synthetic dna spotted onto the second stage pcr array along with primers to amplify this target. this "pcr " control only monitors the function of the second stage pcr. a more important control for pouch function is generated by freeze-drying a small number of cells of the yeast schizosaccharomyces pombe into the well of the pouch fitment that receives the sample. nucleic acid purified from these yeast cells must pass through all the steps of the pouch. outer primers in the first-stage pcr and inner primers spotted onto the second-stage pcr array are designed to amplify a spliced messenger rna from the s. pombe cells (in the filmarray bcid pouch which does not contain reverse transcriptase, the s. pombe target is a genomic dna sequence). biofire has shown during the development of several different pouches that artificially induced failure modes that prevent detection of a pathogen organism in a sample also prevent detection of the yeast control. the filmarray instrument controls the movement of liquid through the pouch using pneumatically-actuated bladders and seals that force liquid from a pouch blister or prevent liquid from leaving a blister, respectively. the hydrated reagents in the pouch fitment are introduced into the pouch blisters via additional pneumatically actuated pistons. the amplification reactions are thermocycled using inch square peltier devices situated adjacent to the first-and second-stage pcrs (# and # of fig. a , respectively). to detect the melting of the second-stage pcr amplicons, a blue led illuminates the array, and a camera with a filter to detect green light observes the signal generated by the dna-binding dye lcgreen® plus. multiplex panels are particularly attractive to clinicians because they provide a comprehensive and accurate test result in a short period of time, and the test panels have been designed to match the clinical syndrome (i.e., respiratory infection, infectious gastroenteritis). however, given the increased cost of these tests, it is important to demonstrate their impact to patient management and their cost-effectiveness. it is intuitive to believe that a rapid, accurate, and comprehensive diagnostic test should improve patient management by shortening the time to the most effective therapy, by preventing inappropriate therapy (especially empiric antimicrobials), by reducing additional diagnostic testing (e.g., imaging studies), by improving the use of infection control measures, and by reducing patient length of stay. of particular importance, these tests can reduce the unnecessary use of empiric antimicrobials by reducing the time to pathogen-directed therapy. use of broad-spectrum antibiotics for patients with serious illnesses and the inappropriate use of antibiotics in the outpatient setting "just in case" are important drivers of antibiotic resistance which is one of the major healthcare threats of our time. in this section, we will review what is known about the clinical utility and cost-effectiveness of these multiplex panels. because the clinical implication for each syndromic panel is different, the discussion is presented by syndrome. currently there are three vendors with multiplex respiratory panels that are both fda-cleared and ce marked (biofire diagnostics, salt lake city, utah; luminex, austin, texas; and genmark, san diego, california) and several more that are ce-marked (seegene, seoul south korea; curetis, holzgerlingen, germany, fast-track diagnostics, sliema, malta). these panels include assays for several viral pathogens (e.g., influenza, respiratory syncytial virus (rsv), human rhinovirus, parainfluenza viruses, adenovirus, coronaviruses, etc.) and some also include selected bacterial targets (e.g., mycoplasma pneumoniae, bordetella spp, legionella pneumophila). all of the fda-cleared test are limited to testing nasopharyngeal swab (nps) samples, while several of the ce-marked tests include a larger range of respiratory sample types (e.g., bronchoalveolar lavage, sputum, etc.). prior to the availability of multiplex respiratory panels, testing for viral respiratory pathogens relied on viral culture, direct fluorescent antigen (dfa) testing, enzyme immunoassays (eias), and traditional pcr assays. while viral culture was the gold standard, it has several limitations, including that it is a complex test requiring highly skilled laboratory workers to both set up the test and interpret the results, it is slow (taking days to complete), and only a limited number of human pathogens can be grown in viral cultures. dfa tests can be performed directly on the patient sample and can have a fast turnaround time; however, these tests are also technically complex, and the range of pathogens is limited. eia assays can be performed in a variety of ways and are used for rapid antigen tests. rapid antigen tests are fast and simple to use but are known to have poor test sensitivity and a limited test menu. traditional pcr assays are highly sensitive and specific; however, they are complex and require highly trained laboratory staff and specialized laboratory facilities. in addition, each test is ordered independently placing a large burden on the ordering clinician to select the correct test or to order multiple individual tests. due to their complexity, these tests are commonly sent to specialized reference laboratories which can increase cost and slows the time to result. the introduction of multiplex respiratory panels has allowed for comprehensive testing (ability to test viral pathogens that do not grow in cell culture and the ability to simultaneously test for bacterial and viral pathogens) in a shorter time frame. the easy-to-use systems allow the testing to be performed by laboratory workers without specialized molecular skills and in laboratories without specialized equipment and facilities. these systems allow testing to be performed closer to the patient and therefore further reduce the time to test result by reducing the need to transport samples and eliminating the delays associated with batch testing. multiplex respiratory panels have the potential to improve patient management and lower overall healthcare costs by improving use of influenza antivirals, reducing inappropriate use of antibiotics and antivirals, reducing use of healthcare resource (e.g., additional laboratory or imaging procedures), informing appropriate infection control practices, and reducing length of hospital, emergency department, and intensive care unit (icu) stay. several studies have evaluated the effect on patient and healthcare outcomes linked to the use of a multiplex respiratory panel. xu et al. [ ] showed that replacing dfa testing with on-demand use of the filmarray rp for children presenting to the emergency department (ed) resulted in dramatic reductions in test turnaround time ( vs . h), timely (defined as within h of discharge from the emergency department) administration of oseltamivir for % of patients testing positive for influenza, effective use of cohorting for admitted patients, and a potential saving of h of ed boarding time. similarly, in a pre-/post-intervention study of pediatric patients admitted through the ed, rodgers et al. [ ] compared several outcome measures when the filmarray rp replaced the use of three clinicianordered traditional pcr tests (prodesse assays for, flua/b/rsv, piv , , , and hmpv). the study demonstrated that use of the filmarray rp resulted in a significant increase in the number of patients with positive test results ( . % vs . %, p < . ) and a % reduction in time to result ( . vs . h, p < . ) when compared to use of traditional pcr tests. these improvements lead to a mean reduction in length of hospital stay of . days for patients with positive test results, reduced duration of antibiotics for patients with positive test results ( . vs . days, p < . ) or when results were reported in < h ( . vs . days, p < . ), and an overall reduction in healthcare costs of $ /patient. another study of pediatric patients reported significant reductions in the duration of antibiotic use ( vs days, p < . ), use of chest radiographs ( % vs %, p < . ), and an increase in appropriate use of isolation measures [ ] . similar findings have been observed in studies of adult patients. brendish et al. [ ] performed a prospective randomized study of adult patients presenting to the emergency department (ed) with respiratory symptoms over two respiratory seasons. in the control arm, patients were tested for respiratory viruses at the clinician's discretion using nine traditional pcr assays performed at a reference laboratory. in the intervention arm, all patients were tested with the filmarray rp, and testing was performed in the ed. the study demonstrated the expected increase in pathogen detection ( % vs %, p < . ) and reduction in time to result ( . vs . h, p < . ) but failed to show the expected reduction in the proportion of patients that received antibiotics ( % vs %, p = . ). however, there was an increase in the proportion of patients that received a short course of antibiotics (< h, % vs %, p = . ) especially for patients with positive filmarray rp test results. patients in the intervention group also had a mean reduction in hospital length of stay of . days ( . vs . d, p = . ) with the shortest length of stay observed in patients with positive filmarray rp results. the use of influenza antivirals was the same in both groups ( % vs %, p = . ); however, the intervention group had a significant increase in the number of influenza-positive patients that received influenza antivirals ( % vs %, p = . ) and a reduction in the use of antivirals for patients that were influenza-negative ( % vs %). in another study evaluating adult patients with a positive influenza result on a multiplex respiratory panel, rappo [ ] reported a significantly lower odds ratio for hospital admission (p = . ), a reduced length of stay (p = . ), reductions in antimicrobial duration (p = . ), and a reduction in the number of chest radiographs (p = . ). there is currently only one study evaluating the use of multiplex panels in an outpatient setting. greene et al. evaluated the difference in use of antibiotics and antivirals for adult outpatients tested with the filmarray rp that were [ ] positive for influenza, [ ] positive for non-influenza pathogen, or [ ] negative for all pathogens [ ] . they observed significant increases in the use of influenza antivirals ( . % vs . - . %, p < . ) and reduced use of the antibiotics ( . % vs . - . %, p = . ) for individuals with a positive result for influenza. however, detection of non-influenza viral pathogens did not lead to a reduction in the use of antibiotics when compared to those with no pathogen detected ( . % vs . %). the authors suggest that either influenza testing alone is more cost-effective for this patient population or that additional education and/or antibiotic stewardship is needed to drive appropriate use of antibiotics in the outpatient setting. blood culture panels are designed to test positive blood cultures with the aim to provide a faster time to organism identification. in addition, these panels include assays for selected antibiotic resistance genes providing important information to guide antibiotic therapy. there are currently three vendors with multiplex blood culture panels that are both fda-cleared and ce-marked (biofire diagnostics; luminex and accelerate diagnostics, tucson, arizona), while genmark (san diego, california, usa) and curetis (holzgerlingen, germany) have panels that are ce-marked. these panels include assays for gram-positive bacteria, gram-negative bacteria, yeast, and antibiotic resistance markers or, in one case (accelerate pheno™ system), antibiotic susceptibility test results. the curetis unyvero bcu blood culture application cartridge® panel is the most comprehensive (with identification of ~ bacteria and resistance markers) followed by the biofire filmarray blood culture identification panel (identification of ~ bacteria and resistance markers). the genmark eplex and luminex verigene systems provide separate panels that are specific to gram-positive bacteria, gram-negative bacteria, or yeast with selection of the appropriate panel determined by blood culture gram stain. all of these tests can be used with a variety of different blood culture media and blood culture systems. prior to the availability of multiplex blood culture panels, pathogen identification was performed using classic standard culture-based systems with phenotypic (or maldi-tof) identification followed by traditional growth-based antimicrobial susceptibility testing. these tests are the gold standard methods and are very reliable; however, they suffer from a slow time to result ( - days after the positive blood culture) and technical complexity. molecular assays for specific pathogen identification, such as staphylococcus aureus and enterococci, have been in use for some time and have shown improvements in patient outcomes [ ] [ ] [ ] [ ] . another method that reduces time to organism identification is using maldi-tof to identify bacteria directly from minimally processed blood cultures without the need to subculture to agar plates. the maldi-tof identification is very comprehensive, and the reduced time to bacterial identification has also been shown to improve patient outcomes [ , ] . while individual molecular assays and maldi-tof identification have both been shown to improve patient outcomes, they are both technically complex and require specialized skills. as a result, these test methods are typically performed during standard laboratory working hours and are typically not used on night shifts when staffing is limited. molecular multiplex panels offer the advantage of a fast time to organism identification along with ease of use. all of the fda-cleared and ce-marked panels use unprocessed blood culture media and provide identification results within - h of test initiation. due to the ease of use, these panels can be used by laboratory staff without specialized molecular biology skills; however, because these panels do not identify all possible pathogens, the results must be interpreted in conjunction with the blood culture gram stain, and traditional culture and sensitives must still be performed. furthermore, appropriate adjustments to antimicrobials rely on proper test interpretation and a good understanding for the local patterns of antimicrobial resistance (e.g., antibiogram). treatment adjustments should be based on local guidelines developed by an antimicrobial stewardship program (asp) team with an in-depth understanding of the capabilities of the test being used, the local antibiogram, and the local patient populations. as with the individual molecular assays and the maldi-tof identification, numerous studies have shown that use of multiplex molecular blood culture panels dramatically reduces the time to organism identification [ ] [ ] [ ] [ ] which drives more appropriate pathogen-directed therapy. pathogen-directed therapy includes antibiotic escalation (the addition or change of dose when the current therapy is ineffective against the identified organism) and antibiotic de-escalation (discontinuation of unnecessary empiric antibiotics). a prospective randomized study conducted at the mayo clinic showed that antibiotic escalation occurred more quickly with or without real-time asp oversight ( h with bcid and asp, h with bcid only, and h without bcid or asp, p = . ); however, optimal antibiotic de-escalation requires oversight by an asp ( h with bcid and asp, h with bcid only, and h without bcid or asp, p < . ) [ ] . the finding that multiplex molecular blood culture panels paired with an asp results in a faster time to optimal antibiotic therapy (most narrow effective therapy) has been confirmed in several additional studies [ , ] . the use of molecular multiplex blood culture panels has also been shown to reduce unnecessary treatment due to contaminated blood cultures [ , ] . reducing the use or duration of unnecessary antibiotics is important to reducing the incidence of antibiotic resistance. the cost of molecular multiplex blood culture panel and the fact that they do not replace existing testing have been raised as reasons to not use them; however, studies of the overall healthcare cost prove the panels to be cost neutral [ ] [ ] [ ] or to reduce overall healthcare cost [ , , [ ] [ ] [ ] [ ] . while the evidence is strong that multiplex panels dramatically reduce time to organism identification and time to optimal antibiotic therapy, the evidence is inconsistent with regard to reductions in patient mortality and length of hospital stay, mostly likely because the management of patients with sepsis is complex and multifactorial. however, a recent meta-analysis [ ] of studies using rapid molecular methods to test positive blood cultures found a small but statistically significant reduction in patient mortality when the results were used as part of an asp (or . , % ci . - . ) but not when used outside of an asp (or . , % ci . - . ). the improvements were seen for patients with gram-positive (or . , % ci . - . ) or gram-negative bacteremia (or . , % ci . - . ), but not for patients with candidemia (or . % ci . - . ). the study also found that time to effective therapy decreased by a weighted mean difference of − . h ( % ci − . to − . ) and that length of hospital stay decreased by − . days ( % ci − . to − . ). currently there are three vendors with multiplex gastrointestinal panels that are both fda-cleared and ce-marked (biofire diagnostics; luminex, and bd, sparks, maryland) and several more that are ce-marked (seegene, soul, south korea; mobidiag, finland; serosep, limerick, ireland). some of these panels include assays for bacteria, viruses, and parasites in one test (filmarray gi panel, biofire diagnostics; luminex ggp, luminex; verigene enteric pathogens test, luminex), while others provide separate panels for bacterial, viral, or parasitic pathogens (allplex™, seegene; bd max®, bd; amplidiag®, mobidiag; entericbio® realtime dx, serosep). most tests are performed with raw stool samples or stool in transport media. the use of fecal swabs with transport media is also common, and direct testing of rectal swabs is desirable. current testing for infectious gastroenteritis includes many tests (stool culture, ova and parasite examination (o&p), enzyme immunoassays) that are technically complex and suffer from low diagnostic yield. the gold standard for stool pathogen testing is stool culture; however, stool culture has low diagnostic yield, is technical complexity, and has a long time to result. the yield for stool cultures is reported to be between . % and . % with a cost per positive result of $ to $ [ ] . another commonly ordered test is o&p, which requires the collection and testing of three different stool samples. this method is also known to be technically difficult, to have low sensitivity, to be improperly used, and to have a low diagnostic yield of . % [ ] . as a result of the low diagnostic yield, clinicians often order multiple tests for the same stool sample, or perform testing sequentially until a causative pathogen is identified. as an example, a study conducted at a children's hospital found that a median of three tests (range - ) were ordered per stool sample [ ] . to make matters worse, several studies have shown that clinician test ordering practices for gastroenteritis are problematic, in part due to the complexity of which pathogens are covered by what test [ , [ ] [ ] [ ] . the use of culture-independent molecular multiplex panels has increased the diagnostic yield for stool testing due both to increased test sensitivity and an expanded test menu. studies using the filmarray gi panel identified a pathogen in - % of stool samples [ , , ] . some of the assay requires specialized molecular laboratories and personnel (bd max, luminex ggp, allplex); however, some are designed to be simple to use (filmarray gi panel, verigene enteric panel) and to provide a fast time to result (as little as h from test initiation). while these tests have the benefits of offering a comprehensive and accurate result in a relatively fast time period, the impact to patient care is largely unknown; however, one recent pre-/post-implementation study highlighted several important improvements when the filmarray gi panel was used to test pediatric and adult inpatients [ ] . these included an increase in diagnostic yield from . % to . % and an improved time to result from a mean of . h to . h when compared to traditional clinician ordered tests. when compared to a matched historical control group, implementation of the filmarray gi panel led to a reduction in the number of additional stool tests ( . vs . , p = . ), a trend toward shorter duration of antibiotics ( . days vs . day, p = . ), significantly fewer imaging studies ( . vs . , p = . ), and a reduction in the length of hospital stay after sample collection ( . days vs . days, p = . ). reduced length of stay was more pronounced for the adult population ( . days vs . days, p = . ). recent studies have also shown that these tests have important advantages for infection control. in a recent retrospective study, the filmarray gi panel was used to test frozen stool samples that had previously been tested for rotavirus and c. difficile for infection control purposes [ ] . the study showed that % of the samples contained pathogens that should have required infection control measures, including norovirus, rotavirus, and c. difficile. of these patients, % were under no or inadequate contact precautions, for a total of patient days. conversely . % of the patients with negative results by the filmarray gi panel were unnecessarily placed under contact precautions for a total of patient days. this study illustrates that without a rapid comprehensive test result, contract precautions are not rationally applied, leading to both an increased risk of nosocomial infections and unnecessary costs associated with inappropriately applied contact precautions. these are important factors when considering the care of patients in hospitals and in long-term care facilities. use of the luminex xtag gastrointestinal pathogen panel (gpp) has been compared with conventional laboratory testing for hospitalized patients and was found to be cost-effective because the increased cost of the laboratory testing was more than offset by the cost saving for elimination of unneeded contact precautions. importantly, the cost savings was directly related to the time to test result [ ] . the national institute for health care excellence (nice) in the uk recently published a very comprehensive health economics assessment of molecular multiplex panels [ ] . they reported that there was considerable uncertainty in their models; however, the luminex ggp panel was determined to be cost-effective for use in community-acquired and traveler diarrhea and both the filmarray gi panel and the luminex ggp were found to be cost-effective for use in inpatients with diarrhea. these models will be updated as new information (such as the recent study by beal [ ] ) becomes available. further clinical utility studies will highlight the importance of the different pathogens detected by the multiplex panels. however, independent of this work, continuing improvements to these ivd systems are likely to increase their value in the clinical infectious disease setting. in contrast to previous generations of infectious disease ivd platforms which used cell culture, microscopy, or immunoassay technology, the current generation of multiplex systems are all highly automated and computerized [ , [ ] [ ] [ ] ] . this opens the possibility of exporting the results of a patient test directly to an internet (or "cloud") database. a pilot version of such a system has been achieved with development of filmarray trend [ ] . trend aggregates result from geographically dispersed clinical laboratories and displays the results on a website (www.syndromictrends.com) in close to real time, resulting in a form of infectious disease "weather map." the pilot project summarized the respiratory pathogen results for the filmarray rp from > , patient samples acquired over years ending in july from clinical laboratories in the united states (fig. ) . similar to social media-based disease reporting systems, the data is syndrome-based [ ] . however, a unique feature of the trend dataset is that analysis is pathogen-specific. the filmarray rp patient test results demonstrate that a number of viruses (rsv, hmpv, piv, and cov) show seasonal occurrence that is similar to influenza and thus can be confused with influenza when a symptomatic diagnosis of influenza-like-illness is made. this has important implications for treatment of influenza and for determining the efficacy of influenza vaccination and thus emphasizes the value of multiplex testing for respiratory symptoms. the filmarray trend data also show that % of the filmarray rp tests detect the presence of two or three pathogens in a single sample. the importance of this result for patient treatment is not currently clear. clinical studies that focus on patients presenting with more than one pathogen are needed. data from the filmarray gi panel are also available at the www.syndromictrends.com website. over time, additional filmarray ivd panels will be added to trend, thus enabling the tracking of the pathogens that those panels detect. in the us fda cleared the filmarray rp-ez panel [ ] . this panel has clinical laboratory improvement act (clia)-waived status and thus can be used in settings close to the patient including low-complexity outpatient settings. in other work, the time to result for the rp panel has been decreased from min for rp v . to min for the rp panel [ ] . speed, ease of use, and a comprehensive test menu are all critical features if the possibilities of point-of-care syndromic testing are to be fully realized [ ] . in the longer term, additional simplification of the test setup procedure as well as reductions in the time to result should further expand the number of outpatient settings able to use multiplex testing. the data from farrar and wittwer [ ] on "extreme" pcr conditions (cycle times below s) suggest that reductions in the time to result are limited by the instrument and not by the chemistry and that substantial improvements are still possible. as noted earlier, the cost of multiplex diagnostic systems is not driven by that of the primers needed for each assay, so the number of assays in a test is limited by assay format and the ability to separate the signal for each analyte. the depth of multiplex achieved in pcr multiplexes for infectious disease has steadily increased from the earliest, manually performed multiplexes, compared to the those being developed for the automated systems of today. the point will soon be reached in which the feasible number of assays in a test begins to exceed the number of distinct pathogens that need to be tested for in any particular syndrome. however, there are situations (e.g., hiv drug resistance testing or hpv serotyping) where the ability to detect a limited number of point mutations would add great value to the test result. there is also great interest in the direct detection of sepsis pathogens from blood because the hours saved by not having to culture the bacteria reduces the risk of incorrect antibiotic treatment. with a combination of direct enrichment of the bacteria from the blood and careful attention to removing endogenous bacteria from the test manufacturing process, it should be possible to achieve the necessary sensitivity to detect bacterial pathogens directly from blood, without the time and labor of culturing the sample. an infectious disease society of america policy paper from [ ] made a number of recommendations for the key characteristics of future infectious disease ivd tests. the current generation of multiplex tests already meets many of these goals (direct testing from easily accessible sample types, able to rule out infection with high 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gastroenteritis in hospitalised patients integrated multiplex pcr tests for identifying gastrointestinal pathogens in people with suspected gastroenteritis (xtag gastrointestinal pathogen panel, filmarray gi panel and faecal pathogens b assay). diagnostics guidance detection of influenza a and b with the alere i influenza a & b: a novel isothermal nucleic acid amplification assay. influenza other respir viruses automated real-time collection of pathogen-specific diagnostic data: syndromic infectious disease epidemiology infectious disease surveillance in the big data era: towards faster and locally relevant systems fda clearance for filmarray respiratory panel ez (rp ez) fda clearance for filmarray respiratory panel (rp the point-of-care laboratory in clinical microbiology extreme pcr: efficient and specific dna amplification in - seconds better tests, better care: improved diagnostics for infectious diseases key: cord- - mhimfsf authors: gray, nicholas; calleja, dominic; wimbush, alexander; miralles-dolz, enrique; gray, ander; de angelis, marco; derrer-merk, elfriede; oparaji, bright uchenna; stepanov, vladimir; clearkin, louis; ferson, scott title: is “no test is better than a bad test”? impact of diagnostic uncertainty in mass testing on the spread of covid- date: - - journal: plos one doi: . /journal.pone. sha: doc_id: cord_uid: mhimfsf testing is viewed as a critical aspect of any strategy to tackle epidemics. much of the dialogue around testing has concentrated on how countries can scale up capacity, but the uncertainty in testing has not received nearly as much attention beyond asking if a test is accurate enough to be used. even for highly accurate tests, false positives and false negatives will accumulate as mass testing strategies are employed under pressure, and these misdiagnoses could have major implications on the ability of governments to suppress the virus. the present analysis uses a modified sir model to understand the implication and magnitude of misdiagnosis in the context of ending lockdown measures. the results indicate that increased testing capacity alone will not provide a solution to lockdown measures. the progression of the epidemic and peak infections is shown to depend heavily on test characteristics, test targeting, and prevalence of the infection. antibody based immunity passports are rejected as a solution to ending lockdown, as they can put the population at risk if poorly targeted. similarly, mass screening for active viral infection may only be beneficial if it can be sufficiently well targeted, otherwise reliance on this approach for protection of the population can again put them at risk. a well targeted active viral test combined with a slow release rate is a viable strategy for continuous suppression of the virus. during the early stages of the united kingdoms sars-cov- epidemic, the british government's covid- epidemic management strategy was been influenced by epidemiological modelling conducted by a number of research groups [ , ] . the analysis of the relative impact of different mitigation and suppression strategies concluded that the "only viable strategy at the current time" is to suppress the epidemic with all available measures, including the lockdown of the population with schools closed [ , ] . similar analysis in other countries lead to over half the world population being in some form of lockdown by april and over % of global schools closed [ , ] . these analyses have highlighted from the beginning that the eventual relaxation of lockdown measures would be problematic [ ] . without a considered cessation of the suppression strategies the risk of a second wave becomes significant, possibly of greater magnitude than the first as the sars-cov- virus is now endemic in the population [ , ] . although much attention was focused on the number of tests being conducted and the effect that testing could have in supressing the disease [ ] [ ] [ ] . not enough attention has been given to the issues of imperfect testing, beyond matt hancock, uk secretary of state for health and social care, stating in a press conference on nd april that "no test is better than a bad test" [ ] . in this paper we will explore the validity of this claim. the failure to detect the virus in infected patients can be a significant problem in highthroughput settings operating under severe pressure, with evidence suggesting that this is indeed the case [ ] [ ] [ ] [ ] [ ] . the public are rapidly becoming aware of the difference between the 'have you got it?' tests for detecting active cases, and the 'have you had it?' tests for the presence of antibodies, which imply some immunity to covid- . what may be less obvious is that these different tests need to maximise different test characteristics. to be useful in ending lockdown measures, active viral tests need to maximise the sensitivity. high sensitivity reduces the chance of missing people who have the virus who may go on to infect others. there is an additional risk that an infected person who has been incorrectly told they do not have the disease, when in fact they do, may behave in a more reckless manner than if their disease status were uncertain. the second testing approach, seeking to detect the presence of antibodies to identify those who have had the disease would be used in a different strategy. this strategy would involve detecting those who have successfully overcome the virus, and are likely to have some level of immunity (or at least reduced susceptibility to more serious illness if they are infected again), so are relatively safe to relax their personal lockdown measures. this strategy would require a high test specificity, aiming to minimise how often the test tells someone they have had the disease when they haven't [ ] . a false positive tells people they have immunity when they don't, which may be worse than if people are uncertain about their viral history. the successes of south korea, singapore, taiwan and hong kong in limiting the impact of the sars-cov- virus has been attributed to their ability to deploy widespread testing, with digital surveillance, and impose targeted quarantines in some cases [ ] . this testing has predominantly been based on the use of reverse transcription polymerase chain reaction (rt-pcr) testing. during the h n pandemic the rapid development of high sensitivity pcr assay were employed early with some success in that global pandemic [ ] . these tests, when well targeted, clearly provide a useful tool for managing and tracking pandemics. these tests form the basis of much of the research into the incidence, dynamics and comorbidities of sars-cov- , but few, if any, of these studies give consideration to the impact of false test results [ ] [ ] [ ] [ ] [ ] . increasing reliance on lower-sensitivity tests to address capacity concerns is likely to make available data on confirmed cases more difficult to accurately utilise [ ] . it may be the case that false test results contribute to some of the counter-intuitive disease dynamics observed [ ] . there is evidence that both active infection [ ] [ ] [ ] [ ] [ ] and antibody [ ] [ ] [ ] tests lack perfect sensitivity and specificity even in best-case scenarios. alternative screening methods such as chest x-rays may be found to have high sensitivity based on biased data [ ] or may simply perform poorly even compared to imperfect rt-pcr tests [ ] . the foundation for innovative in order to answer this question there are a number of important statistics: • sensitivity σ-out of those who actually have the disease, that fraction that received a positive test result. • specificity τ-out of these who did not have the disease, the fraction that received a negative test result. the statistics that characterise the performance of the test are computed from a confusion matrix (table ) . we test n infected people who have covid- , and n healthy people who do not have covid- . in the first group, a people correctly test positive and c falsely test negative. among healthy people, b will falsely test positive, and d will correctly test negative. from this confusion matrix the sensitivity is given by ( ) and the specificity by ( ). s ¼ a n infected ð Þ sensitivity is the ratio of correct positive tests to the total number of infected people involved in the study characterising the test. the specificity is the ratio of the correct negative tests to the total number of healthy people. importantly, these statistics depend only on the test itself and do not depend on the population the test is intended to be used upon. when the test is used for diagnostic purposes, the characteristics of the population being tested become important for interpreting the test results. to interpret the diagnostic value of a positive or negative test result the following statistics must be used: • prevalence p-the proportion of people in the target population that have the disease tested for. • positive predictive value ppv-how likely one is to have the disease given a positive test result. • negative predictive value npv-how likely one is to not have the disease, given a negative test result. the ppv and npv depend on the prevalence, and hence depend on the population you are focused on. this may an entire nation or region, a sub-population with covid- compatible symptoms, or any other population you may wish to target. the ppv and npv can be calculated using bayes' rule: to illustrate the impact of prevalence on ppv, for a test with σ = τ = . , if prevalence p = . , then the ppv = . . therefore, a positive result only indicates a % chance that an individual will have the disease given that they have tested positive, even though the test is highly accurate. fig shows why, for test subjects there will be similar numbers of true and false positives even with high sensitivity and specificity of %. in contrast, using the same tests on a sample with a higher prevalence p = . we find the ppv = . , see fig . similarly, the npv is lower when the prevalence is higher. sir models offer one approach to explore infection dynamics, and the prevalence of a communicable disease. in the generic sir model, there are s people susceptible to the illness, i people is "no test is better than a bad test"? infected, and r people who are recovered with immunity. the infected people are able to infect susceptible people at rate β and they recover from the disease at rate γ [ ] , fig shows how people move between the different states of an sir model. once infected persons have recovered from the disease they are unable to become infected again or infect others. this may be because they now have immunity to the disease or because they have unfortunately died. to explore the effect of imperfect testing on the disease dynamics when strategies testing regimes are employed to relax lockdown measures, three new classes were added to the model. the first is a quarantined susceptible state, q s , the second is a quarantined infected state, q i , and the third is people who have recovered but are in quarantine, q r , as shown in is "no test is better than a bad test"? the present model is similar to other sir models that take into account the effect of quarantining regimes on disease dynamics, such as lipsitch et al. ( ) [ ] or giordano et al. ( ) [ ] . lipsitch et al. implement quarantine in their model but do not incorporate the effects on the dynamics from imperfect testing, nor do they consider how the quality and scale of an available test affect the spread of a disease. diagnostic uncertainty plays no part in the model they present. likewise, giordano et al reduce population based diagnostic strategies to two parameters which confound test capacity, test targeting, and diagnostic uncertainty. again, they do not investigate the role that diagnostic uncertainty plays in the spread of a disease. the intent of this model is not to create a more sophisticated sir model, but to investigate how diagnostic uncertainty affects the dynamics of an epidemic. the model evaluates each day's population-level state transitions. there are two possible tests that can be performed: • an active virus infection test that is able to determine whether or not someone is currently infectious. this test is performed on some proportion of the un-quarantined population (s + i + r). it has a sensitivity of σ a and a specificity of τ a . • an antibody test that determines whether or not someone has had the infection in the past. this is used on the fraction of the population that is currently in quarantine but not infected (q s + q r ) to test whether they have had the disease or not. this test has a sensitivity of σ b and a specificity of τ b . each test is defined by a number of parameters. testing each day is limited by the test capacity c, the maximum number of tests that can be performed each day. each day a population n will be submitted for testing. the targeting capability of the test, t indicates the probability that an individual submitted for testing is positive, this is effectively the ppv of the initial screening effort. this results in a number of individuals m being considered for screening who are negative, of which k will be tested. targeting must be imperfect, as if it were perfect there would be no need for testing. unless otherwise stated, scenarios consider a default targeting of t = . , representing an extremely effective screening capability that is nonetheless imperfect. if daily testing targets are a goal regardless of the prevalence of the illness, t can be overruled to ensure n � c for example. this condition is referred to as strict capacity and is denoted with boolean parameter g, defaulting to true for all scenarios. tests can also be conducted periodically by changing the test interval parameter d. these default to , i.e. daily testing. each test has unique parameters, so for example test a (active virus infection test) has a targeting parameter t a whilst test b (antibody test) has t b . the parameters σ, τ, t, c, g and d define a test. a person in any category who tests positive in an active virus test transitions into the corresponding quarantine state, where they are unable to infect anyone else. a person, in q s or q r , who tests positive in an antibody test transitions to s and r respectively. any person within i or q i who recovers transitions to r, on the assumption that the end of the illness is clear and they will know when they have recovered. for this parameterisation the impact of being in the susceptible quarantined state, q s , makes an individual insusceptible to being infected. similarly, being in the infected quarantined state, q i , individuals are unable to infect anyone else. in practicality there is always leaking, no quarantine is entirely effective, but for the sake of exploring the impact of testing uncertainty these effects are neglected from the model. other situations may require including this effect. the sir model used in this paper uses discrete-time binomial sampling for calculating movements of individuals between states. for a defined testing strategy these rates are defined as follows: in eq , bin(n, p) refers to a binomial distribution with count n and rate p, h(n, k, m) refers to a hypergeometric distribution with populations n and k and a sample size m. the model must be initialised with a defined population split between the six states. at each time step t, the model calculates the number of persons moving between each state in the order defined above. the use of binomial and hypergeometric sampling was prompted by a desire to incorporate aleatory uncertainty in each movement. the current approach does not account for epistemic uncertainty, fixing the model parameters σ, τ, c, t and d. a discrete time model was selected to allow for comparisons against available published data detailing recorded cases and recoveries on a day-by-day basis. if the tests were almost perfect, then we can imagine how the epidemic would die out very quickly by either widespread infection or antibody testing with a coherent management strategy. a positive test on the former and the person is removed from the population, and positive test on the latter and the person, unlikely to contract the disease again, can join the population. more interesting are the effects of incorrect test results on the disease dynamics. if someone falsely tests positive in the antibody test, they enter the susceptible state. similarly, if an infected person receives a false negative for the disease they remain active in the infected state and hence can continue the disease propagation and infect further people. in order to explore the possible impact of testing strategies on the relaxation of lockdown measures several scenarios have been analysed. these scenarios are illustrative of the type of impact, and the likely efficacy of a range of different testing configurations. • immediate end to lockdown scenario: this baseline scenario is characterised by a sudden relaxation of lockdown measures. • immunity passports scenario: a policy that has been discussed in the media [ ] [ ] [ ] . analogous to the international certificate of vaccination and prophylaxis, antibody based testing would be used to identify those who have some level of natural immunity. • incremental relaxation scenario: a phased relaxation of lockdown is the most likely policy that will be employed. to understand the implications of such an approach this scenario has explored the effect of testing capacity and test performance on the possible disease dynamics under this type of policy. under the model parameterisation this analysis has applied an incremental transition rate from the q s state to the s state, and q r to r. whilst the authors are sensitive to the sociological and ethical concerns of any of these approaches, the analysis presented is purely on the question of efficacy. for the purpose of the analysis we have selected a population similar in size to the united kingdom, . × people, β and γ were set to . and . respectively, this was ensure that r value of the model was broadly in line with other models [ , ] . under the baseline scenario, characterised by the sudden and complete cessation of lockdown measures, we explored the impact of infection testing. under this formulation the initial conditions of the model in this scenario is that the all of the population in q s transition to s in the first iteration. the impact of infection testing under this scenario was analysed in fig using the parameters shown in table . these scenarios consider the impact of attempts to control the disease through increased testing capacity and a more sensitive test. a test capacity range between × and × was considered as representative of the capabilities of a country such as the uk. to illustrate the sensitivity of the model to testing scenarios an evaluation was conducted with a range of infection test sensitivities, from % (i.e of no diagnostic value) to %. the specificity of these tests has a negligible impact on the disease dynamics in these scenarios. a false positive would mean people are unnecessarily removed from the susceptible population, but the benefit of a reduction in susceptible population is negligibly small. as would be expected the model indicates a second wave is an inevitability and as many as million people could become infected within days. a high-sensitivity test has little impact table . https://doi.org/ . /journal.pone. .g is "no test is better than a bad test"? beyond quarantining a slightly higher percentage of the population if capacities are low. at higher capacities this patterns remains, though peak infection counts are marginally reduced. overall it is clear that reliance on infection testing, even with a highly sensitive test and high capacities, is not enough to prevent widespread infection. the immunity passport is an idiom describing an approach to the relaxation of lockdown measures that focuses heavily on antibody testing. wide-scale screening for antibodies in the general population promises significant scientific value, and targeted antibody testing is likely to have value for reducing risks to nhs and care-sector staff, and other key workers who will need to have close contact with covid- sufferers. the authors appreciate these other motivations for the development and roll-out of accurate antibody tests. this analysis however focuses on the appropriateness of this approach to relaxing lockdown measures by mass testing the general population. antibody testing has been described as a 'game-changer' [ ] . some commentators believe this could have a significant impact on the relaxation of lockdown measures [ ] , but others note that there are severe ethical, logistical and medical concerns which need to be resolved before antibody testing could support a strategy such as this [ ] . much of the discussion around antibody testing in the media has focused on the performance and number of these tests. the efficacy of this strategy however is far more dependent on the prevalence of antibodies (seroprevalence) in the general population. without widescale antibody screening it is impossible to know the seroprevalence in the general population, so there is scientific value in such an endeavour. however, the seroprevalence is the dominant factor to determine how efficacious antibody screening would be for relaxing lockdown measures. presumably, only people who test positive for antibodies would be allowed to leave quarantine. the more people in the population with antibodies, the more people will get a true positive, so more people would be correctly allowed to leave quarantine (under the paradigms of an immunity passport). the danger of such an approach are false positives. we demonstrate the impact of people reentering the susceptible population who have no immunity. we assume their propensity to contract the infection is the same as those without the false sense of security a positive test may engender. on an individual basis, and even at the population level, behavioural differences between those with false security from a positive antibody test, versus those who are uncertain about their viral history could be significant. the model parametrisation here does not include this additional confounding effect. to simulate the seroprevalence in the general population the model is preconditioned with different proportions of the population in the q s and q r states. this is analogous to the proportion of people that are currently in quarantine who have either had the virus and developed some immunity, and the proportion of the population who have not contracted the virus and is "no test is better than a bad test"? have no immunity. of course the individuals in these groups do not really know their viral history, and hence would not know which state they begin in. the model evaluations explore a range of sensitivity and specificities for the antibody testing. these sensitivity and specificities, along with the capacity for testing, govern the transition of individuals from q r to r (true positive tests), and from q s to s (false positive tests). each of the plots in figs and show the effect of different seroprevalence in the population. to be clear, this is the proportion of the population that has contracted the virus and recovered but are in quarantine. the analysis has explored a range of seroprevalence from . % to %. fig explores the impact of a variation in sensitivity, from a test with % sensitivity to tests with a high sensitivity of %. it can be seen, considering the top row of fig , that the sensitivity of the test has no discernible impact on the number of infections. the seroprevalence entirely dominates. this is possibly counter intuitive, but as was discussed above, even a highly accurate test produces a very large number of false positives when seroprevalence is low. in this case that would mean a large number of people are allowed to re-enter the population, placing them at risk, with a false sense of security that they have immunity. the bottom row of fig shows the proportion of the entire population leaving quarantine over a year of employing this policy. at low seroprevalence there is no benefit to better table . performing tests. this again may seem obscure to many readers. if you consider the highest seroprevalence simulation, where % of the population have immunity, higher sensitivity tests are of course effective at identifying those who are immune, and gets them back into the community much faster. a more concerning story can be seen when considering the graphs in fig . now we consider a range of antibody test specificities. going from % to %. low specificities (τ < . ) table . https://doi.org/ . /journal.pone. .g lead to extreme second peaks, and could possibly lead to more. this is due to the progressive release of false-positives from the quarantined population, which eventually swells the susceptible population to a size where the infection count can resume exponential growth. high specificities avoid this at the cost of a prolonged lockdown, which is naturally limited by the lower false-positive rate. clearly some means of release beyond immunity passports would be required to avoid this scenario. notably, a reasonably specific test (τ b = . ) is capable of restraining a second peak to reasonably low levels regardless of seroprevalence. this may allow for other means of reducing lockdown measures, though with very low seroprevalence this could still be a potentially risky strategy. the dangers of neglecting uncertainties in medical diagnostic testing are pertinent to this decision [ ] . considering the above, some form of incremental relaxation of lockdown seems appropriate. this could take many forms, it could be an incremental restoration of certain activities such as school openings, permission for the reopening of some businesses, the relaxation of stay-athome messaging, etc. under the parameterisation chosen for this analysis the model is not sensitive to any particular policy change. we consider a variety of rates of phased relaxations to quarantine. to model these rates we consider a weekly incremental transition rate from q s to s, and q r to r. in fig , three weekly transition rates have been applied: %, % and % of the quarantined population. whilst in practice the rate is unlikely to be uniform as decision makers would have the ability to update their timetable as the impact of relaxations becomes apparent, it is useful to illustrate the interaction of testing capacity and release rate. the model simulates these rates of transition for a year, with a sensitivity and specificity of % for active virus tests. the specifics of all the runs are detailed in table . fig shows five analyses, with increasing capacity for the active virus tests. in each, the incremental transition rates are applied with a range of targeting capabilities. the value of . used previously represents an unrealistically extreme case of effective targeting. the ppv, as discussed above, has a greater dependence on the prevalence (at lower values) in the tested population than it does on the sensitivity of the tests, the same is true of the specificity and the npv. it is important to notice that higher test capacities cause a higher peak of infections for higher release rates. this has a counterintuitive explanation. when there is the sharpest rise in the susceptible population (i.e., high rate of transition), the virus rapidly infects a large number of people. when these people recover after around two weeks they become immune and thus cannot continue the spread of the virus. however, when the infection testing is conducted with a higher capacity up to , units per day, these tests transition some active viral carriers into quarantine, so the peak is slightly delayed providing more opportunity for those released from quarantine later to be infected, leading to higher peak infections. this continues until the model reaches effective herd immunity after which the number of infected in the population decays very quickly. having higher testing capacities delays but actually has the potential to worsen the peak number of infections. at % release rate, up to a capacity of testing of , these outcomes are insensitive to the prevalence of the disease in the tested population. this analysis indicates that the relatively fast cessation of lockdown measures and stay-home advice would lead to a large resurgence of the virus. testing capacity of the magnitude stated as the goal of the uk government would not be sufficient to flatten the curve in this scenario. the % release rate scenario indicates that a slow release by itself is sufficient to lower peak infections, but potentially extends the duration of elevated infections. the first graph of the top row in fig shows that the slow release rate causes a plateau at a significantly lower number of infections compared to the other release rates. poorly targeted tests at capacities less than , show similar consistent levels of infections. however, with a targeted test having a prevalence of % or more, the % release rate indicates that even with , tests per day continuous suppression of the infection may be possible. the per-day testing capacity is varied across the five columns of graphs. rate, the percentage of the initial quarantined population being released each week is varied among rows. the prevalence of infections in the tested population is varied among different colours. to facilitate comparison within each column of graphs, the gray curves show the results observed for other rates and prevalences with the same testing intensity. model parameters are shown in table . https://doi.org/ . /journal.pone. .g at the rate of % of the population in lock-down released incrementally each week the infection peak is suppressed compared to the % rate. the number of infections would remain around this level for a significantly longer period of time, up to months. there is negligible impact of testing below a capacity of , tests. however, with a test capacity of , tests the duration of the elevated levels of infections could be reduced if the test is extremely well targeted (t a = . ), reducing the length of necessary wide-scale lockdown. if this level of targeting is not achieved, increasing capacity may again increase peak infections, so care must be taken to ensure a highly targeted testing strategy. this analysis does support the assertion that a bad test is potentially worse than no tests, but a good test is only effective in a carefully designed strategy. more is not necessarily better and over estimation of the test accuracy could be extremely detrimental. this analysis is not a prediction; the numbers used in this analysis are estimates and the sirq model used is unlikely to be detailed enough to inform policy decisions. as such, the authors are not drawing firm conclusions about the absolute necessary capacity of tests. nor do they wish to make specific statements about the necessary sensitivity or specificity of tests or the recommended rate of release from quarantine. the authors do, however, propose some conclusions that would broadly apply when testing and quarantining regimes are used to suppress epidemics, and therefore believe they should be considered by policy makers when designing strategies to tackle covid- . • diagnostic uncertainty can have a large effect on the dynamics of an epidemic. and, sensitivity, specificity, and the capacity for testing alone are not sufficient to design effective testing procedures. policy makers need to be aware of the accuracy of the tests, the prevelence of the disease at increased granularity and the characteristics of the target population, when deciding on testing strategies. • caution should be exercised in the use of antibody testing. assuming that the prevalence of antibodies is low, it is unlikely antibody testing at any scale will support the end of lockdown measures. and, un-targeted antibody screening at the population level could cause more harm than good. • antibody testing, with a high specificity may be useful on an individual basis, it has scientific value, and could reduce risk for key workers. but any belief that these tests would be useful to relax lockdown measures for the majority of the population is misguided. • the incremental relaxation to lockdown measures, with all else equal, would significantly dampen the increase in peak infections, by order of magnitude with a faster relaxation, and orders of magnitude with a slower relaxation. • as the prevelence of the disease is suppressed in different regions, it may be the case that small spikes in cases could be the result of false positives. this problem is potentially exacerbated by increased testing in localities in response to small increases in positive tests. policy decisions that depend on small changes in the number of positive tests may, therefore, be flawed. • for infection screening to be used to relax quarantine measures the capacity needs to be sufficiently large but also well targeted to be effective. for example this could be achieved through effective contact tracing. untargeted mass screening at any capacity would be ineffectual and may prolong the necessary implementation of lockdown measures. epidemiological models used for policy making in real time will need to take into account the impact of diagnostic uncertainty of testing, as well as the dynamical behaviour and sensitivity analyses of modelled parameters in an appropriately complex model that may need to include quarantining, contact tracing and other surveillance strategies, test availability and targeting, and multiple subpopulations of susceptible, infected and recovered categories. covid- : government announces moving out of contain phase and into delay phase scaling up our testing programmes. department of health and socal care impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand. imperial college covid- response team pm address to the nation on coronavirus half of humanity now on 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passports' could speed up return to work after covid- britain has millions of coronavirus antibody tests, but they don't work the reproductive number of covid- is higher compared to sars coronavirus euro surveillance: bulletin europeen sur les maladies transmissibles = european communicable disease bulletin boris johnson and donald trump talk up potential'game-changer' scientific advances on coronavirus developing a national strategy for serology (antibody testing) in the united states calculated risks: how to know when numbers deceive you key: cord- -m l t e authors: lucas, t. c.; pollington, t. m.; davis, e. l.; hollingsworth, t. d. title: responsible modelling: unit testing for infectious disease epidemiology date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: m l t e infectious disease epidemiology is increasingly reliant on large-scale computation and inference. models have guided health policy for epidemics including covid- and ebola and endemic diseases such as malaria and tuberculosis. yet a single coding bug may bias results, leading to incorrect conclusions and wrong actions that could cause avoidable harm. we are ethically obliged to ensure our code is as free of error as possible. unit testing is a coding method to avoid such bugs, but unit testing is rarely used in epidemiology. we demonstrate through simple examples how unit testing can handle the particular quirks of infectious disease models. modelling is an important tool for understanding fundamental biological processes in infectious disease dynamics, evaluating potential intervention efficacy and forecasting disease burden. at the time of writing, infectious disease modellers are playing a central role in the interpretation of available data on the covid- pandemic to inform policy design and evaluation [ ] [ ] [ ] . similarly, policy on endemic infectious diseases, such as duration and frequency of control programmes and spatial prioritisation, is also directed by models [ ] . such research builds on a long history of modelling for policy [ ] and a general understanding of the dynamics of infectious disease systems. given the importance of modelling results, it is vital that the code they rely on is both coded correctly and trusted. bugs can be caused by typos, code behaving in unexpected ways, or logical flaws in the construction of the code. outside of epidemiology, bugs have been found in code that had been used by many researchers [ ] and may lead to retractions [ ] . bugs have also been found in highly influential work; a paper that informed austerity policies globally was found to have a fatal computational mistake [ ] . in engineering bugs caused the mars climate orbiter and the mariner spacecraft to become lost or destroyed [ , ] . we do not know of high profile cases of infectious disease models being found to have bugs once published, but as code is not always shared and little post-publication testing of code occurs, this likely represents a failure of detection. the issue of trust was highlighted recently when neil ferguson, one of the leading modellers informing uk covid- government policy, tweeted: "i'm conscious that lots of people would like to see and run the pandemic simulation code we are using to model control measures against covid- . to explain the background -i wrote the code (thousands of lines of undocumented c) + years ago to model flu pandemics. . . " [ ] . the code that was released did not include any tests [ ] but subsequent work has added documentation, while independent code reviews have supported the results of the study [ , ] . the tweet and lack of tests garnered considerable backlash (some of which may have been politically motivated [ ] ), with observers from the software industry noting that code should be both documented and tested to ensure its correctness [ ] . it is understandable that during the fastmoving, early stages of a pandemic, other priorities were put above testing and documenting the code. however, this simply reinforces that time should be taken to test and document code when it is first written so that it is already well tested for when it is needed under short deadlines. it is also important to note that a lack of tests is not unusual in our field, or for some of the authors of this article. to guard against error, policy-makers now standardly request analyses from multiple modelling groups (as is the case in the uk for covid - [ ] ) as a means to provide scientific robustness and reliability [ ] , yet this is not enough if the models themselves lack internal validity. infectious disease modellers are rarely trained as professional programmers [ ] and recently some observers have made the case that this has been due to a lack of funding [ ] . it is also notable that there are few texts available which demonstrate the use of unit testing to check infectious disease models. infectious disease modellers have sought to address these issues (as in the case above) by having multiple, independently developed models to inform policy, to address structural and parameter uncertainty [ , ] . whilst there many drivers and attempts to address this problem with code robusteness, today's models are increasingly moving from mean-field ordinary differential equation approximations to individual-based models with complex, data-driven contact processes [ , ] . these increases in model complexity are accompanied with growing codebases. as the mathematical methods depend increasingly on numerical solutions rather than analytical pen-and-paper methods, it becomes more difficult to tell if a bug is present based on model outputs alone. traditionally, the workflow is to write the complete code, run the model and examine plots of the output. this crude ad hoc testing approach can miss many bugs. furthermore, this workflow is biased as models that show expected behaviour are assumed bug-free, whereas the opposite gets more scrutiny. unit testing is a formally-defined, principled framework that compares comprehensive output scenarios from code to what the programmer expected to happen ( [ ] chapter , [ ] , [ ] ). ready-to-run frameworks for unit testing are available in r [ ] , julia [ ] and python [ ] and are standard practice in the software industry. these testing concepts also apply to many other scientific fields but here we focus on infectious diseases. infectious disease modelling presents specific challenges, such as stochastic outputs, which are difficult to test and not covered in general unit testing literature. in this primer we introduce unit testing with a demonstration of an infectious disease model. we also outline the available testing frameworks in various languages commonly used by modellers. at the heart of every unit test is a function output, its known or expected value and a process to compare the two. for the square root function ( √ x or sqrt(x) in r), we could write a test that runs the function for the number , i.e. sqrt(x = ), and compares it to the correct answer i.e. . however, often our function arguments will cover an infinite range of possibilities and we cannot exhaustively check them all. instead we devise tests that cover standard usage as well as corner case scenarios: what do we want our function to do if given a negative number e.g. sqrt(- ), or a vector argument containing strings or missing values e.g. sqrt(c( ,"melon",na))? in r, the testthat package [ ] , provides a simple interface for testing. while a variety of test functions can make different comparisons, the two main ones are expect_true() and expect_equal(). expect_true() takes one argument: an expression that should evaluate to true. for our square root example . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . above, we would write expect_true(sqrt( ) == ). expect_equal() takes two arguments, an expression and the expected output; so we would write expect_equal(sqrt( ), ). there are a number of ways to incorporate unit testing into your programming workflow. . each time you write code for a new, discrete chunk of functionality, you should write tests that confirm it does what you expect. these tests should be kept in the same directory as the code it is testing. . whenever a bug is found in the code outside of the existing testing framework, a new test should be written to capture it. then if the bug re-emerges it will hopefully be quickly flagged so that the developor can fix it. . all of these tests should be regularly run as you develop new code. if a change causes the older tests to break, this points to the introduction of an error in the new code, or implies that the older code could not generalise to the adapted environment. here we define a toy epidemiological model and then demonstrate how to effectively write unit tests for it in r code. consider a multi-pathogen system, with a population of n infected individuals who each get infected by a new pathogen at every time step (fig. ). in this toy example, we imagine that individuals are infected with exactly one pathogen at a time. some aspects of this model could reflect the dynamics of a population where specific antibiotics are used regularly i.e. each time step an individual is infected, diagnosed and treated suboptimally, leaving the individual susceptible to infection from any pathogen, including the one they were just treated for. the aim of this model however is not to be realistic but serve as a learning tool with succinct code. each individual i, at time t, is defined by the pathogen they are currently infected with i it ∈ {a, b, c} for a -pathogen system. the population is therefore defined by a length n state vector i t = (i it ) i= [ ,n ] . at each time step, every . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint individual's infection status is updated as: that is, at each iteration, the new infection status of each individual is a uniform random sample from the set of infection statuses in the previous iteration (including itself i i,t− ). certainly this toy model is naïve as it is governed by mass-action principles, ignoring contact and spatial dynamics. nevertheless it will serve its purpose. code shows our first attempt at implementing this model. usually we would make some output plots to explore if our code is performing sensibly. plotting the time course of which pathogen is infecting one individual shows repeated infection with different pathogens as expected (fig. ) . however, if we look at the proportion of each pathogen through time (not shown here) we quickly see that the pathogen proportions are identical through time and so . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . there must be a bug that we had not originally noticed. this simple example demonstrates a number of points. firstly, bugs can be subtle. secondly, it is not easy to notice an error, even in just lines of code. thirdly, it is much easier to debug code when you know there is a bug. fourthly, while plotting simulation runs is an excellent way to check model behaviour, if we had only relied on fig. we would have missed the bug. additionally, manually checking plots is a time consuming and non-scalable method because a human has to perform this scan every test run. in summary this ad hoc plotting approach reduces the chances that we will catch all bugs. the cause of the bug is that sample() defaults to sampling without replacement sample(..., replace = false); this means everyone transmits their infection pathogen on a one-to-one basis rather than one-to-many as required by the model. setting replace = true fixes this (code ) and when we plot the proportion of each pathogen ( fig. ) we see the correct behaviour (a single pathogen drifting to dominance). in the subsequent sections we will develop this base example as we consider different concepts in unit testing, resulting in well-tested code by the end. write small functions to ensure the unit tests are evaluating the exact code as run in the analysis, code should be structured in functions, which can be used to both run unit tests with and to generate results as part of a larger model codebase. make your functions compact with a single clearly-defined task. we have defined a function, initialisepop(), to initialise the population and another, updatepop(), to run one iteration of the simulation (code ). organising the codebase into these bite-sized operations makes following the programming flow easier as well as understanding the structure of the code. at this stage we have also enabled the varying of the number of pathogens . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint if we start with a small population with few pathogens, we can then easily work out exactly what the initialised population should look like (code ). when we initialise a population with three individuals and three pathogens, we will get the sequence "a", "b", "c" as seen in the first test. when the number of individuals is greater than the number of pathogens, the sequence will be repeated as seen in the second test. finally, when the number of individuals is greater than the number of pathogens, but is not a multiple of the number of pathogens, the sequence will have an incomplete repeat at the end as seen in the third test. in this sequence of tests, we have taken our logical understanding of what the function should do, and used it to make predictions of what the results should be. we then test that the result is the same as what we expect. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint code : using simple parameter sets we can work out beforehand what results to expect pop <-initialisepop(t = , n = , pathogens = ) expect_equal(pop [ ,], c("a", "b", "c")) pop <-initialisepop(t = , n = , pathogens = ) expect_equal(pop [ ,], c("a", "b", "c", "a", "b", "c")) pop <-initialisepop(t = , n = , pathogens = ) expect_equal(pop [ ,], c("a", "b", "c", "a", "b")) initialisepop() has three arguments to check. first we initialise the population, and then alter each argument in turn (code ). arguments t and n directly change the expected dimension of the returned matrix so we check that the output of the function is the expected size. for the pathogens argument we test that the number of pathogens is equal to the number requested. we can also cover cases that expose deviations from the logical structure of the system. after initialising our population, we expect all the rows other than the first to contain na. we also expect each of the pathogens a, b and c to occur at least once on the first row if pathogens = and n ≥ . finally, updatepop() performs a single simulation time step, so we expect only one additional row to be populated. instead of testing by their numerical values, we verify logical statements of the results within our macro understanding of the model system (code ). code : test more complex cases using your understanding of the system . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint .na(pop [- ,]) )) # expect all pathogens at t = expect_true(all(c("a", "b", "c") %in% pop [ ,])) pop <-updatepop(pop , t = , n = ) # after update expect st & nd row not to have nas expect_true(all (!is.na(pop [ : ,]) )) # and also expect that rows other than the st & nd are still nas. expect_true(all(is. na(pop [-c( : ) ,]))) in the end an entire model only runs when its functions work together seamlessly. so we next check their connections; achieved through nesting functions together, or defining them at a higher level and checking the macro aspects of the model. we define a function fullsim() that runs both initialisepop() and updatepop() to yield one complete simulation. we would expect there to be no nas in the output from fullsim() and every element to be either a, b or c. # expect no nas expect_true(!any(is.na(pop))) # expect all pathogens contained within expect_true(all(pop %in% c("a", "b", "c"))) stochastic simulations are a common feature in infectious disease models. stochastic events are difficult to test effectively because, by definition, we do not know beforehand what the result will be. we can check very broad-scale properties, like code , where we check the range of pathogen values. however, code could still pass and be wrong (for example the base example (code ) would still pass that test). there are however a number of approaches that can help. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint isolate the stochastic parts of your code. for example, updatepop() performs stochastic and deterministic operations in one line (code ). firstly, updatepop() stochastically samples who gets infected by whom at iteration t. then it takes those infection events and assigns the new infectious status for each individual. we demonstrate in code how this could be split. we accept this is a fairly exaggerated example and splitting a single line of code into two functions is rare! the more common scenario is splitting a multi-line function into smaller functions which also brings benefits of code organisation so it does not feel like extra effort. x <-updateinfectionstatus(x, t, infector_pathogen) return(x) } now, half of updatepop() is deterministic so can be checked as previously discussed. we still have chooseinfector() that is irreducibly stochastic. we now examine some techniques for directly testing the stochastic parts of a model. in the same way that we used simple parameters values in code , we can often find simple cases for which our stochastic functions become deterministic. for example, samples from x ∼ bernoulli(p) will always be zeroes for p = or ones for p = . in the case of a single pathogen (code ), the model is no longer stochastic. so initialisation with one pathogen means the second time step should equal the first. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint vector with the indices of the infector for each infectee. paste () then turns this length- vector into a length- string with two characters; we expect this to be one of " ", " ", " " or " ". replicate() runs the expression times, but in your unit test you should choose a value high enough so that you are confident that all of the distinct outcomes will have occurred at least once. # collapse each draw into a single string to make comparisons easier. manypops <-replicate( , paste (chooseinfector(n = ), collapse = "")) expect_true(all(manypops %in% c(" ", " ", " ", " "))) while the previous example worked well for a small set of possible outputs, testing can conversely be made easier by using very large numbers. this typically involves large sample sizes or numbers of stochastic runs. for example, the clearest test to distinguish between our original, buggy code (code ) and our correct code (code ) is that in the correct code there is the possibility for an individual to infect more than one individual in a single time step. in any given run this is never guaranteed, but the larger the population size the more likely it is to occur. with a population of one thousand, the probability that no individual infects two others is vanishingly rare (code ). as this test is now stochastic we should set the seed of the random number generator so that the test is reproducible. setting the seed with set.seed means that each time the code is run, the same pseudo-random numbers will be generated. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint set.seed( ) n <- e infector_pathogen <-chooseinfector(n) if we have an event that we know should never happen, we can use a large number of simulations to provide stronger evidence that it does not stochastically occur. however, it can be difficult to determine how many times is reasonable to run a simulation, especially if time is short. this strategy works best when we have a specific bug that occurs relatively frequently (perhaps once every ten simulations or so). if the bug occurs every ten simulations and we have not fixed it we would be confident that it will occur at least once if we run the simulation or times. conversely, if the bug does not occur even once in or simulations we can be fairly sure we have fixed it. similarly, a bug might cause an event that should be rare to happen very regularly or even every time the code is run. in our original buggy code (code ) we found that the proportions remained identical for entire simulations. we would expect this to happen only very rarely. we can run a large number of short simulations to check that this specific bug is not still occurring by confirming that the proportion of each pathogen is not always the same between the first and last time point. as long as we find at least one simulation where the proportions of each pathogen are different between the first and last iteration, we know the bug has been fixed. sapply(manysims, diffproportions) )) . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint as well as testing that functions work when given the correct inputs, we must also test that they behave sensibly when given wrong ones. this typically involves the user inputting argument values that do not make sense. this may be, for example, because the inputted argument values are the wrong class, in the wrong numeric range or have missing data values. therefore it is useful to test that functions fail gracefully if they are given incorrect inputs. this is especially true for external, exported functions, available to a user on a package's front-end. however, it is not always obvious what constitutes an 'incorrect value' even to the person who wrote the code. in some cases, inputting incorrect argument values may cause the function to fail quickly. in other cases code may run silently giving false results or take a long time to give an error. both of these cases can be serious or annoying and difficult to debug afterwards. often for these cases, the expected behaviour of the function should be to give an error. there is no correct output for an epidemiological model with - pathogens. instead the function should give an informative error message. often the simplest solution is to include argument checks at the beginning of functions. we then have to write slightly unintuitive tests for an expression where the expected behaviour is an error. if the expression does not throw an error the test should throw an error (as this is not the expected behaviour). conversely, if the expression does throw an error the test should pass and not throw an error. we can use the expect_error() function for this task. this function takes an expression as its first argument and reports an error if the given expression does not throw an error as expected. we can first check that the code sensibly handles the user inputting a string instead of an integer for the number of pathogens. because this expression throws an error, expect_error() does not throw an error and the test passes. now we contrast what happens if the user inputs a vector of pathogens to the initialisepop() function. here we are imagining that the users intent wass to run a simulation with three pathogens: , and . this test fails because the function does not throw an error. instead the code takes the first element of pathogens and ignores the rest. therefore, a . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . population is created with one pathogen, not three, which is almost certainly not what the user wanted. here, the safest fix is to add an explicit argument check at the top of the function as implemented below. the same test now passes because initialisepop() throws an error when a vector is supplied to the pathogens argument. we can similarly check how the code handles a user inputting a vector of numbers to the t argument (perhaps thinking it needed a vector of all time points to run). in code , initialisepop() does not throw an error if a vector is supplied to t. however, fullsim() does throw an error if a vector is supplied to t. while it is a good thing that fullsim() throws an error, the error message is not very informative. if the code that runs before the error is thrown (in this case the initialisepop() function) takes a long time, it can also be time consuming to work out what threw the error. it is also a signature of fragile code that the error is coincidental; a small change in the code might stop the error from occurring. to remedy this we can add an additional argument check to initialisepop(). importantly, we then want to check that fullsim() errors in the correct place (i.e. in initialisepop() rather than afterwards). we can achieve this using the regexp argument of expect_error() that compares the actual error message to the expected error messages. the test will only pass if the error message contains the string provided. similarly, special cases can be triggered with parameter sets that do not match the extrema of parameter space. this is where understanding of the functional form of the model can help. consider a function divide(x, y) that divides x by y. we could test this function by noting that y * divide(x, y) should return x. if we write code that tests standard values of x and y such as * divide( , ) == we would believe the function works for nearly all values of division, unless we ever try y = . we checked earlier if the pathogens argument of initialisepop() worked by verifying that the returned population had the correct number of pathogens. however, if we set the pathogens argument to be greater than the number of individuals in the population we get a population with n pathogens. the function does not therefore pass the test we defined in code . for edge cases like this it may be rather subjective what the correct behaviour should be. it might be appropriate for the function to throw an error or give a warning if the user requests more pathogens than individuals. here however, we will decide that this behaviour is acceptable. the test above was still useful to highlight this unusual case. as our expected output from the function has changed, we should change our test; we now expect a population with n pathogens. we should however retain the test in code so that we have two tests: one test checks that when pathogens < n, the number of unique . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . pathogens in the population is equal to pathogens; the other test checks that when pathogens > n, the number of unique pathogens is equal to n. most programming languages have established testing packages. for r, there is the testthat package as already discussed. when structuring r code as a package, tests should be kept in the directory tests/testthat; further requirements to the structure can be found in [ ] chapter . all the tests in a package can then be run with test() from the devtools package [ ] or check() for additional checks relevant to the package build. if the code is to be part of a package then these tools are essential to run the code within the context of a build environment. these tools also provide a clean environment to highlight if a test was previously relying on objects defined outside of the test script. other programming languages have similar testing frameworks. their specifics differ but the main concept of comparing a function evaluation to the expected output remains the same. in julia there is the test package [ ] . the basic structure for tests with this package is demonstrated below. we name the test and write a single expression that evaluates to true or false. for a julia package, unit tests reside in test/runtests.jl and tests are run with pkg.test(). code : julia test example @testset "my_test_name" begin @test sqrt( ) == end finally, in python we have the unittest framework [ ]; tests must be written into a class that inherits from the testcase class. the tests must be written as methods with self as the first argument. an example test script is shown below. tests should be kept in a directory called lib/test, and the filename of every file with tests should begin with "test_". code : python test example . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint import unittest import math class testmaths(unittest.testcase): def test_sqrt(self): self.assertequal(math.sqrt( ), ) unittest.main() if your code is under version control [ , ] and hosted on github, gitlab or bitbucket, you can automate the running of unit tests-also known as continuous integration. in this setup, whenever you push code changes from your local computer to the online repository, any tests that you have defined get run automatically. furthermore these tests can be automated irrespective of changes to your code or tests: since dependencies with other packages and knock-on changes from them into a bug in your code can be automatically found and notified to you by email. there are various continuous integration services such as travis-ci.org, github actions and gitlab pipelines. these services are often free on a limited basis, or free if your code is open source. we briefly describe the setup of the simplest case usign travis ci. setting testing up is very straightforward for r code already organised into a package and hosted openly on github. within your version-controlled folder that contains the r code, you add a one-liner file named ".travis.yml" that contains a description of which language the code uses. code : a basic travis yml file. this file can also be created with use_travis() from the usethis package. you then sign up to travis-ci.org and point it to the correct github repository. to authenticate and trigger the first automatic test you need to make a minor change to your code, commit and push to github. more details can be found in [ ] chapter . . it is vital that infectious disease models are coded to minimise bugs. unit testing is a well-defined, principled way we can do this. there are many frameworks that make aspects of unit testing automatic and more informative and these should be used where possible. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . the basic principles of unit testing are simple but writing good tests is a skill that takes time, practice and thought. however, ensuring your code is robust and well-tested saves time and effort in the long run and helps prevent spurious results. these qualities are important for the reproducibility of science, but are particularly relevant where code may be shared between individuals or groups, or where you wish to publish your code as a package to be used by others. our aim in this paper was to demonstrate tailored results for infectious disease modelling. there are number of standard programming approaches to unit testing which would be good followup reading ( [ ] chapter , [ ] , [ ] ). as demonstrated here, it is initially time consuming to program in this way, but over time it will become habitual and both you and the policy-makers who use your models will benefit from it. please see the fully-reproducible and version-controlled code at www.github. com/timcdlucas/unit_test_for_infectious_disease. tmp, tdh, tcdl and eld gratefully acknowledge funding of the ntd modelling consortium by the bill & melinda gates foundation (bmgf) (grant number opp ). views, opinions, assumptions or any other information set out in this article should not be attributed to bmgf or any person connected with them. tmp's phd is supported by the engineering & physical sciences research council, medical research council and university of warwick (grant number ep/l / ). tmp thanks the big data institute for hosting him during this work. all funders had no role in the study design, collection, analysis, interpretation of data, writing of the report, or decision to submit the manuscript for publication. is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint ihme covid- health service utilization forecasting team, murray cj. forecasting covid- impact on hospital bed-days, icu-days, ventilator days and deaths by us state in the next months impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand feasibility of controlling covid- outbreaks by isolation of cases and contacts modelling for policy: the five principles of the neglected tropical diseases modelling consortium. plos neglected tropical diseases modeling infectious disease dynamics in the complex landscape of global health characterization of leptazolines a-d, polar oxazolines from the cyanobacterium leptolyngbya sp., reveals a glitch with the "willoughby-hoye" scripts for calculating nmr chemical shifts. organic letters does high public debt consistently stifle economic growth? a critique of reinhart and rogoff. cambridge journal of economics mars climate orbiter mishap investigation board phase i report november tweet from @neil_ferguson mrc centre for global infectious disease analysis impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand the chartered institute for it. professionalising software development in scientific research critiqued coronavirus simulation gets thumbs up from codechecking efforts guidelines for multi-model comparisons of the impact of infectious disease interventions pandemic response shines spotlight on coding in science learning from multi-model comparisons: collaboration leads to insights, but limitations remain lessons from a decade of individual-based models for infectious disease transmission: a systematic review strategies for mitigating an influenza pandemic r packages: organize, test, document, and share your code ten simple rules for effective computational research best practices for scientific computing r v . . : a language and environment for statistical computing austria: r foundation for statistical computing julia: a fresh approach to numerical computing python core team. python v . . : a dynamic, open source programming language : get started with testing key: cord- -jzwwses authors: kaul, karen l.; sabatini, linda m.; tsongalis, gregory j.; caliendo, angela m.; olsen, randall j.; ashwood, edward r.; bale, sherri; benirschke, robert; carlow, dean; funke, birgit h.; grody, wayne w.; hayden, randall t.; hegde, madhuri; lyon, elaine; murata, kazunori; pessin, melissa; press, richard d.; thomson, richard b. title: the case for laboratory developed procedures: quality and positive impact on patient care date: - - journal: acad pathol doi: . / sha: doc_id: cord_uid: jzwwses an explosion of knowledge and technology is revolutionizing medicine and patient care. novel testing must be brought to the clinic with safety and accuracy, but also in a timely and cost-effective manner, so that patients can benefit and laboratories can offer testing consistent with current guidelines. under the oversight provided by the clinical laboratory improvement amendments, laboratories have been able to develop and optimize laboratory procedures for use in-house. quality improvement programs, interlaboratory comparisons, and the ability of laboratories to adjust assays as needed to improve results, utilize new sample types, or incorporate new mutations, information, or technologies are positive aspects of clinical laboratory improvement amendments oversight of laboratory-developed procedures. laboratories have a long history of successful service to patients operating under clinical laboratory improvement amendments. a series of detailed clinical examples illustrating the quality and positive impact of laboratory-developed procedures on patient care is provided. these examples also demonstrate how clinical laboratory improvement amendments oversight ensures accurate, reliable, and reproducible testing in clinical laboratories. the field of pathology offers the opportunity to better understand the science behind the mechanisms of disease, to lead innovation of new diagnostic technologies, to provide quality oversight of these developments, and to have enormous impact on the lives of patients every day. patients benefit from laboratory medicine testing throughout their lives as every medical decision can be impacted by the result of a laboratory test. laboratory results constitute the majority of data in a patient's electronic medical record, and our procedures dictate the majority of downstream medical decisions for patients. , clinical laboratory medical professionals have the unique responsibility to patients for assessing the performance of technologies in providing the most accurate information to ensure the most appropriate and efficient course of care. it is an understatement to say that the medical field is rapidly changing. technology and new genomic data developed as a result of the human genome project are leading to an explosion of knowledge applicable to individual patient care; this is the promise of precision medicine. we must continue to innovate and integrate novel diagnostic tools, genomic information, and new treatments into clinical practice. considerable technologic advances allow clinical laboratory professionals to offer new testing that provides more information than ever before and often within a time frame that allows rapid patient care and better outcomes. next-generation sequencing (ngs) in genetics and oncology, maldi-tof in the clinical microbiology laboratory, and a variety of mass spectroscopy-based methods in clinical chemistry now allow precise and rapid testing with demonstrated improvements in patient care. it is often thought that when "laboratory tests" are done to reach a diagnosis, they are done with a kit or on a machine, but in fact, most are procedures done with the direct involvement of a laboratory professional or physician. laboratory tests are generally not fully encompassed by a "test kit" but often start with the pathologist examining the tissue section, bone marrow aspirate, or gram stain and determining what additional information is needed to provide the clinician with the best scenario so that the patient can be treated most effectively. often, clinical laboratory professionals lead the development and optimization of these approaches to improve care and fill a clinical need, and their involvement in the process helps ensure that the highest quality standards are maintained. ongoing development of these novel methods is critical to medicine and must be done with the highest level of safety and accuracy, yet simultaneously addressing growing demands to lower the cost of medical care in the united states. the regulatory oversight of laboratory-developed testing procedures (ldps) has a critical impact on patients' access to testing and diagnosis. currently, there is national discussion regarding the optimal regulatory oversight of laboratory tests and procedures that will balance the needed accuracy and safety with ensuring that new tests are made available to patients safely and expeditiously. oversight provided by the clinical laboratory improvement amendments (clia) and the food and drug administration (fda) currently exists in the clinical laboratory. it must be noted that a spectrum of testing activities take place in clinical laboratories. these activities range from complex procedures, such as evaluation of a tissue biopsy, classification of a tumor, or culture of a microbe, to more automated or standardized tests for which an fdaapproved kit is utilized. all of these activities take place under the direction of a laboratory professional and in accordance with the detailed requirements of clia. the fda review process is well suited for diagnostic assays that are commercially marketed as kits designed to operate across a spectrum of laboratory settings, in laboratories with a range of expertise. currently, fda approval or clearance requires prospective clinical trial data and a lengthy review process, and thus, fda approval takes considerable effort and time. the investment needed for this process impacts the types of tests, and also sample types, that are submitted for approval, as manufacturers must recover their investment afterward. additionally, fda approval for an in vitro diagnostic (ivd) specifies the sample type, clinical purpose, and other aspects of performance of the assay. when a new clinical need for the ivd arises, the need to use a new sample type arises, or any needed modification that arises in response to the ongoing and sometimes rapid advancements seen in medicine, incorporation of these improvements renders the test an ldp, with the validation needs of an ldp under clia. laboratories can be caught between the regulations and the needs to best serve their patients. the clia provide for oversight of clinical laboratories by defining all aspects of laboratory operation, including the quality programs required for clinical tests, personnel requirements, and the validation requirements for ldps. the clia certification of laboratories can be accomplished through several deemed agencies such as the college of american pathologists (cap) or the new york state department of health (nys-doh). these organizations provide operational guidelines and perform on-site inspections based upon checklists developed via consensus of laboratory experts, which include hundreds of pages of requirements and data points. compliance with clia has been built into clinical laboratory operations, mechanisms for data collection, training, proficiency testing (pt), and test implementation. laboratories are subject to unannounced inspections and must demonstrate satisfactory performance characteristics for any test offered to ensure that results are accurate. for testing not reviewed by the fda, such as ldps, laboratories must go through a rigorous validation process before offering the test for clinical use. under clia, the validation data collected by these laboratories are subject to ongoing peer review. in particular, organizations with deemed status overseeing laboratories (such as cap and nysdoh) conduct rigorous peer-inspection using detailed criteria developed specifically for molecular pathology. laboratories also participate in required pt to demonstrate assay quality, with interlaboratory data sharing and assessment (most often led by the cap) that leads to ongoing broad improvement in ldps. recent public documents have presented examples of specific ldps in which the clinical validity of the test, the interpretation or use by clinicians, or the reproducibility of the laboratory data was questioned, raising concern about the safety and efficacy of this category of tests. , enhanced regulatory oversight has been proposed to help ensure laboratories are delivering meaningful, high-quality results to patients. however, additional regulations have the potential to slow innovation and to limit and delay patient access to novel testing that impacts their clinical care, as well as add redundant reporting efforts and significant cost. expanded oversight of laboratories through a revised clia process has also been proposed (http://www.cap.org/showproperty?nodepath=/ucmcon/con tribution% folders/webcontent/pdf/ -cap-ldt-legisla tive-proposal.pdf. accessed april , ). in an effort to illustrate the need for and positive impact of laboratorydeveloped procedures on patient care, the following series of vignettes have been assembled. in each case, timely and highquality laboratory-developed procedures filled a key clinical need. the impact on patient care has been summarized. as possible, data describing interlaboratory comparisons are provided to demonstrate the quality of these ldps, as validated and performed in accordance with clia. these examples also serve to highlight the quality efforts and interlaboratory comparisons that take place before ldps are offered by laboratories for clinical use; these activities and data are often unknown to the clinicians who utilize these testing services. table provides a guide to the examples included and summarizes the impact of each assay along with key points about its utility. encephalitis is the most serious complication of herpes simplex virus (hsv) infection. while rare, hsv is commonly included among causes of viral encephalitis. since hsv infection can be treated effectively with acyclovir, it is critical to rapidly and accurately establish the diagnosis and initiate treatment to reduce morbidity and mortality. culture of cerebrospinal fluid (csf) is insensitive for the diagnosis of hsv encephalitis, so brain biopsy, a very invasive procedure with significant morbidity, was historically required to make a diagnosis, with results not available for days afterward. several studies demonstrated that detection of viral dna by polymerase chain reaction (pcr) using csf samples performed equivalently to brain biopsy, including a landmark study in . [ ] [ ] [ ] given the ease of collecting csf samples, the lower risk of complication, the lower cost, and speed of results, pcr became the standard of care for diagnosing hsv cns infections in the mid- s, with ldps used for nearly years. it was not until that the first fda-cleared pcr test for the diagnosis of hsv encephalitis became available, with a second test cleared in . laboratory-developed testing procedures dramatically improved the quality of care for many patients and continue to be used successfully today, as the cleared tests have limitations, requiring specific instrumentation not standard in many laboratories. additionally, one of the tests is highly multiplexed, which may not be appropriate in all clinical situations. herpes simplex virus can also cause infections in neonates, with a frequency of : to : deliveries in the united states. the infection is acquired by exposure to maternal genital secretions. the presentation of neonatal hsv varies and includes skin, eye, and mouth infection, with encephalitis and disseminated disease in over % of cases. again, rapid diagnosis is needed to prevent morbidity and sequelae from encephalitis. the diagnosis of encephalitis is made via pcr of csf samples, while testing of plasma or serum is critical to diagnose disseminated disease. the ability to use plasma or serum is very important as it may be difficult to obtain enough csf from a newborn to assess all diagnoses in the differential. although there are fdacleared assays to test csf for hsv, there are no assays cleared for testing serum and plasma. laboratory-developed testing procedures continue to play a critical role in the diagnosis and management of disseminated hsv infection in newborns. additionally, ldps have performed with a high degree of accuracy and interlaboratory agreement. blinded pt samples were distributed to laboratories as part of a cap pt survey for analysis of hsv; . % correctly identified hsv- , and . % identified hsv, but not noting the subtype; an overall accuracy of . % was obtained. previous proficiency surveys showed similar results for samples containing hsv . over % of the laboratories used ldps. bk virus infection is very common, with a seroprevalence in the adult population of * %. after primary infection, the virus colonizes the renal and urinary tracts; healthy individuals will occasionally shed virus in their urine without consequence. however, in renal transplant recipients, bk virus is the major cause of polyomavirus-associated nephropathy (pvan), putting % to % of kidney transplant patients at risk of premature allograft failure. given the lack of effective antiviral therapy for bk virus, the key to preventing allograft loss is to identify at-risk renal transplant recipients early and reduce immunosuppressive therapy before pvan develops. reduction of immunosuppressive therapy helps control viral replication and in most cases prevents the development of pvan. there is a critical balance between too much immunosuppressive therapy, which can lead to pvan, and too little immunosuppression causing rejection. the ability to monitor bk virus levels in the blood allows for informed clinical decisions. studies have shown that monitoring patients with viral load testing during the first years after transplant can dramatically reduce the development of pvan. consensus guidelines recommend that screening for bk replication be performed at least every months during the first years posttransplant and then annually until the fifth year posttransplant. when the plasma viral load value rises above a threshold ( to copies/ml), a renal biopsy may be performed to assess for pvan, and immunosuppressive therapy is reduced based on the results of the biopsy. viral load testing is also done if there is an increase in serum creatinine, as the level of bk virus aids in distinguishing rejection from pvan. although bk viral load testing has been the standard of care for several years and is used in transplant centers across the country, there is no fda-cleared or fda-approved test available. all testing is performed using ldps. if these ldps were not available, most cases of pvan would not be identified promptly, leading to negative patient outcomes such as allograft loss or rejection. cytomegalovirus (cmv) can cause a wide range of complications among both solid organ transplant and hematopoietic stem cell transplant recipients, as well as in other immunocompromised patients. cytomegalovirus has a high seroprevalence, and large numbers of transplant patients experience reactivation or primary infection, with probability increasing based on pre-transplant serostatus, severity of pretransplant conditioning, and allograft relatedness. , although infection can be subclinical, high or increasing viral load signals increased the risk of symptomatic disease, which can range from relatively mild constitutional symptoms to severe end-organ infection or potentially fatal disseminated disease. preemptive therapy of high-risk patients based on the detection of increasing cmv load in peripheral blood was shown to be effective in the s , ; however, the first fda-approved ivd test did not appear on the market until . in the intervening years, laboratory-developed assays played a critical role in bridging the gap. the presence of such methods and their adoption across the country enabled the routine use of cmv screening for asymptomatic patients in transplant centers soon after data supported its utility. the availability of such methods has likely saved many lives over the years, supporting early diagnosis, preemptive treatment strategies, and the assessment of therapeutic treatment efficacy. , [ ] [ ] [ ] the widespread use of ldp cmv quantitative methods produced a generation of transplant physicians comfortable with the use of such methods and changed the epidemiology of posttransplant cmv disease, markedly reducing the incidence of early disease in such patients. over the years of ldp use, numerous studies focused on continuous improvement and optimization of methods, including the development of international quantitative standards in . the ability to rapidly incorporate advances in technology (including the advent of real-time quantitative methods) has been demonstrated by the improvement in sensitivity and other performance characteristics of such tests over time. the data accumulated throughout these experiences informed the development of the first commercially available cmv ivd assays. in fact, the absence of ldps and the vast clinical and laboratory experience that they provided likely would have delayed the availability of commercial methods, and their performance characteristics taken longer to optimize to today's levels. human papilloma virus (hpv), the causative agent of genital warts, has been implicated in the development of * % of cervical cancers. more than hpv genotypes have been described, and approximately are capable of infecting the human genital tract. of these, a relative few are known to cause cervical cancer and other malignancies; these can be identified by genotyping. today, assays are fda approved for detecting high-risk hpv genotype strains in cervical specimens. [ ] [ ] [ ] [ ] these tests are routinely used to confirm the presence of an hpv infection, screen for cervical cancer, and refer cases with an indeterminate cytology examination. during the past decade, a rise in oropharyngeal squamous cell cancer, primarily in to -year-old caucasian males with limited alcohol and tobacco exposure, has been described. unexpectedly, investigators discovered the frequent presence of high-risk hpv genotype strains in these lesions. human papilloma virus-positive head and neck cancer is biologically distinct from hpv-negative disease. patients with hpv-driven tumors have a significantly better prognosis, including response to chemoradiation therapy and overall survival, compared to hpv-negative patients. therefore, testing head and neck cancer specimens for high-risk hpv genotypes has become standard of care and is used to guide treatment. , however, the hpv tests that are fda approved for cervical specimens have not been approved for head and neck cancer, leaving a critical gap for patient care. clinical laboratories have thus had to develop new assays or modified the existing fda-approved ones to detect high-risk hpv genotypes in head and neck cancer specimens. inclusion of patients in several clinical trials is based on these ldps (www.clinicaltrials.gov. accessed april , ). without laboratory-developed tests, patients with head and neck cancer cannot benefit from personalized treatment strategies. clinical laboratories must be highly vigilant for infectious disease outbreaks, since they are likely the first to recover the pathogen and recognize the potential for an outbreak. recent examples of emerging or reemerging pathogens causing substantial human morbidity and mortality include avian influenza virus ("bird flu"), chikungunya virus, ebola virus, middle eastern respiratory syndrome virus, severe acute respiratory syndrome virus, and zika virus. , at the time of their emergence, no fda-approved tests were available to detect any of these pathogens. in response, many clinical laboratories developed, validated, and implemented the ldps needed to care for patients at their institutions. , these assays were based on extensive data sets and reported in peer-reviewed journals, supporting their quality claims. since performance characteristics such as analytic sensitivity (limit of detection) may vary between different assay designs, as was recently discussed for several different zika virus tests, these sorts of collaborative efforts are essential. in many cases, laboratories leading these efforts collaborated with one another to share validation materials, perform interlaboratory comparisons, and exchange blinded testing samples (http://www.usatoday.com/story/ news/ / / /texas-hospitals-develop-rapid-zika-test/ /. accessed april , ). while perhaps not ideal, there is an urgent need for a more integrated and coordinated mechanism for rapid diagnosis of novel infectious agents that incorporates both the public health and hospital laboratories. the recent emergence of zika virus, which has been linked to severe birth defects, underscores the need for clinical laboratories to have rapid access to diagnostic tools. when the secretary of health and human services declared zika virus to be a public health emergency, the first fda emergency use authorization for zika virus testing was granted to a test available only to the public health laboratory system, not to hospital laboratories on the front lines of patient care (https://www.fe deralregister.gov/documents/ / / / - /authori zation-of-emergency-use-of-an-in-vitro-diagnostic-device-fordiagnosis-of-zika-virus. accessed april , ). as a result, the public health system quickly became overwhelmed, as it has been during past outbreaks, such as influenza. in many areas, turnaround times for zika virus testing exceeded to weeks (http://www.nytimes.com/ / / /us/zika-testdelays-florida-pregnant.html?_r¼ . accessed april , , http://medicalxpress.com/news/ - -lab-constraints-zikaresults.html. accessed april , , http://www.miamiher ald.com/news/health-care/article .html. accessed april , ). these delays critically impact patient care, particularly for pregnant women with possibly affected fetuses. in comparison, many hospital-based and national reference laboratories are able to report results within hours (http:// www.usatoday.com/story/news/ / / /texas-hospitalsdevelop-rapid-zika-test/ /. accessed april , , http://www.nytimes.com/ / / /us/zika-test-delays-flor ida-pregnant.html?_r¼ . accessed april , ). for example, in miami-dade florida, where more than people have been confirmed zika positive and the virus is circulating in the local mosquito population, the public health laboratory system encountered a backlog of nearly untested specimens (http://www.miamiherald.com/news/health-care/arti cle .html. accessed april , ). diagnostic assays for zika and other emerging pathogens will continue to evolve, but it is clear that rapid identification of pathogens during other outbreaks facilitates rapid treatment and appropriate isolation of patients, leading to improved patient outcomes and potentially slowing the spread of infections such as influenza (http://www.cdc.gov/flu/professionals/diagnosis/molecu lar-assays.htm. accessed april , ). implementation of the first rapid diagnostic tests for influenza was directly associated with reduced length of hospital stay, decreased mortality, and reduced costs. access to diagnostic tests, early in the course of an outbreak and in hospital laboratories, has a positive public health impact. the kras gene encodes a gtpase critical in signal transduction that is known to be mutated in a wide range of tumor types. a landmark study presented at the american society of clinical oncology (asco) meeting in demonstrated that patients with metastatic colorectal cancer harboring a mutated kras failed to respond to targeted therapy with cetuximab. , at the time, there were no clinical tests for kras mutations available. molecular pathology laboratories worked quickly to fill this need, to define the best analytic approaches, and to ensure that test results done in one laboratory matched those done in another. [ ] [ ] [ ] within a few months, laboratories were able to offer fully validated kras assays that worked reliably and were safe for patient care. under clia, the validation data collected by these laboratories were subject to ongoing peer review, and laboratories participate in ongoing pt to demonstrate consistent assay quality. in , the asco and the national comprehensive cancer network (nccn) recommended mutational profiling of kras exons and before institution of anti-epidermal growth factor receptor (egfr) therapy for patients with metastatic colorectal cancer; it became standard of care to assess formalin-fixed paraffin-embedded tumor tissues from patients with metastatic colon cancer for kras mutation status. , it was not until years later that the fda cleared qiagen's therascreen kras test, designed to detect the presence of mutations in the kras gene in colorectal cancer. by this time, new data demonstrated that kras analysis alone was not enough; mutation analysis of other genes was necessary, , and the fda-approved assay was already inadequate for patient testing compliant with national treatment guidelines. without ldps, an estimated % of patients with non-exon kras mutations would be overtreated with expensive anti-egfr therapy. the use of ldps has thus persisted in clinical practice to provide patients with the most complete information to guide treatment. in the cap kras-b- mailing, laboratories reported results from testing blinded proficiency-testing specimens. the specimens contained recurring somatic mutations in kras exons or (nm_ . ), c. g>t (p.g v), and c. g>a (p.g d). an acceptable response was reported by over % of the laboratories for both mutations ( / for p.g v and / for p.g d). the vast majority of reporting laboratories utilized ldps. kras and ras family gene mutation analysis is also critical in the management of patients with non-small-cell lung cancer (nsclc) and other tumors, for which fda approval of kits has not occurred; ldps or off-label use of kits is required. braf belongs to a family of serine-threonine protein kinases that participate in signal transduction cascades involving ras, raf mek, and erk family members. this pathway is important in the regulation of normal cell proliferation and differentiation. activating mutations in braf can lead to increased proliferation and prolonged cell survival in a variety of tumor types. laboratories will typically test for braf mutations in low-grade gliomas (for diagnosis), colorectal cancer (to establish the sporadic origin of msi-h tumors and response to anti-egfr therapy), hairy cell leukemia (for diagnosis), lung adenocarcinomas (to predict response to therapy), thyroid cancer (for preoperative detection of thyroid cancer in fna samples and prognosis in papillary thyroid carcinoma), or melanoma (to predict response to braf kinase inhibitors). for one of these indications, malignant melanoma, fdaapproved companion diagnostics are available. vemurafenib (zelboraf) is a kinase inhibitor indicated for the treatment of patients with unresectable or metastatic melanoma with braf v e mutation. dabrafenib (tafinlar) is a kinase inhibitor indicated as a single agent for the treatment of patients with unresectable or metastatic melanoma with braf v e mutation or in combination with trametinib (mekinist) for the treatment of patients with unresectable or metastatic melanoma with braf v e or v k mutations (www.fda.gov. accessed april , ). the cobas braf v mutation test (roche molecular systems, pleasanton, ca, usa) sporadically cross reacts with braf v k and braf v d mutations , and thus is neither sensitive for braf v mutations nor specific for braf v e mutations, confounding accurate outcome evaluations and preventing its usefulness in selecting patient for tafinlar therapy. the thxid braf kit (biomerieux, boston, ma, usa) does detect both braf v e and braf v k mutations (but not other braf v mutations) and is necessary to distinguish between alternate therapeutic options (single agent vs combination therapy). it is important to note that increased cell proliferation has been seen in tumors treated with braf inhibitors with normal braf. it is therefore important to identify all braf activating mutations to assist in the selection of appropriate therapy. the fda-approved assays are therefore not adequate for current clinical needs. in a european multicenter study, consecutive tumor samples of histologically proven melanoma tumor tissue were assessed for braf mutation status by the cobas system and a variety of laboratory developed procedures. testing was concordant for ( . %) of samples but discordant for ( . %). among the discordant cases, had invalid results ( samples with the cobas and with ldps). of samples with braf v mutations detected by the ldps (but not by the cobas mutation test), were v k, d, or r mutations, and contained only % tumor cells. for the samples with braf v mutations detected by the cobas but not by the ldps, were confirmed with retesting, was not mutated, and were considered invalid results. this study documents similar results between the performance of braf ldps and ivds. further data can be gathered from the cap pt program. in the braf-b- cap proficiency survey, laboratories reported on the detection of v e and other braf mutations by a variety of analytic methods. two of the well-characterized specimens in the proficiency test contained braf v e alleles, and . % and . % of laboratories correctly reported the mutation. the majority of these laboratories used ldps. there are no currently available braf mutation tests approved for use in other tumor types such as those mentioned above, and use of the existing ivd tests would constitute offlabel use and hence ldps. microsatellite instability is the presence of hypermutability in repetitive dna sequences resulting from impaired dna mismatch repair. microsatellite instability can be an inherited or acquired feature of tumors. microsatellite instability occurs in approximately % of all colorectal carcinomas and is a consistent feature of colorectal and other tumors in patients with lynch syndrome. tumors are classified as showing high levels of msi (msi-h phenotype) if or more of microsatellite markers (or ! %) exhibit instability, a microsatellite-stable phenotype if none of the markers show instability, and an msilow phenotype if only of or less than % of the markers show instability. studies have confirmed that the appropriate cutoff for determining an msi-h phenotype is the finding of instability in % or more of the markers tested. the finding of an msi-h phenotype is consistent with the presence of defective dna mmr in the tumor. the finding of an msi-h phenotype in a crc increases the likelihood that the patient has ls but is not specific for ls. the definitive establishment of a diagnosis of ls requires the finding of a pathogenic germline mutation in one of the dna mmr genes. additional testing that can be offered to determine whether a patient with an msi-h crc is likely to have ls includes testing the tumor for dna mmr protein expression using ihc, braf v e point mutation analysis (since braf-mutated msi-h colorectal carcinomas are known to have sporadic mmr gene mutations), and mlh promoter hypermethylation. studies have shown that an msi-h phenotype is a favorable independent prognostic indicator in patients with crc. in addition, some reports indicate that msi-h tumors may not be responsive to -fluorouracil-based therapies. recent draft guidelines developed collaboratively by professional societies recommend that deficient mismatch repair/microsatellite instability testing must be performed in all colorectal cancers for prognostic stratification and identification of patients with lynch syndrome. although numerous laboratories offer msi testing using ldps, there are currently no fda-approved tests for the evaluation of microsatellite instability. a summary of cap pt results demonstrates excellent performance of laboratories participating in the msi proficiency surveys. this good performance of laboratories over the years may be partly due to the educational nature of the cap pt, which provides laboratories with an external mechanism to monitor the quality status of their testing. epidermal growth factor receptor is a membrane-bound tyrosine kinase which activates several signaling pathways known to be altered in human cancer, including nsclcs. [ ] [ ] [ ] nonsmall cell lung cancer tumors with egfr-activating mutations are responsive to gefitinib and erlotinib, small molecule tyrosine kinase inhibitors of egfr. , the fda approval of anti-egfr therapies based on clinical trial outcomes data resulted in the need for clinical laboratories to test tumor tissue for the egfr-sensitizing mutations in order for patients to be eligible for treatment. with no fda-approved "companion" diagnostic test on the market, clia-licensed laboratories developed and validated ldp tests for the most common egfr mutations as early as . the fda followed with approval of the roche cobas egfr mutation test in along with the qiagen therascreen egfr rgq kit. both assays tested for the exon deletions and the exon l r point mutation. of note was that each test was approved for specific therapeutic indications and specimen types. as new drugs became available, approval for new claims was needed. laboratory-developed procedures continue to be the method of choice due to the limitations of claims made for fda-approved assays and performance characteristics, including types of mutations being detected. clinical laboratories participate in twice-yearly proficiency test challenges of unknown samples that must be analyzed and reported, with results graded and compared to other laboratories performing the testing. in the cap egfr-b- proficiency test, laboratories reported results from testing unknown proficiency-testing specimens in late . the specimens con- note: some laboratories do not test for certain mutations, hence, the denominator is often less than . as patients being treated with these new targeted anti-egfr therapies began to relapse, further studies revealed that egfr harbors both sensitizing and resistance mutations. the clia laboratories have demonstrated the ability to detect all mutations in the egfr gene as well as in other genes using ngs assays to sequence panels of cancer-related genes. this panel approach allows the laboratory to provide the oncologist with a more comprehensive profile of the tumor, using a costeffective technology that makes maximal use of small tissue samples and thus makes treatment strategies more effective. in addition, the time saved by testing a broader panel of gene targets can result in better outcomes for the patient as well as fewer adverse drug reactions. for the payer, the cost savings of such an approach versus algorithm-based testing with single gene assays is significant. currently, there are no fdaapproved sequencing assays for egfr mutation status, and ldps are solely used for the detection of these mutations that define therapy selection. the complexity of cancer biology and the ever-evolving therapeutic approach to management of the patient with cancer more often requires expanded knowledge of the tumor beyond single-gene mutation status. over the past several years, the laboratory's ability to multiplex testing for several genes or genetic variants has been limited by the available technologies. next-generation sequencing or massively parallel sequencing has allowed the laboratory to provide a more comprehensive genomic profile of tumor cells in a single assay than previous methods. the ability to detect numerous mutations in multiple genes results in information that can allow the oncologist to develop a more accurate treatment strategy including therapies selected based on a "responsive" tumor profile and those not selected based on the presence of resistance mutations. [ ] [ ] [ ] instrumentation from thermo fisher (thermo fisher life-technologies, carlsbad, ca, usa) and illumina (illumina, san diego, ca, usa), the personal genome machine (pgm), and miseq, have made ngs suitable for routine clinical laboratory testing. [ ] [ ] [ ] in , the miseq dx obtained fda approval. despite this approval and the routine use of ngs in ldps setting, there are no currently fda-approved ngs tests for application in oncology. although many drug package inserts require or allude to the use of a companion diagnostic for eligibility, very few companion diagnostic tests are fda approved and none using ngs technology. as an ldp, clinical laboratories are required to demonstrate rigorous performance criteria for wet-bench testing and analysis pipelines to ensure the test is functioning properly for its intended clinical purpose. , [ ] [ ] [ ] most ngs testing for therapeutic selection in cancer consists of panels of genes that range from to or more genes. each test can be designed to detect hotspots of known mutations in those genes, to sequence the entire coding region of the genes, or to sequence the entire gene. the end result is a comprehensive profile of the tumor genome that can then be used to tailor therapy for the individual patient. although ngs assays cost more than single-gene assays, the cost per gene sequence is dramatically reduced and results in cost savings over using multiple single-gene tests. furthermore, ngs panels can be applied to very small specimen samples, using as little as to ng of input dna depending on the analytic platform utilized. since evaluation of therapeutic biomarkers is usually needed in the setting of advanced disease and such patients often have only limited tissue samples available for testing, ngs assays allow for much more extensive genomic information to be obtained compared to single-gene assays, each of which can require dna input comparable to that of an entire ngs panel. a total of laboratories recently participated in a capsponsored proficiency assessment of ngs cancer panel testing (ngsst-a- ), with data collection on gene mutations (akt , alk, braf, egfr, fbxw , idh , kit, kras, nras, and pik ca). of genotyping calls across the spectrum of mutations tests, ( . %) were called concordantly (unpublished data). no other ldp in the field of oncology has had a greater impact on patient care than has the quantitation of rna in chronic myelogenous leukemia (cml). one of the first (and arguably most successful) molecularly targeted cancer therapies is the bcr-abl -targeted tyrosine kinase inhibitor, imatinib, which was fdaapproved in . in those very early days of targeted therapy, long before the advent of fda-approved "companion diagnostics," the ubiquitous and obvious method to determine the efficacy of novel leukemia treatments was to directly quantitate the target of the inhibitor drug, namely, the cancer cellspecific bcr-abl fusion gene. a reduction in posttreatment bcr-abl rna levels, as measured by sensitive laboratorydeveloped pcr-based methods, was shown to be the best available test for predicting therapeutic response and long-term progression-free survival in tki-treated patients with cml. consensus oncology practice guidelines in both the united states (nccn) and europe (eln), going back at least a decade, have universally recommended that tki-treated patients with cml should be serially monitored with a (laboratory-developed) bcr-abl rt-pcr blood test at least every to months during their lifelong course of tki therapy. the nccn and eln guidelines have also long recommended serial bcr-abl rna testing to directly inform not only the appropriate dose of tki (to overcome developing resistance) but also the therapeutic switch from one tki to another (depending on the drug's known resistance profile). to directly support optimal therapeutic decision-making in the routine care of patients with cml, clinical laboratories have been offering accurate and sensitive pcr-based laboratory-developed procedures for bcr-abl for at least the last years. recognizing that standardization of these ldp's was necessary to promote uniform therapeutic decisionmaking, the laboratory community undertook an extensive multiyear project to create a standardized "international scale" (is) of measurement for bcr-abl messenger rna. follow-up efforts resulted in the creation of a world health organization-recognized panel of reference materials directly linked to the bcr-abl is and the subsequent creation of secondary is-calibrated reference materials that could be used for routine daily qc in clinical laboratories. , recognizing the additional need for pt, the cap has been offering semiannual bcr-abl pt surveys for at least years, with a progressive increase in the number of participating laboratories (from * in to * in ). as proof of the nearuniversal recognition of assay standardization, approximately % of these accredited laboratories now report their pcr results using the standardized is. a cap survey confirmed excellent interlaboratory precision, with over % of laboratories reporting a bcr-abl is result within internationally acknowledged acceptable tolerance limits ( . logs) for is reporting of a sample with an approximate -to -fold reduction in pretreatment bcr-abl levels the primary driving force behind the remarkable increase in longevity and quality of life for patients with cml over the past years has no doubt been the availability of noveltargeted tki therapies. this has become the paradigm for personalized/precision cancer medicine programs, coupled with parallel effort of the laboratory community toward building, improving, and standardizing accurate, precise, and sensitive laboratory-developed tests for bcr-abl . of note, this year targeted therapy program for cml occurred entirely without the availability of fda-approved bcr-abl diagnostic reagents, which have only become available in . these fda-approved assays were based upon those developed in clinical laboratories; they are not approved for diagnosis of cml nor do they cover the spectrum of breakpoints that occur in the disease. during those ground-breaking first years of the targeted cancer therapy era, if the laboratory community had been prohibited from providing high-quality, standardized ldp-based testing under existing clia guidelines, the negative consequences to patient care in the past and the future would have been substantial. fragile x (fx) syndrome is one of the most common inherited causes of intellectual disability. the causative molecular mechanism is an expansion of a cgg repeat region of the regulatory region of the fmrp gene. when the cgg repeat expands beyond approximately cgg repeats, the gene is methylated and silenced. laboratory testing for fx includes sizing the number of repeats as well as methylation analysis and has been available for clinical diagnostic and carrier status testing for over years. the american college of medical genetics and genomics (acmg) has published practice guidelines for appropriate test ordering. it is a first tier test for individuals and families in which an x-linked inheritance pattern of intellectual disability is suspected. once an expanded fx allele has been identified, other family members can be tested to identify premutation carriers at risk of having affected offspring. prenatal (fetal) or preimplantation genetic diagnostic testing is available for known fx carriers. according the genetic test registry, over laboratories in the united states offer testing for fx (https://www.ncbi.nlm. nih.gov/gtr/; accessed - - ). currently, all fx testing is performed as ldps: no fda-cleared assay is available. pcr primers and southern blot reagents are available commercially as analyte-specific reagents (asr) or as investigational use only. clinical laboratories use these commercial reagents, or design primers or probes, combine them internally to develop the assay and establish performance characteristics. the acmg has published standards and guidelines for clinical laboratories that perform this test. reference materials to standardize sizing were developed through the genetic testing reference material program sponsored by the centers for disease control and prevention (cdc), the national institute of standards and technology (https://www.nist.gov/node/ , accessed november , ), and the world health organization. proficiency testing through the cap has demonstrated the excellent performance of clinical laboratories of this high-complexity ldp. as the genetic basis for many human diseases became apparent, sequence-based diagnostic testing was implemented as a way to provide definitive diagnoses for patients and their families. many laboratories began offering sequence-based testing for heritable disorders in the s, using a variety of mutationscanning techniques, such as single-strand conformation polymorphism, denaturing hplc, mlpa, and others. sanger-based sequencing was the gold standard, despite being slow and expensive. the multigenic nature of some of these disorders made these sequencing approaches challenging due to the sheer number of genes and size of the sequence requiring analysis. in recent years, however, most of this testing has been converted to ngs, which offers significant advantages in terms of analytic capabilities, quality, speed, and cost. the repetitive sequence reads in a single region ensure an enhanced level of quality, and ngs assays can be designed to interrogate anything from small to large gene panels, whole exomes, and beyond, depending on the clinical need being addressed. consensus guidelines for ngs assays have been developed by multiple professional societies and address the development, validation, and quality control of these assays. , the cap has developed inspection checklists for laboratories performing ngs for detection of somatic mutations in cancers as well as germline mutations that cause heritable diseases. progress has also been made in the planning and production of reference materials and proficiency samples. together, these practices and resources have yielded laboratory-developed assays that can be demonstrated to meet the quality levels needed for patient care. in addition to continuous quality assessment of the "wet laboratory" procedures, ongoing national and international efforts to share data, and construct and maintain up-to-date curated databases for variant interpretation, are critical for quality care. as new mutations and variants are detected, interpretation and assessment of clinical impact, including determination of the clinical importance of variants of undetermined significance, is critical. rapid generation of genomic data, disorganized data sharing, and a lack standardization have created challenges, and a more consistent approach to clinical sequence interpretation is needed, along with centralized and openly accessible databases for sequence and clinical information. in recognition of the urgent need for up-to-date variant classification resources, the acmg and association for molecular pathology released a landmark guidance document in , which has been implemented by us and international laboratories. additional resources are outlined and include ncbi's clinvar database (https://www.ncbi.nlm.nih.gov/clinvar/), which has quickly become a valuable centralized resource for clinically classified variants, and the clinical genome resource (clingen, www.clinicalgenome.org), which serves as a centralized site for managing genomic knowledge surrounding genes and variants. with exome and genome sequencing being increasingly implemented, guidance has been issued by the acmgg on how to deal with the incidental identification of variants in the so-called "actionable" genes in patients tested for unrelated conditions. additionally, quality assessment focusing on the informatics pipeline and variant interpretation could effectively utilize sequence data sets, as has been recently outlined. the genetics and pathology communities are increasingly embracing data sharing, which will lead to needed improvements in divergent interpretation of gene sequence variants. these interpretative tasks would be beyond the scope of an fda approval for a kit, or the clia oversight of an ldp, but have a critical impact on patient care based on genomic information. next-generation sequencing analysis of a variety of gene panels has become routine in clinical care and has had a positive impact on the diagnosis and treatment of patients and families with complex syndromes and disorders. examples of of the most common clinical settings in which gene panels are tested for potential germline mutations are provided below, along with information on the clinical setting, potential benefits, and also challenges in utilizing these approaches. inherited cardiomyopathies are common disorders and include hypertrophic cardiomyopathy (hcm), dilated cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy, and restrictive cardiomyopathy. , several characteristics of all inherited cardiomyopathies provide compelling reasons for genetic testing and include ( ) a substantial genetic component with detection rates currently ranging between % and %, , ( ) long presymptomatic phases with acute disease onset typically not before adolescence, and ( ) a predisposition to sudden cardiac death (scd), which can be the first presenting sign. frequent and heartbreaking publicity following cases of sudden death of competitive athletes has brought these diseases to public attention, and a recent study shows that % of scd cases are due to an underlying unrecognized inherited cardiomyopathy. the importance of these heritable abnormalities is underscored by the fact that nearly a third of the genes for which the acmg recommends return of results, regardless of the test indication, are made up of these cardiomyopathy genes. these disorders are heterogeneous, which can lead to clinical diagnostic uncertainty or error; hence, large multigene panels are particularly useful to cover the spectrum of genes that may cause a clinical disorder. importantly, the identification of pathogenic variants in affected individuals can inform medical management of family members and can identify those at risk early and also release negative individuals from clinical screening. genetic testing can also identify phenocopies such as fabry disease, which can masquerade as isolated hcm. while fabry disease is rare, disease-modifying treatment is available, and therefore, genetic testing provides essential clinical information for these patients. epilepsy is a common disorder of the central nervous system characterized by periodic loss of consciousness with or without convulsions associated with abnormal electrical activity in the brain. this can significantly affect the quality of life and has major psychological and socioeconomic consequences. it is estimated that there are more than million people with epilepsy worldwide, and an estimated in people in the united states will develop epilepsy at some point in their lifetime. a significant proportion of cases show a familial distribution, and there is an increased risk of epilepsy with a family history. the prime requirements for successful management of epilepsy are a complete diagnosis and selection of an optimal treatment to benefit the patient. development of epilepsy may involve multiple gene abnormalities or a gene abnormality in concert with an environmental trigger. more than genes have been shown to be associated with epilepsy, and a precise genetic diagnosis can help in deciding the accurate treatment and follow-up. , evaluation of all genes implicated in epilepsy is most efficiently accomplished using an ngs panel to provide accurate information to the physician for treatment planning. nextgeneration sequencing assays are performed as ldps under clia. an example of such one gene is scn a, which causes dravet syndrome and can be successfully treated. it is important to avoid treatment with sodium channel blockers as these can worsen seizures in dravet syndrome. these include phenytoin (dilantin), fosphenytoin (cerebyx, prodilantin), carbamazepine (tegretol), and other medications. as ongoing research reveals new genes and mutations relevant to these diseases, it is important to classify newly found variant quickly and accurately. open access to new information and consensus efforts to define standards for classification and reporting of variants and vuss will be critical in ensuring that patients get the most upto-date and complete information from genomic testing. , another example is the recently discovered gene tbckrelated epilepsy. tbck-related intellectual disability syndrome is rare with developmental delay, hypotonia, and seizures. children with lower levels of the tbck protein have slower cell mtor signaling, which can be improved by the addition of leucine, which may provide future therapeutic options. it is important that clinical laboratories adapt their ngs panels to incorporate new targets as clinical utility is established. neuromuscular diseases (nmds) refer collectively to the many disorders that affect the peripheral nervous system, either by impairing the proper development or functioning of muscles or by damaging the associated nerves or neuromuscular junctions. muscular dystrophies that form the majority of inherited nmds share clinical, genetic, and pathological characteristics, including muscle degeneration and wasting, progressive muscle weakness, hypotonia, and variably elevated serum creatine kinase levels. cardiac involvement is often present, accounting for high morbidity and mortality. there are different genetically defined types of muscular dystrophies categorized based on the age of onset, the specific muscles involved, and common characteristic clinical features. [ ] [ ] [ ] [ ] congenital muscular dystrophies and limb-girdle muscular dystrophies are the major subgroups; these are genetically heterogenous, with many new genes being implicated in recent years. lack of pathognomonic signs or specific biochemical markers and the presence of high phenotypic overlap with other forms of nmds make diagnosis difficult. molecular assessment is critical not only to establish a diagnosis but also to allow participation in clinical trials of therapeutic treatments that are designed for a specific set of variants or variant types. an extensive diagnostic workup involving protein studies on muscle biopsy may be used to narrow the number of single genes to be tested, but many patients never are specifically diagnosed. comprehensive approaches to expedite molecular diagnosis now include ngs-based panel testing for sequence analysis of all disease-associated genes in a single analysis. [ ] [ ] [ ] heritable cancer panel genomic testing for familial cancer syndromes has become routine over the past decades. approximately heritable cancer syndromes are recognized and are causative of % to % of all cancers. although familial breast cancer has perhaps become the most publicly known example of testing, genes for other inherited cancer syndromes may be included in ngs multigene panels. patients who carry a germline mutation of brca or have a lifetime risk of breast cancer of % to %. the us preventative task force recommends brca and testing for women who have family members with breast, ovarian, fallopian tube, or peritoneal cancer or meet other criteria. numerous studies have demonstrated the psychosocial benefits of genetic counseling and testing. , for patients who carry a germline mutation of brca or , surgical interventions may significantly reduce the risk of cancer or death. contralateral mastectomy has been shown to reduce the risk of death in carriers by %. prophylactic salpingooophorectomy has been shown to dramatically reduce the mortality due to ovarian cancer or breast cancer in brca mutation carriers. similarly, identification of lynch syndrome mutations can permit surveillance leading to earlier detection and marked improvement in survival in patients developing colorectal, endometrial, or ovarian cancer. although more than decades have passed since sequencebased analysis of high-penetrance cancer genes has been performed, only laboratory-developed procedures have been available. countless patients and families have benefited from the availability of these ldps. epidermolysis bullosa (eb) is an inherited skin and connective tissue disease that causes skin and oral blistering with only mild trauma (http://www.niams.nih.gov/health_info/epidermolysis_ bullosa/epidermolysis_bullosa_ff. accessed november , ) . the severity of the disorder depends on the layer of skin where the tissue separation occurs. approximately % of patients with biopsy-proven eb will have mutation(s) in of genes known to cause the disorder (http://www.niams.nih.gov/health_info/epider molysis_bullosa/epidermolysis_bullosa_ff. accessed november , ). knowledge of the specific gene can direct therapy and provide reproductive options for the family. for many years, it was possible only to sequence the suspect genes one by one, taking months to years, and only on a research basis. recently, with the advent of ngs technology, a small number of clinical laboratories have stepped in to develop a rapid multigene ngs approach that provides answers quickly in time to make treatment decisions as well as to provide carrier and prenatal testing in at-risk families. , as new candidate genes have been identified, ngs has been validated and offered for clinical testing. under clia, the validation data collected by the laboratory was subject to ongoing peer review, and the laboratory participates in ongoing pt to demonstrate assay quality. as the disease is rare ( children born with eb annually), the cost of bringing such a test through fda for approval is prohibitive. without an available ldp, patients and families affected by this disease would go without specific diagnoses, be unable to enroll in gene/mutation specific therapies (currently in development by at least pharmaceutical companies and academic centers) (http://www.debra.org/research-trials. accessed november , ), or have control over their reproductive lives. whole-exome sequencing (wes) involves evaluating the coding regions of all * human genes at once, to search for the underlying molecular cause of an undiagnosed but presumed genetic disorder. these tests are used for patients who already have undergone extensive genetic diagnostic testing and exhausted the (limited) fda and ldp singlegene tests or in cases where it is more cost-and timeeffective to start with wes. whole-exome sequencing is used for the so-called "diagnostic odyssey" patient and has a high diagnostic yield for these patients, with % to % of studies yielding a diagnosis. , the tests are highly complex and involve capture of the relevant dna segments, sequencing of those segments, bioinformatics approaches to sequence alignment and identification of variants (differences between patient dna and reference), interpretation of the identified variants, and report generation. under clia and nysdoh, the technical validation data collected by the laboratory prior to offering wes are required, and the laboratory participates in ongoing pt (through cap and sample exchanges) to demonstrate assay quality. as this is cutting-edge science and medical practice, the capture and sequencing technology, bioinformatics, and interpretation tools are evolving at a very fast pace. to provide the best service to patients, laboratories must frequently update, revalidate, and offer new services. whole-exome sequencing is offered as an ldp by laboratories which have extensive experience in genetic testing. the time delay involved in bringing this test and its frequent modifications to the fda is prohibitive. as these tests serve the rare disease community, and reimbursement is limited by the lack of pricing for a specific cpt code, the cost of bringing wes through fda approval would be a major deterrent. innovation would be slowed, and likely several laboratories would remove the test from test menus. with affected individuals in the united states, , huntington disease (hd) falls under the category of a rare (or orphan) disorder, and given its limited market, no commercial genetic testing platform has been developed or submitted to the fda for review. the relatively small number of laboratories offering diagnostic or predictive (presymptomatic) testing for this disorder must therefore rely entirely on ldps, without which patients with hd and their at-risk relatives would have no access to testing and diagnosis. despite the characteristic clinical features (the movement disorder [chorea] along with intellectual decline), and lack of preventive or curative treatment for hd, genetic testing is widely relied upon by hd families and their physicians. onset of symptoms is often insidious and nonspecific, and definitive early diagnosis can only be accomplished at the dna level. presymptomatic testing, which is offered to the adult offspring of patients with hd (who are at % risk of inheriting this autosomal dominant disease), can only be accomplished using ldps and allows crucial life-planning decisions, such as educational pursuits and career choices, marriage, and whether to have children (and if so, affording the ability to pursue prenatal diagnosis) and whether to begin planning for inevitable disability. without this test, all of these at-risk relatives (of which there are an estimated in the united states) would lead their lives anxiously waiting for the symptoms to begin, when half of them are actually at no risk because they did not inherit the mutant gene from their affected parent. although there are at-risk relatives who choose not to avail themselves of the predictive test, the many who do opt to be tested credit it with freeing them of years of obsessive uncertainty. the results can afford the affected patients the opportunity to enroll in clinical trials (involving drugs or neuronal stem cells), with the aim of preventing or delaying the onset of symptoms. although these studies are still in an early phase with no outcome data yet available, they give patients some hope for the future, perhaps for themselves but also for future patients. given the mechanism of gradual neuronal cell death in the basal ganglia, it stands to reason that the earlier such intervention is initiated-ideally in the presymptomatic stage-the higher the chances of success. huntington disease is one of the trinucleotide repeat disorders, caused by expansion of a tandem repeat of cag in the first intron of the huntingtin (htt or it ) gene. in contrast to fx syndrome and some of the other trinucleotide repeat disorders, the difference between the mutated and nonmutated repeat length can be as little as a single repeat (ie, nucleotides). thus, extreme care is required in the sizing of the repeat, especially when it falls near the cutoff length of repeats or higher which is diagnostic or predictive of hd, with % penetrance. fortunately, the ldps in current use, relying on capillary electrophoresis, are very accurate in determining repeat length, as attested by the excellent performance in cap proficiency surveys. busulfan is a bifunctional dna alkylating agent typically given to patients as a conditioning agent prior to hematopoietic cell transplantation (hct) for the treatment of hematologic malignancies. therapeutic drug monitoring (tdm) is crucial for the safe and efficacious use of busulfan due to a narrow therapeutic index based on area under the curve (auc) calculations. too low a dose places the patient at risk of either graft failure or early relapse. , on the other hand, too high a dose increases the risk of neurotoxicity as well as a severe and life-threatening complication termed hepatic sinusoidal obstruction syndrome (sos). , hepatic sos, previously termed hepatic veno-occlusive disease (vod), refers to the occlusion of terminal hepatic venules and hepatic sinusoids. severe cases of vod can lead to hepatorenal syndrome, causing multi-organ failure, hepatic encephalopathy, and death. veno-occlusive disease typically occurs in the context of hct, particularly after administration of conditioning regimens prior to hct. it is one of the most feared complications of hct and accounts for a significant fraction of hct-related mortality. severe cases, which account for approximately % to % of sos, are almost always fatal. , , despite a clear need for busulfan tdm, there are currently no fda-approved assays available for the quantitation of busulfan in blood. for this reason, various bioanalytical methods have been developed and are currently in use by multiple laboratories. data from a busulfan proficiency program organized by the university of washington/seattle cancer care alliance show a total of participating laboratories at the present time. of these, laboratories use gas chromatography (gc) methods, use hplc methods, and use liquid chromatography-tandem mass spectrometry (ms) methods. all of these methods are non-fda-approved tests independently developed and validated for clinical use by their respective clinical laboratories. the use of these methods is also driven by the need for high precision and accuracy. current criteria for acceptable laboratory performance in the analysis of busulfan is + % of the known concentrations for medium and high concentrations and within + % of the known concentration for low concentrations. this is due to the fact that dosing change decisions are based on auc calculations, which depend on blood concentrations of busulfan measured from multiple timed blood draws. multiple small analytical errors can easily add up to big differences in calculated auc values. busulfan testing is currently available from reference laboratories. however, many busulfan regimens call for intravenous infusions every or hours for to days. bone marrow transplant teams need quicker turnaround times than can be reasonably provided by sendout testing in order to be able to make dosing adjustments within this limited timespan. guidelines have also been recently published by the american society for blood and marrow transplantation guidelines committee advocating for personalized busulfan dosing using busulfan tdm in certain busulfan regimens. for these reasons, laboratory-developed methods for busulfan will continue to play key roles in the management of hematologic malignancies at cancer centers throughout the world. very sensitive measurements of serum androgens are important in adult and pediatric endocrinology and oncology. very-low-level testosterone (te) measurements are needed for adult women, whose values are routinely < ng/dl, in children, and men undergoing antiandrogen therapy whose values are usually < ng/dl. the most commonly used methods for steroid analysis are fda-approved immunoassays because they are rapid and sensitive enough for most routine applications involving healthy adult males. however, te immunoassays lack the sensitivity requirements for chemically castrated males, women, and children. many immunoassays also lack specificity and accuracy as immunoassays may show cross-reactivity with structurally similar compounds. [ ] [ ] [ ] in addition, most immunoassays are not standardized against internationally recognized standards. for these reasons, a number of sensitive and specific assays using ms have been described for te. [ ] [ ] [ ] the lack of sufficient accuracy and standardization of te assays is a major concern for the clinical and public health communities. several years ago, the endocrine society, in partnership with the cdc, convened a meeting with various relevant professional societies and industrial partners to create the partnership for the accurate testing of hormones (path) whose mission is to improve the accuracy and standardization of a variety of steroid hormone tests. [ ] [ ] [ ] the path has worked with the cdc and begun to address this concern through its host program, which provides laboratories with specimens spanning their analytical measurement range that have been previously analyzed using the cdc reference method. many assays using ms have been approved by the cdc host program, however not a single fda-approved immunoassay has met the performance requirements. testosterone is a perfect example of an ldp that is indispensable for patient care and allows for accurate measurements to be made on children, women, and male patients with cancer receiving antiandrogen medication. ethylene glycol is a colorless, sweet-tasting liquid commonly encountered in automobile antifreeze. because of this widespread availability, it is also a commonly encountered toxicological agent in both accidental and self-inflicted poisonings with exposures in . ethylene glycol poisoning classically presents with a metabolic acidosis caused by the production of toxic metabolites, primarily glycolic acid and oxalic acid. this is also often accompanied by an anion gap and osmolal gap. untreated ethylene glycol poisoning can also progress to acute renal failure when high levels of oxalate anions combine with calcium to develop crystals in the kidneys and urinary tract. ethylene glycol poisoning is an urgent, toxicological emergency. once ethylene glycol is identified, the drug fomepizole is typically administered. fomepizole inhibits alcohol dehydrogenase, the enzyme that metabolizes ethylene glycol, to slow the accumulation of toxic metabolites. fomepizole and ethanol dramatically lengthen the half-life of ethylene glycol, and therefore, hemodialysis is often required to clear the poison. both the diagnosis and treatment of ethylene glycol poisoning are heavily dependent on laboratory measurements. no fda-approved assays for ethylene glycol are currently available, and all testing is performed by laboratory-developed procedures. the most common methods for the analysis of ethylene glycol are gc with flame ionization detector, gc with ms, and enzymatic assays. , gas chromatography with mass spectrometry is considered the gold standard for the analysis of ethylene glycol, as it can differentiate it from interferences that plague the other methods. , in addition to initial detection needed for diagnosis, the ethylene glycol blood concentration is used to determine when hemodialysis has cleared ethylene glycol to undetectable levels. measurement of thyroglobulin (tg) in serum has proven useful for detecting recurrence of treated differentiated thyroid carcinoma (dtc). according to the american cancer society, the united states has over new thyroid cancer cases each year. the death rate is almost per year. differentiated thyroid cancer accounts for over % of cases. differentiated thyroid cancer produces tg, making its measurement useful as a tumor marker for detecting recurrence. the nccn and american thyroid association (ata) guidelines recommend tg testing following total thyroidectomy and radioiodine ablation treatment, including tests at baseline, to weeks after treatment, months, months, and annually thereafter. patients free of disease have undetectable tg. older competitive tg-ria methods are available but produce falsely high tg results in the presence of tg autoantibodies (tg-ab). newer fda-cleared tg assays are immunometric immunoassays (tg-ia) and can detect tg at concentrations down to approximately . ng/ml. generally, tg is captured with a solid-phase antibody, then quantitated using a detection anti-tg reagent. the signal is directly proportional to the amount of tg. the assay design is susceptible to interference from endogenous anti-tg-ab. the intended use of these tg-ia are tg measurement in tg-ab-negative (tg-ab À ) patients. the fda requires tg-ab testing whenever tg is measured using these cleared methods. depending on the method used, up to % of treated patients with dtc are tg-ab positive (tg-ab þ ). thus, many of these patients have falsely low or even falsely negative tg results when measured by ia. four tg-ab assays are in common use and are not harmonized, detecting tg-ab in widely divergent numbers of treated patients with dtc. in addition, the degree of tg interference cannot be predicted from the magnitude of the tg-ab result. thus, up to % of patients with recurrence are missed by tg-ia testing. to circumvent the tg-ab interference, hoofnagle and wener developed and validated a ms tg method (tg-ms) using tryptic digestion and immunocapture of tg-specific peptides followed by ms focused on those peptides. they demonstrated the tg-ms method accurately measures tg in the presence of tg-ab. the tryptic digestion destroys the tg-ab, eliminating their interference with the assay. four national reference laboratories have adopted versions of this method, and harmonization efforts are underway. a recent clinical outcome study compared tg-ia, tg-ria, and tg-ms in both tg-ab À and tg-ab þ patients. as predicted from the assay designs, all methods were equivalent for tg-ab À cases, but the tg-ms was more accurate for tg-ab þ cases. tg-ia methods had more false negatives and tg-ria had more false positives. although tg-ms has not yet been incorporated into the current guidelines, the ata guideline mentions it as a promising new technique. without tg-ms, thyroid cancer recurrence in tg-ab þ patients can be missed, thus delaying follow-up and creating patient harm. antimicrobial susceptibility testing, used to determine whether antibiotic treatment will be successful, is an essential component of the microbiology culture report. emerging resistance among pathogenic bacteria and new antimicrobial agents require frequent updates to both testing methods and interpretation of the results. most laboratories use automated instruments to perform minimal inhibitory concentration (mic) testing to determine whether a patient's isolated bacteria are susceptible, susceptible dose dependent, intermediate, or resistant to a panel of antibiotics. these interpretations are based on fda breakpoint criteria published at the time of drug approval and periodically updated to respond to the appearance of new resistance mechanisms. the fda also clears automated instrumentation used to determine mic values (via the k process). although the mic testing process may not be changed, new breakpoints added to the instrument software require a revised k application. because the fda does not have the authority to require manufacturers to submit data for revised breakpoints within a specified time frame, manufacturers may elect to use outdated breakpoints rather than face the expense of a k resubmission. a recent example was the year delay between the release of updated breakpoints for diagnosing carbapenem-resistant enterobacteriaceae in and the ability to use these breakpoints in the clinical laboratory. this delay was used to calculate the potential for additional carriers of multidrug-resistant enterobacteriaceae in southern california health-care systems. as many as additional carriers of mdro enterobacteriaceae were estimated to have occurred in orange county, california because of this delay. the disastrous spread of mdro enterobacteriaceae can be mitigated by laboratories validating testing methods that enable use of updated antimicrobial breakpoint interpretations before fda-cleared testing is available. specifically, modifying a manufacturer's instructions, including interpreting mic results using a revised breakpoint other than that listed in the product insert, is a change that renders the procedure an ldp. without the option of using an ldp, one is left reporting outdated interpretations that miss resistant strains leading to unacceptable patient care. as illustrated, ldps are an integral part of the spectrum of tests and procedures performed by clinical laboratories which fulfill a critical need for patient care, particularly in rapidly evolving areas such as testing for personalized medicine. laboratory testing should be consistent with national/international consensus treatment guidelines, which may require development of procedures earlier or for new clinical purposes not fulfilled by fda-approved kits. in such cases where clinical testing needs exist beyond the original fda purpose, laboratories must be able to perform additional validation of new sample types or develop additional assays to include new mutations or analytes that are needed. as illustrated by these case examples, laboratories and professional organizations often work together to broadly compare and optimize assay performance, creating consensus standards that raise the quality of testing overall. in contrast, the current structure for fda approval requires review of assay kits individually, or in comparison with the predicate method, rather than assessing and improving performance across the spectrum of assay options available. the science of laboratory medicine has advanced dramatically in the almost decades since clia was enacted, and updates and expansions to clia regulations could be useful. additional resources, such as reference materials, and consensus practice guidelines would extend the quality framework that all laboratories and manufacturers utilize. for example, consensus guidelines that include such details as the target for percent allele frequency detectable, requirements for percent tumor cell content, what mutations and variants should be included, and sample types to be tested would be useful as a guide for assay validation as well as in standardization of the practice. professional expert groups are already generating assay and practice guidelines. , , [ ] [ ] [ ] [ ] ideally, clinical laboratories and kit manufacturers would utilize appropriate reference materials to help standardize the results obtained for any particular analyte regardless of technology platform or laboratory setting. to address the needs for reference materials to facilitate assay result standardization, a multistakeholder initiative, the diagnostic quality assurance pilot, has been launched to design, develop, and evaluate traceable reference sample materials (referred to as reference materials) to better provide molecular pathology laboratories with the means to demonstrate equivalent performance of ldps and companion diagnostic ivds for targeted cancer therapy. this quality pilot emerged from the sustainable predictive oncology therapeutics and diagnostics working group, launched in by tapestry networks (waltham, massachusetts), which was composed of diverse stakeholders (oncologists, pathologists, patient advocates, third party payers, and regulators) for the purpose of designing a quality pilot to advance these goals (http://www.ta pestrynetworks.com/initiatives/healthcare/oncology-therapeu tics-and-diagnostics/diagnostic-quality-assurance-pilot.cfm. accessed april , ). the tapestry pilot proposes that laboratories would be allowed to utilize assays that best serve the needs of their patients based upon performance, quality, clinical needs, and the test menus and volumes of that particular laboratory. it is not critical that laboratories all use the identical assay or test platform, provided that all are able to get the correct answer. to close, the overarching goal is the efficacy and safety of our clinical laboratory tests and procedures for patients. pathologists and laboratory professionals need the best and most upto-date tools to do their jobs and optimize patient care. some of these will be fda approved or cleared kits, and others will be laboratory-developed procedures performed under clia; both have their place. laboratories have a long history of success performing ldps, as illustrated by these case studies. as much as possible, these capabilities need to be performed on-site to insure that the results can be integrated with other clinical and laboratory findings, interpreted as a whole and completed in a timely fashion. also important is the handson training of the next generation of physicians, for whom, we hope, maximal use of genomic and other laboratory information will be a way of life as they treat human disease. that is the promise of personalized medicine! the author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. the author(s) received no financial support for the research, authorship, and/or publication of this article. the ' % claim': what is the evidence base? evidence-based laboratory medicine the public health evidence for fda oversight of laboratory developed tests: case studies the public health evidence for fda oversight of laboratory developed tests: case studies proposal for modernization of clia regulations for laboratory developed testing procedures (ldps) viral encephalitis herpes simplex virus infections of the central nervous system: 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carbapenem-resistant enterobacteriaceae the spectrum of clinical utilities in molecular pathology testing procedures for inherited conditions and cancer next-generation sequencing for infectious disease diagnosis and management: a report of the association for molecular pathology laboratory practice guidelines for detecting and reporting jak and mpl mutations in myeloproliferative neoplasms the role of mgmt testing in clinical practice diagnostic quality assurance pilot: a model to demonstrate comparative laboratory test performance with an oncology companion device assay the authors would like to thank the college of american pathologists, dr jason merker and ms patty vasalos, for facilitating access and allowing use of data from cap interlaboratory proficiency testing programs. ms mary williams, dr barbara zehnbauer, dr peter hulick, and dr david klimstra provided valuable comments on the manuscript. ms laura metz provided clerical support. key: cord- -q lda authors: hanson, kimberly e; caliendo, angela m; arias, cesar a; englund, janet a; lee, mark j; loeb, mark; patel, robin; el alayli, abdallah; kalot, mohamad a; falck-ytter, yngve; lavergne, valery; morgan, rebecca l; murad, m hassan; sultan, shahnaz; bhimraj, adarsh; mustafa, reem a title: infectious diseases society of america guidelines on the diagnosis of covid- date: - - journal: clin infect dis doi: . /cid/ciaa sha: doc_id: cord_uid: q lda background: accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease (covid- ). direct detection of severe acute respiratory syndrome coronavirus (sars-cov- ) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. the numbers of available sars-cov- nucleic acid detection tests are rapidly increasing, as is the covid- diagnostic literature. thus, the infectious diseases society of america (idsa) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance. objective: the idsa’s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of sars-cov- nucleic acid amplification tests. in addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings, and highlight important unmet research needs in the covid- diagnostic testing space. methods: idsa convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of sars-cov- molecular diagnostics. grading of recommendations assessment, development and evaluation (grade) methodology was used to assess the certainty of evidence and make testing recommendations. results: the panel agreed on diagnostic recommendations. conclusions: universal access to accurate sars-cov- nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the covid- pandemic. information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered low to very low. recognizing these limitations, the idsa panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having covid- . in addition, testing is recommended for asymptomatic individuals with known or suspected contact with a covid- case. testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (ppe) usage decisions, dictate eligibility for surgery, or inform administration of immunosuppressive therapy. ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations. a c c e p t e d m a n u s c r i p t background in late december , an outbreak of pneumonia cases of unclear etiology was reported in wuhan city, hubei province, china [ ] . unbiased next generation sequencing (ngs) using lower respiratory tract (lrt) specimens collected from affected patients subsequently identified a novel coronavirus as the cause of illness now known as coronavirus disease . the entire viral genome was shared online within days and phylogenetic analyses established close relationship to human severe acute respiratory syndrome coronavirus (sars-cov) as well as several other sars-like bat coronaviruses [ , ] . based on genetic similarities, the novel coronavirus was officially named sars-cov- [ ] . by march th , , the virus had spread to at least countries and killed more than , people, prompting the world health organization (who) to officially declare a global pandemic [ ] . public availability of the sars-cov- genome was an essential first step enabling development of accurate molecular diagnostic assays. nucleic acid amplification tests (naats) designed to detect one or more gene sequences specific to sars-cov- are essential for confirming covid- to date, multiple commercial test manufacturers and clinical laboratories, including academic medical centers, have received eua for a sars-cov- -specific molecular diagnostic test. the first home-based test collection kit was also recently granted an eua [ ] . it is important to recognize, however, that eua guidance differs substantially from the standard fda approval process. in the setting of a public health emergency, the fda only requires test developers to establish acceptable analytical accuracy. clinical test performance (i.e., sensitivity and specificity) has yet to be determined or comprehensively compared across eua platforms. as a result, most of the naat performance data used to inform this guideline was derived from a c c e p t e d m a n u s c r i p t studies evaluating assays not widely used in the u.s. we assumed, therefore, that performance of standard naat methods to be comparable across countries (which may or may not be correct). given increasing test availability combined with a rapidly growing number of naat-focused studies published online or in academic journals, the infectious diseases society of america table . at the time of this review, there was little evidence to inform use of serologic testing. therefore, the first version of the idsa diagnostic guideline focuses only on the use of targeted naat applied directly respiratory tract specimens. it is anticipated that these guidelines will be frequently updated as substantive new information becomes available; subsequent versions will also address sars-cov- serology due to the rapidly evolving information and uncertainty of the reliability of serological tests. m a n u s c r i p t this guideline was developed using the grading of recommendations assessment, development and evaluation (grade) approach for evidence assessment. in addition, given the need for rapid response to an urgent public health crisis, the methodological approach was modified according to the gin/mcmaster checklist for development of rapid recommendations [ ] . the the conflict of interest (coi) review group included two representatives from idsa who were responsible for reviewing, evaluating and approving all disclosures. all members of the expert panel complied with the coi process for reviewing and managing conflicts of interest, which required disclosure of any financial, intellectual, or other interest that might be construed as constituting an actual, potential, or apparent conflict, regardless of relevancy to the guideline topic. the assessment of disclosed relationships for possible coi was based on the relative weight of the financial relationship (i.e., monetary amount) and the relevance of the relationship (i.e., the degree to which an association might reasonably be interpreted by an independent observer as related to the topic or recommendation of consideration). the coi review group ensured that the majority of the panel and chair was without potential relevant a c c e p t e d m a n u s c r i p t (related to the topic) conflicts. the chair and all members of the technical team were determined to be unconflicted. clinical questions were developed into a population, intervention, comparison, outcomes (pico) format [ ] prior to the first panel meeting (table s ) . idsa panel members prioritized questions with available evidence that met the minimum acceptable criteria (i.e., the body of evidence reported on at least test accuracy results can be applied to the population of interest). panel members prioritized patient-oriented outcomes related to sars-cov- testing such as requirement for self-quarantine, eligibility for investigational covid- treatment, timing of elective surgery or procedures, and management of immunosuppressive therapy. we also considered the impact of sars-cov- results on infection prevention and public health practices, including the use of personal protective equipment (ppe) and contact tracing. the national institute of health and care excellence (nice) and the center of disease control (cdc) highly-sensitive search was reviewed by the methodologist in consultation with the technical team information specialist and was determined to have high sensitivity. an additional term, covid, was added to the search strategy used in addition to the terms identified in the pico questions (table s ) . ovid medline and embase were searched from through april , . horizon scans were performed daily during the evidence assessment and recommendation process to locate additional grey literature and manuscript preprints from the following sources litcovid, medrxiv, ssrn, and trip database. reference lists and literature suggested by panelists were reviewed for inclusion. no restrictions were placed on language or study type. two reviewers independently screened titles and abstracts, as well as eligible full-text studies. we included studies reporting data on diagnostic test accuracy (cohort studies, cross sectional a c c e p t e d m a n u s c r i p t studies and case-control studies). when questions compared the performance of different tests (e.g., different testing or sampling methods) or testing strategies, we included studies that provided direct test accuracy data about both tests in the same population. when these direct studies where lacking, we included studies that assessed a single test and compared its results to a reference standard. we did not limit our inclusion to a specific reference standard due to sparsity of data. we also included studies that assessed the prevalence of covid- in different populations. reviewers extracted relevant information into a standardized data extraction form. two reviewers completed data extraction independently and in duplicate. disagreements were resolved by discussion to reach consensus and in consultation with expert clinician scientists. data extracted included general study characteristics (authors, publication year, country, study design), diagnostic index test and reference standard, prevalence of covid- , and parameters to determine test accuracy (i.e., sensitivity and specificity of the index test). accuracy estimates from individual studies were combined quantitatively (pooled) for each test using openmetaanalyst (http://www.cebm.brown.edu/openmeta/). we had planned to conduct a bivariate analysis for pooling sensitivity and specificity for each of the test comparisons to account for variation within and between studies. however, this was not feasible due to the sparsity of available data and lack of information on specificity in most instances, so we either presented data as a range of the extreme sensitivity and specificity presented in the studies or pooled as proportions to facilitate decision making. we had also planned to use the breslow-day test to measure the percentage of total variation across studies due to heterogeneity (i ) but were not able to do that due to the sparsity of data. forest plots were created for each comparison. to calculate the absolute differences in effects for different testing or sampling strategies, we applied the results of the sensitivity and specificity to a range of plausible prevalence in the population. we then calculated true positives, true negatives, false positives, and false a c c e p t e d m a n u s c r i p t negatives. to determine the prevalence for each question, we considered the published literature in consultation with the clinical experts. in general, for questions addressing symptomatic individuals we considered the following prevalence: % which is typically seen in symptomatic outpatients who have not reached a hospital facility [ ] [ ] [ ] ; % which is typically seen in patients meeting clinical definition for covid- who were hospitalized [ , ] ; and % which is typically seen in patients meeting clinical definition for covid- who were admitted to intensive care units. for questions addressing asymptomatic individuals who were exposed to covid- , we considered that the prevalence may range from % to % based on household clusters, nursing home outbreak, active surveillance of passengers quarantined on a cruise ship or passengers of repatriation flights, hospital employees with close contact with covid- positive patients and customers and employees of a restaurant that had a covid- outbreak [ ] [ ] [ ] [ ] [ ] [ ] [ ] . for questions addressing asymptomatic individuals, we considered that the prevalence may range from < % in general population who are not in hotspots to % in asymptomatic patients in hotspots [ , , ] . we conducted the risk of bias assessment for diagnostic test accuracy studies using the quality assessment of diagnostic accuracy studies (quadas)- revised tool (table s ) [ ] . grade framework was used to assess overall certainty by evaluating the evidence for each outcome on the following domains: risk of bias, imprecision, inconsistency, indirectness, and publication bias [ , ] . grade summary of findings tables were developed in gradepro guideline development tool [ ] . the panel considered core elements of the grade evidence in the decision process, including a c c e p t e d m a n u s c r i p t as per grade methodology, recommendations are labeled as "strong" or "conditional". the words "we recommend" indicate strong recommendations and "we suggest" indicate conditional recommendations. figure provides the suggested interpretation of strong and weak recommendations for patients, clinicians, and healthcare policymakers. rarely, low certainty evidence may lead to strong recommendations. in those instances, we followed generally recommended approaches by the grade working group, which are outlined in five paradigmatic situations (e.g., avoiding a catastrophic harm) [ ] . for recommendations pertaining to good practice statements, appropriate identification and wording choices were followed according to the grade working group [ ] . a "good practice statement" represents a message perceived by the guideline panel as necessary to health care practice, that is supported by a large body of indirect evidence difficult to summarize, and indicates that implementing this recommendation would clearly result in large net positive consequences. for recommendations where the comparators are not formally stated, the comparison of interest was implicitly referred to as "not using the test". some recommendations acknowledge the current "knowledge gap" and aim at avoiding premature favorable recommendations for test use and to avoid encouraging the rapid diffusion of potentially inaccurate tests. detailed suggestions about the specific research questions that should be addressed are found in table . a c c e p t e d m a n u s c r i p t a c c e p t e d m a n u s c r i p t committee reviewed and approved the guideline prior to dissemination. regular, frequent screening of the literature will take place to determine the need for revisions based on the likelihood that new data will have an impact on the recommendations. if necessary, the expert panel will be reconvened to discuss potential changes. in addition, future searches will include critical appraisal of the sars-cov- serology literature. systematic review and horizon scan of the literature identified , references of which informed the evidence base for these recommendations (figure s ). characteristics of the included studies can be found in table s . figure summarizes a testing algorithm for covid- diagnosis guidelines. however, testing is not widely available in some areas.  this recommendation does not address testing a combination of specimen types due to lack of evidence.  the panel considered symptomatic patients to have at least one of the most common symptoms compatible with covid- ( table ) . thirteen studies informed this recommendation [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] and they provided varying descriptions of specimen type (supplement c). in an effort to maintain consistency in the analysis of evidence, reported specimen types were grouped into nasopharyngeal (np), mid-turbinate (mt), nasal, throat, or saliva. in studies that did not define collection techniques for "nasal", we assumed it to mean anterior nasal and not deep-nasal or a c c e p t e d m a n u s c r i p t nasopharyngeal. saliva collection methods were also inconsistent. saliva studies incorporating a "coughed-up" sample were excluded from the urti and ili analysis under the assumption that they likely included some mixture of pure saliva and sputum. analyses of "tongue" swabs were also excluded. it is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing sars-cov- positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). a total of reports presented data about test accuracy of a specific sample type(s); eight of these [ , , - , , ] provided comparative data for two or more sample collection sites; and three others [ , , ] provided data for one site only. studies with comparative data showed a lower sensitivity for oral sampling in comparison to np, mt, or nasal sampling. summary statistics different specimen type are shown in table . two studies [ , ] a c c e p t e d m a n u s c r i p t types are false negative results, which could promote unchecked sars-cov- transmission. one potential benefit of the alternative methods are the less-invasive nature of nasal, mt and throat swabs or saliva as compared to np sampling. in addition, the ppe requirements for healthcare providers collecting non-cough inducing specimen types may be less. lastly, the non-np sampling is amendable to patient self-collection, which has the potential to further reduce healthcare worker exposure to infectious droplets and possible droplet nuclei. additional considerations: indirect evidence from influenza and respiratory syncytial virus studies suggest that alternative nasal cavity collection sampling methods such as anterior nasal and mt swabs provide comparable sensitivity to np swabs [ ] . using np swab collection as the reference method will bias evaluation of the comparator method by definition. saliva is an easily obtained specimen and there is significant recent interest in its use for sars-cov- detection. at the time of this literature review we identified a single study assessing true saliva as a specimen type. this is a promising specimen type given the simplicity of collection. the panel anticipates multiple additional studies to follow, which will be included in future guideline updates. the panel considered indirect evidence for nasal swabs and mt swabs from other respiratory viruses in the decision to list these specimen types are preferred over saliva. in addition, saliva is complex matrix and clinical laboratories will need to carefully assess rna stability during specimen transport and the efficiency of nucleic acid extraction using their own specific methods. we did not identify any studies assessing combinations of specimen types. although oropharyngeal swabs or saliva can be utilized for the diagnosis of covid- , the available evidence combined with indirect evidence from other respiratory viruses suggests that collection of anterior nares, mt, or np swabs has higher sensitivity. at the current time, there is little evidence to support use of oropharyngeal swabs or saliva alone. however, future studies of saliva as a specimen type for sars-co- detection are anticipated. a c c e p t e d m a n u s c r i p t evaluation of alternative collection devices and methods are critically needed as we are facing shortages in test collection supplies such as swabs, transport media and ppe. while np swab collection is widely used and the primary specimen type for commercial direct sars-cov- test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. clinical laboratories will need to validate use of individual specimen types. future studies of saliva should clearly describe collection methods, specimen transport media and processing requirements. moving forward, it will be critical to standardize these processes. ( to ) ( to ) ( to ) ( to ) ( to ) ( to ) explanations: this table is based on applying the sensitivity and specificity estimates to calculate true and false positives and negatives in a hypothetical population of individuals. *no studies reported on the specificity of oral and np a. the case-control design leads to a serious study population bias. b. some studies compared two or more of the specimen types, but no studies compared all specimen types in the same patient population. studies reported test accuracy results but did not report on patient-important and population-important outcomes based on the results. c. there is serious unexplained heterogeneity.  appropriate specimen collection and transport to the laboratory is critical. general instructions for swab-based sars-cov testing are shown in table . additional resources are available on the idsa website.  a clear, step-by-step protocol needs to be presented to patients attempting self-collection. this could be in the form of a short video or printed pamphlet with illustrations.  the majority of self-collection studies were performed in the presence of a healthcare worker.  the available evidence for nasal and mt swabs as alternatives to healthcare personnel collection is based on assessment of symptomatic patients. data on self-collection in asymptomatic individuals is currently unavailable. a c c e p t e d m a n u s c r i p t  the panel considered symptomatic patients to have at least one of the most common symptoms compatible with covid- ( table ) . this recommendation is based on three cohort studies (supplement d). in the first study, test accuracy results were provided for self-collected non-invasive specimens compared to healthcare-collected np swabs as the standard [ ] . for self-collection, participants were provided with instructions and asked to self-collect tongue, nasal, and mt swabs, in that order. tongue samples were collected with a nylon flocked swab. nasal samples were collected with a foam swab bilaterally. mid-turbinate samples were collected with a nylon flocked swab bilaterally. after patient sampling was completed, np samples were collected by a healthcare worker using a polyester tipped swab on a skinny wire. in the second study, patients attending dedicated covid- collection clinics were offered the option to first self-collect nasal and throat swabs followed by healthcare provider collection of nasal, throat or oropharyngeal swabs [ ] ; concordance of results were presented. the third study compared positivity for supervised oral fluid sampling, supervised self-collected deep nasal swabs, unsupervised oral fluid sampling and provider collected np swabs [ ] . in this analysis, any positive test, obtained from any of the reported sampling methods including the index test, was considered to be a true positive. although the study reported the results for "oral fluid", it is likely these samples were mixed with sputum. lastly, the panel considered unpublished data submitted to the fda on home collection, which demonstrated good stability of specimens stored in universal transport media (utm) during transport from homes to laboratories and comparable quantities of virus in self-collected compared to healthcare provider collected swabs. summary statistics for self-collected versus health-care worker collected nasal swabs are shown in table . the studies used to inform the recommendation were small and heterogeneous. sources of heterogeneity included variable swab and transport media types as well as use of unilateral versus bilateral nares self-collection. the timing of collection relative to symptom onset is also important but was not well documented in available data. due to the mentioned concerns with a c c e p t e d m a n u s c r i p t the studies and the lack of direct comparisons between different specimen types in the same patient population, the panel agreed that overall certainty of evidence was low. benefits and harms: the panel placed a high value on avoiding the close exposure of healthcare providers to patient droplets and possible droplet nuclei generated during specimen collection. we assumed that self-collected specimens including anterior nasal swabs, mt swabs and saliva (without cough) would reduce provider exposure and could reduce mask or respirator use. the overall sensitivity of testing when samples were collected by patients was comparable to those collected by healthcare providers. other potential benefits of self-collection include increasing the availability of testing outside the healthcare system and increased patient satisfaction with selfcollection. concerns with self-collection include lack of experience or documentation for actual collection methods by patients; inappropriate sample collection and/or handling could then lead to inaccurate results. although data is limited, both healthcare provider collected, and self-collected nasal or mt swabs appear to result in similar rates of detection of sars-cov- . self-collection of np swabs is unlikely to be an option as a self-collection method. there are advantages of having multiple strategies to collect clinical specimens, particularly in times of ppe shortages when limiting exposure to healthcare personnel or other patients is important, or when testing in specific populations without access to the healthcare system is required. further comparative studies of self-collected non-invasive specimens (i.e., nasal, mid-turbinate, and throat swabs, as well as saliva) compared with m a n u s c r i p t abbreviations: np = nasopharyngeal; op = oropharyngeal; mt = nasal mid-turbinate; ns = anterior nares swab. ^c autions: do not use calcium alginate swabs or swabs with wooden shafts, which may contain substances that interfere with nucleic acid amplification. rayon swabs may not be compatible with all molecular platforms. clinical laboratories should confirm compatibility of collection devices during assay validation. # pediatrics: swab insertion distance will differ for pediatric patients. swabs with stoppers make estimating distance easier for mt self-collection. two-sided mt sampling not always performed. we identified nine studies that performed both an upper respiratory tract (urt) swab and lower respiratory tract (lrt) sample collection consecutively on the same patient (supplement e). two reported on viral load and did not report on sensitivity [ , ] . seven studies reported on sensitivity, of which three had a case control design [ , , ] and one reported results per sample and not per patient [ ] . the three cohort studies [ , , ] were used to inform the panel's decision-making process. the sample type varied by study and included throat and nasal swabs for urt sampling and sputum and bronchoalveolar lavage (bal) fluid specimens for lrt sampling. summary statistics for urt versus lrt sampling in cohort studies are shown in table . the timing of specimen collection with regards to clinical course was not reported for all these studies and different diagnostic reference standards were a c c e p t e d m a n u s c r i p t m a n u s c r i p t a c c e p t e d m a n u s c r i p t ( to ) ( to ) ( to ) ( to ) explanations: this table is based on applying the sensitivity and specificity estimates to calculate true and false positives and negatives in a hypothetical population of individuals a. studies reported test accuracy results but did not report on patient-important and population-important outcomes based on the results. b. considering the lower vs upper limit of the sensitivity confidence interval may lead to different clinical decision, and the low number of patients lead to very serious imprecision c. typically seen in symptomatic outpatients who have not reached a hospital facility d. typically seen in patients meeting clinical definition for covid- who were hospitalized e. certainty of evidence (coe) m a n u s c r i p t missing data in the studies included timing of specimen collection in relationship to onset of clinical symptoms and specimen type used for testing. additionally, the performance and accuracy of different rapid tests was very inconsistent. given all these issues, the overall certainty of the effect of using rapid tests on patients was very low. the major benefit of a rapid result is the ability to make clinical decisions while the patient is present in a timely manner and implement interventions to protect others. a possible harm of rapid tests is the potential for increased numbers of false negative results, which could lead to missed diagnoses and patients not being isolated when they are indeed infected, if sensitivity is lower than non-rapid tests. diagnostic accuracy should be stratified by duration of symptoms and severity of disease. furthermore, the diagnostic reference standard must be clearly defined. performance characteristics of eua rapid tests, especially those that are clia-waived, should be collected in the field and performed by the non-laboratory staff running the test (which is how they are used in real life). ideally, studies should assess the impact of rapid results on clinical outcomes, such as time to appropriate treatment or therapeutic intervention. individuals who are either known or suspected to have been exposed to covid- (conditional recommendation, very low certainty of evidence).  known exposure was defined as direct contact with a laboratory confirmed case of covid-  suspected exposure was defined as working or residing in a congregate setting (e.g., longterm care, correctional facility, cruise ship, factory, among others) experiencing a covid- a c c e p t e d m a n u s c r i p t  the risk of contracting sars-cov- may vary under different exposure conditions.  this recommendation assumes the exposed individual was not wearing appropriate ppe.  the decision to test asymptomatic patients will be dependent on the availability of testing resources. summary of the evidence: we did not identify any studies that directly assessed a strategy of testing versus no testing of asymptomatic individuals exposed to sars-cov- . therefore, the effect of testing on the pre-specified outcomes could not be directly assessed. we also did not identify test accuracy studies directly assessing the performance of sars-cov- naats in asymptomatic individuals. however, based on evidence that asymptomatic or pre-symptomatic patients may have similar viral loads and shedding compared to those who are symptomatic [ , , ] , the panel agreed that it is reasonable to apply test accuracy data based on symptomatic patients to the asymptomatic populations. hence, it was essential to determine the pre-test probability or prevalence of covid- in the asymptomatic groups. we assessed studies that reported the prevalence of covid- among asymptomatic individuals in household clusters [ , , ] , a nursing home outbreak [ ] , active surveillance of passengers quarantined on a cruise ship or passengers of repatriation flights [ ] , hospital employees with close contact to covid- positive patients [ ] , and customers and employees of a restaurant that had a covid- outbreak [ ] . overall, prevalence ranged from to % in settings where substantial transmission was suspected prior to testing. summary statistics for single versus repeated testing are shown in table and supplement h. we acknowledge that information on individual exposure was limited in the evidence base. all these limitations led to very low certainty in the evidence overall. testing asymptomatic individuals who have been exposed, or suspected to have been exposed, allows for isolation for those who are positive. whether in an institutional cluster or a wider community outbreak, isolation will help reduce further transmission. there is potential harm in a false negative naat result collected from an exposed individual who is a c c e p t e d m a n u s c r i p t actually infected; these individuals may incorrectly consider themselves non-infected, and unknowingly expose others to sars-cov- as a result. given the lack of evidence, a negative test post-exposure does not mean quarantine can be discontinued. some individuals may still be in the incubation phase, subsequently develop active viral shedding, and incorrectly consider themselves non-infected. as a result, a negative post-exposure test cannot necessarily be used to avoid quarantine. a positive result, however, would reinforce the importance of isolation as well as inform contact tracing, cohorting, or other mitigation strategies. additional considerations: diagnostic test performance in asymptomatic individuals has not been established. assuming an overall test sensitivity between %- % [ , , [ ] [ ] [ ] ] , false negative test results are expected. there is also cost to testing asymptomatic exposed individuals; since quarantine may still be indicated regardless of test results, such testing may add cost without changing practice. data are limited to define definitions of close contact. risk stratification of a given exposure can be made in consultation with public health authorities. in addition, the cdc has published guidance on defining healthcare exposures and categorizing exposure risks [ ] .the ideal time to test an asymptomatic contact of a known or suspected covid- case is also unknown. timing also becomes complicated for household contacts with ongoing exposure. the average incubation period for sars-cov has been determined to be five days [ ] . thus, - days following exposure may be a reasonable time frame to consider post-exposure testing. in addition, data to inform the definition of a significant exposure or close contact are limited. considerations when assessing the risk of a known contact include the duration of exposure and the clinical symptoms (e.g., cough) of the person with covid- . with known or suspected exposures should be coordinated with local public health officials. this indication for testing is especially important in situations where knowledge of asymptomatic or pre-symptomatic infection is essential for determining medical follow-up, defining risks for other vulnerable individuals in the household, congregate setting or hospital. special consideration should also be given to healthcare personnel exposed without a c c e p t e d m a n u s c r i p t appropriate ppe in healthcare settings. definitions of appropriate ppe can be found on the cdc website [ ] . comparative studies (preferably randomized controlled trials) along with cost-effectiveness analyses of testing strategies in asymptomatic populations are needed. studies on the ideal time and collection method to test asymptomatic individuals who have been exposed to covid- should be performed. in addition, what constitutes an exposure that would justify testing requires further research. whether early diagnosis of covid- might provide an opportunity to intervene therapeutically and change the ultimate course of infection (i.e., prevent severe pneumonia) is unknown. if this is shown to be the case, the opportunity for therapeutic intervention might justify screening exposed individuals. this table is based on applying the sensitivity and specificity estimates to calculate true and false positives and negatives in a hypothetical population of individuals a. reference standard considered to be nasopharyngeal specimen rt-pcr. b. studies report test accuracy results but do not report on patient-important outcomes based on these results. c. a small number of patients included. d. we assessed studies that reported the prevalence of covid- among asymptomatic individuals who were exposed to covid- and determined that the prevalence may range from % to % based on household clusters, nursing home outbreak, active surveillance of passengers quarantined on a cruise ship or passengers of repatriation flights, hospital employees with close contact with covid- positive patients and customers and employees of a restaurant that had a covid- outbreak. e. certainty of evidence (coe)  asymptomatic individuals are defined as those with no symptoms or signs of covid- .  a high prevalence of covid- in the community was considered communities with a prevalence of  %. a c c e p t e d m a n u s c r i p t  the decision to test asymptomatic patients (including when the prevalence is between and %) will be dependent on the availability of testing resources. we did not identify any studies that directly assessed a strategy of nucleic acid testing for sars-cov- versus no testing before hospitalization for non-covid- related reasons. we also did not identify test accuracy studies directly assessing the performance of sars-cov- viral rna tests in asymptomatic individuals. however, based on existing evidence suggesting that asymptomatic or pre-symptomatic patients may have similar virus loads and shedding as those who are symptomatic [ , ] , the panel agreed to infer test accuracy for asymptomatic populations before being hospitalized. it was also essential to determine the pre-test probability or prevalence of the disease in asymptomatic patients admitted to the hospital. we assessed studies that reported prevalence  this recommendation defines immunosuppressive procedures as cytotoxic chemotherapy, solid organ or stem cell transplantation, long acting biologic therapy, cellular immunotherapy, or high-dose corticosteroids.  testing should ideally be performed as close to the planned treatment/procedure as possible (e.g. within - hours).  many of these patients require frequent, repeated or prolonged visits to receive treatment.  this recommendation does not address risks or strategies to deal with sars-cov- transmission in outpatient settings such as infusion centers. we did not identify any studies that directly assessed a strategy of testing for sars-cov- versus no testing of asymptomatic individuals before receiving chemotherapy or transplantation. in addition, we were unable to evaluate the risks of delaying necessary treatments or transplants if testing was not available and quarantine/delay of treatment was then required. we also did not identify any test accuracy studies directly assessing the performance of naat in asymptomatic individuals. based on existing evidence supporting that asymptomatic or pre-symptomatic patients may have similar virus loads and a c c e p t e d m a n u s c r i p t shedding as those who are symptomatic [ , ] , the panel agreed that test accuracy data from symptomatic patients would apply to asymptomatic populations being hospitalized. it was essential to determine the pre-test probability or prevalence of covid- in asymptomatic patients who will be receiving chemotherapy. we assessed studies that evaluated prevalence of covid- among asymptomatic individuals and patients with cancer to estimate prevalence a between < to %. we identified three studies reporting data on the prevalence of cancer among covid- patients and the percentage of complications (e.g., icu admission, death) among these patients. liang et al [ ] showed that the prevalence of cancer among covid- patients to be %, which was higher compared to their general population ( . %). yu et al [ ] showed the prevalence of covid- among patients admitted to the radiation and medical oncology floor to be . %. lastly, a systematic review conducted by desai et al. ( ) [ ] showed the pooled prevalence of cancer among covid- cases to be - %. the overall certainty of the evidence about testing effects in immunocompromised individuals was very low due to extremely limited data in this population. the panel determined that a maximum threshold of < - missed cases per would be acceptable. not testing individuals regardless of low versus high prevalence areas would lead to higher numbers of missed cases which the panel considered to exceed the acceptable threshold. the threshold was set very low due to concern about catastrophic outcomes in this population. although data is limited, there are reports documenting outbreaks of respiratory viruses in hospitalized immunocompromised hosts [ ] . in addition, increased risks of severe adverse respiratory virus-related outcomes in this population are documented [ ] . for false negative test results, so caution should be exercised by those who will be in close contact with/exposed to the upper respiratory tract (e.g., anesthesia personnel, ent procedures). the decision to test asymptomatic patients will be dependent on the availability of testing resources.  the panel defined time-sensitive procedures as medically necessary procedures that need to be done within three months.  procedures considered to be aerosol generating are listed in table .  decisions about ppe will be dependent on test results because of limited availability of ppe. however, there is a risk for false negative test results, so caution should be exercised for those who will be in close contact with/exposed to the patient's airways.  procedures considered to be aerosol generating are listed in table .  the decision to test asymptomatic patients will be dependent on the availability of testing resources.  this recommendation does not address the need for repeat testing if patients are required to undergo multiple procedures over time. the panel did not identify any studies that directly assessed a strategy of testing for sars-cov- versus no testing of asymptomatic individuals before undergoing major surgery or aerosol generating procedures (agps). the panel also did not identify test accuracy studies directly assessing the performance of sars-cov- naats in asymptomatic individuals. however, based on existing evidence supporting that asymptomatic or presymptomatic patients may have similar viral loads and shedding as those who are symptomatic, the panel agreed that test accuracy data from symptomatic patients could be applied to asymptomatic populations before surgery. it was essential to determine the pre-test probability or prevalence of disease in the asymptomatic patients who will undergo surgery. we assessed studies that evaluated the a c c e p t e d m a n u s c r i p t prevalence of covid- among asymptomatic individuals and determined that the range of prevalence would be between < to % based on assessing rates of infection in asymptomatic individuals in the general population in low prevalence and in "hotspot" areas [ , , ] . the panel recommendation was based on emphasizing the importance of preventing infection in healthcare providers during major time-sensitive surgeries and agps. in addition, the limited data showing poor outcomes in covid- positive patients undergoing a major surgical procedure requiring intubation informed decisions to reduce this risk for asymptomatic patients [ ] . there are no data that assess the outcome of agps in sars-cov- positive patients. the benefit of suggesting testing for sars-cov- in asymptomatic patients undergoing major time-sensitive surgery is that it allows for the identification of infected patients before the procedure; thus allowing surgery to delayed based on the limited data suggesting that patients testing positive may have poor outcomes [ ] . this approach also has the potential to inform healthcare workers in terms of ppe use, particularly in areas where ppe is limited. of note, there is very low certainty evidence from retrospective case series suggesting poor outcomes of time-sensitive surgeries for those with covid- . the surgeries included were variable in complexity and it was not clear if the poor outcomes came mostly from major or minor surgeries. however, it is plausible that poor outcomes were driven by the major surgeries. a potential harm of testing of immunocompetent, asymptomatic patients before a major surgery or agp is depletion of testing supplies and the diversion of all associated resources away from symptomatic patients. an additional harm of testing is related to the sensitivity of the naats for sars-cov- , which will not detect all asymptomatic patients with covid- infection. therefore, some patients may be missed and healthcare workers at high risk could be exposed. thus, the panel suggests that healthcare workers at the highest risk during surgical procedures (e.g., those performing intubation or ent procedures) consider wearing ppe at all times, regardless of test results. this would be especially important in high prevalence areas a c c e p t e d m a n u s c r i p t (i.e., "hotspots"). an additional harm is that false positive tests for sars-cov- may unnecessarily delay a major time-sensitive surgery. there is no standard definition of what constitutes a major surgery. in general, the panel in consultation with surgical colleagues, agreed that major surgeries would be defined as more complicated and/or prolonged surgeries that require general anesthesia and intubation (which is an agp). additionally, time-sensitive surgeries/procedures were defined as those for which a delay greater than months would negatively affect outcomes. in addition to the clinical questions addressed above, there is significant interest in the use of serologic sars-cov- tests both for diagnosis and public health surveillance. at the time of our literature review, however, additional data were needed to formulate recommendations. important areas that need to be addressed include assessment of the sensitivity and specificity of commercial antibody tests, determinations of protective immunity and measures of antibody responses over time. whether seroconversion can inform return to work or hospital staffing policies needs to be assessed. in the absence of evidence to guide the use of sars-cov- serologic testing, the idsa diagnostics committee published a serology primer for clinicians which highlights potential benefits, limitations and unmet research needs [ ] . antigen detection tests may be on the horizon. how these will compare with naat needs to be defined. in addition, current naats detect viral rna but cannot distinguish infectious from noninfectious virus. this determination requires viral culture, which is not routinely performed in clinical laboratories for biosafety reasons and is likely less sensitive than naat. it will be important to define whether individuals who remain nucleic acid positive after symptom resolution, and potentially seroconversion, are infectious to others because this will have important ramifications for quarantine and reducing restrictions around social distancing. some "test of cure" algorithms require two sequential negative naats, yet some studies describe a c c e p t e d m a n u s c r i p t prolonged rna positivity. future studies are required to determine the significance of nucleic acid or antigen shedding after clinical recovery. molecular tests designed to detect sars-cov- nucleic acids are essential both for confirming covid- diagnosis and for public health responses aimed at curbing the pandemic. several countries have deployed naat on a massive scale as the cornerstone of a successful containment strategy. although the u.s. was hampered by limited test availability early in the outbreak, there are now more than different commercially available sars-cov- assays and multiple clinical laboratories have developed their own laboratory-developed tests. aggressive efforts are underway to assure access to testing, but regional differences in availability persist. individual medical centers and clinics are likely to have different testing capacity as well. furthermore, which test a laboratory or facility chooses to perform will vary based on the resources of a given setting (e.g., near-patient versus high complexity laboratory) and turnaround-time to result requirements (i.e., rapid versus standard). the primary recommendations set forth in this guideline assume that sars-cov- testing is available to healthcare providers on the front lines. however, the panel also recognized that resources may vary, and contingency recommendations were developed for situations where naat supplies or ppe are limited. individual institutions will need to prioritize testing based on available resources and unique patient populations. testing for symptomatic patients should be prioritized. when testing capacity for symptomatic individuals is considered sufficiently robust, testing for asymptomatic individuals should be considered. there will undoubtedly be challenges prioritizing and implementing testing strategies for asymptomatic groups. the strongest recommendation for testing in asymptomatic individuals in this guideline pertains to immunocompromised patients being admitted to the hospital or in advance of immunosuppressive procedures. a c c e p t e d m a n u s c r i p t molecular tests have been central to our understanding of sars-cov- . however, much about the biology of sars-cov- remains unknown. early experience suggests that sars-cov- is detectable in the upper respiratory tract, with peak levels typically measurable during the first week of symptoms [ , , ] . rna detection rates, however, appear to vary from patient to patient and change over time. some patients with pneumonia, for example, have negative upper respiratory tract samples but positive lower airway samples [ , ] . much less it known about the frequency of viral detection in asymptomatic individuals, although the concentration of detectable virus in some people with infection may be quite high [ , ] . a better understanding of the spectrum of viral load kinetics over time at different anatomic sites is needed to inform decisions about the optimal testing strategies, including when and how to repeat if the first test is negative. like other respiratory viruses, shedding of viral rna in respiratory secretions may persist beyond resolution of symptoms and seroconversion [ ] . whether such patients remain infectious to others is uncertain and this is an important area for future study. the clinical performance of commercially available sars-cov- molecular diagnostic tests has not yet been defined and will depend in large part on the biology of the virus. typically, when tests for the detection of viral respiratory pathogens are submitted to the fda, both analytical and clinical performance data are provided. under eua, however, only analytical data are required. diagnostic developers may test contrived specimens, by spiking viral rna or inactivated virus into the desired matrix, rather than using real clinical specimens collected from patients with covid- . thirty contrived positive and negative specimens tested, with % sensitivity and % specificity required for eua. therefore, while we have information regarding the limit of detection of the test and evidence (both in vitro and in silico studies) that the primer design is specific for sars-cov- , there is no information on how each test performs clinically at the time the eua is issued. clinical laboratories using commercial eua tests must verify analytic test performance at some level in their own hands, including evaluation of different specimen types and collection methods (e.g., swab types and transport media). a c c e p t e d m a n u s c r i p t clinical performance metrics include sensitivity, which is the ability of the test to correctly identify those with infection, and specificity, the ability of the test to correctly identify those without the disease. in practice, the positive and negative predictive values of the test are also essential for interpreting test results. estimations of community prevalence and patient pre-test probability combined with knowledge of test sensitivity and specificity are essential for determining the likelihood that an individual has covid- . in practice, however, the true prevalence of covid- in the community may not be well-defined and may be underestimated when test availability is limited. in addition, while sars-cov- rna tests are highly specific, their respective sensitivities are likely to vary. recognizing these complexities, estimates of prevalence/pre-test probability and assay sensitivity were varied in our analyses based on the available literature in an attempt to mirror what may be encountered in clinical practice. going forward, robust prevalence studies are needed. clinical test performance should also ideally be determined in prospective multicenter studies using a well-defined reference standard as the benchmark for test comparisons. table outlines the type of clinical studies needed to address the most pressing covid- diagnostic knowledge gaps. one of the most important problems with current covid- diagnostic literature is the lack of a standard definition to define covid- . the studies included in the systematic reviews that informed this guideline used variable case definitions and many classified disease based in part on the results of the index test under investigation. incorporation of the investigational index test into the diagnostic "gold" standard falsely inflates sensitivity and specificity estimates (i.e. incorporation bias). table outlines options for defining a confirmed covid- case in diagnostic trials. it is recognized that not all individuals with covid- will have detectable sars-cov- nucleic acid. therefore, a "probable" case definition is also proposed. false negative naat results may be due to a variety of factors, including assay limit of detection, anatomic location and adequacy of specimen collection, timing of sampling relative to symptom onset, and underlying biology of disease. to fully understand sars-cov- viral dynamics, studies need to be designed to obtain specimens from multiple sites, ideally from the same a c c e p t e d m a n u s c r i p t patient at the same time. in addition, information on the duration of symptoms (if present), assessment of potential exposures and longitudinal follow-up of outcomes will be essential to define optimal diagnostic test strategies across a variety of patient populations. nucleic acid sequencing matches sars-cov- reference sequences positive results from at least different naats (one of the two may be the index test) option dual positive results from a single naat targeting different genes (cannot be the index test) compatible clinical signs and symptoms in a setting with known community transmission, negative reference naat and documented sars-cov- seroconversion. compatible clinical signs and symptoms in a setting with known community transmission, negative reference naat and positive index test from two different anatomic sites. compatible clinical signs and symptoms in a setting with known community transmission, negative reference naat and positive sars-cov- -specific serology. the guideline panel used a methodologically rigorous process to critically appraise the available diagnostic literature and formulate sars-cov- testing recommendations. the quality of existing evidence, however, was limited and not all of the data used to inform these recommendations had undergone peer-review. based on low certainty evidence, the idsa panel recommends nucleic acid testing for all symptomatic individuals suspected of having covid- . in addition, testing selected asymptomatic individuals is suggested when the results will have significant impact on isolation/quarantine/ppe usage, dictate eligibility for surgery, or inform use of immunosuppressive therapy. ultimately, institutional resources will dictate test this project was funded by idsa. the following list displays what has been reported to the idsa. to provide thorough transparency, the idsa requires full disclosure of all relationships, regardless of relevancy to the guideline topic. evaluation of such relationships as potential conflicts of interest is determined by a review process which includes assessment by the board of directors liaison to the standards and practice guideline committee and, if necessary, the conflicts of interest (coi) and ethics committee. the assessment of disclosed relationships for possible coi is based on the relative weight of the financial relationship (i.e., monetary amount) and the relevance of the relationship (i.e., the degree to which an association might reasonably be interpreted by an independent observer as related to the topic or recommendation of consideration). the reader of these guidelines should be mindful of this when the list of disclosures is reviewed. k.h. serves as an advisor for biofire and quideland and receives centers for disease control and prevention. health care infection prevention and control faqs for covid- prevention strategies for seasonal influenza in health care settings advice on the use of masks in the context of covid- epidemic-and pandemic-prone acute respiratory diseases -infection prevention and control in health care day zero, visby, and chroma code; receives research funding from arcbio and hologic; and has served as an advisor for luminex. c.a. receives royalties from uptodate and receives research funding from merck entasis pharmaceuticals and the national institute of allergy and infectious diseases (niaid)/nih. j.e. serves as a consultant for sanofi pasteur; an advisor/consultant for meissa vaccines; and receives research funding from the centers for serves as an advisor for sanofi, seqirus, and medicago; has served as an advisor for pfizer, sunovion, and md brief; and receives research funding from the canadian institutes of health research and the medical research council (united kingdom). r.p. receives grants from shionogi the infectious diseases society of america (idsa), the national board of medical examiners, uptodate, and the infectious disease board review course; y.f.y. receives honoraria for evidence reviews and teaching from the evidence foundation, honoraria for evidence reviews for the american gastroenterological association, and serves as a director for the evidence foundation and for the u.s a novel coronavirus from patients with pneumonia in china genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding the species severe acute respiratory syndromerelated coronavirus: classifying -ncov and naming it sars-cov- novel coronavirus- events-as-they happen adminsitration fad development of rapid guidelines: . gin-mcmaster guideline 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doi: . /bpp. . sha: doc_id: cord_uid: oyfx ij widespread testing is key to controlling the spread of covid- . but should we worry about self-selection bias in the testing? the recent literature on willful ignorance says we should – people often avoid health information. in the context of covid- , such willful ignorance can bias testing data. furthermore, willful ignorance often arises when selfish wants conflict with social benefits, which might be particularly likely for potential ‘super-spreaders’ – people with many social interactions – given people who test positive are urged to self-isolate for two weeks. we design a survey in which participants (n = ) choose whether to take a costless covid- test. we find that % would take a test. surprisingly, the people most likely to widely spread covid- – the extraverts, others who meet more people in their daily lives and younger people – are the most willing to take a test. people's ability to financially or emotionally sustain self-isolation does not matter to their decision. we conclude that people are selfless in their decision to test for covid- . our results are encouraging – they imply that covod- testing may succeed in targeting those who generate the largest social benefits from self-isolation if infected, which strengthens the case for widespread testing. covid- rapidly developed into a pandemic, and by march , the usa had the highest reported number of infected people in the world. a general message from public health experts is that effective control of the spread of covid- requires widespread medical testing (who, ) . the testing will serve to determine whether people are infected or not, and ideally also if they have been infected and have reached immunity status. three reasons motivate widespread testing. first, if a person learns that they are infected, they can take appropriate measures to reduce the probability of infecting others, such as the recommended -day self-isolation (harvard medical school, ) . second, the data provided by widespread testing will better inform the need for the current social distancing policies (e.g., sheltering at home, avoiding gatherings of or more people, keeping at least feet away from other people and temporarily closing schools, universities, daycare centers, major sports leagues, cultural events and public spaces) (stock, ) . third, testing provides data about the asymptomatic rate in the usa (the share of infected people who show no or very mild symptoms) and insight into how close americans are to developing herd immunity to covid- . this information is useful in order to determine when and where it makes sense to relax these costly social distancing measures. while the usa has increased its capacity to conduct more testing, around . % of the population had been tested by april (covid tracking project, ) . the effectiveness of testing in controlling covid- depends largely on how the tests are conducted. the ideal scenario is to test everyone, but that is infeasible. a second-best scenario is random sample testing (stock, ) . but for random testing to be effective, all sampled people would either need to voluntarily agree to be tested (which is unlikely, as we explain) or be forced to do so (which is illegal in the usa). the third-best (and first-best feasible) strategy is voluntary random testing. this strategy, however, could lead to a systematic selection biaswe will only test those individuals who prefer to learn their health status regarding covid- ; a significant fraction of people might not want to know. these individuals might find that their private costs outweigh any social benefits from not infecting others. this implies that they might want to avoid testing. if their private costs include above-average opportunity costs of social interactions, then individuals who decline to be tested may also be disproportionately likely to become superspreaders. to understand why this might happen, consider the ongoing literature on willful ignorance of health information (also called strategic ignorance). while standard economic theory suggests people never ignore information that enables them to adjust behavior (stigler, ) , many new studies find that people willfully ignore medical diagnoses, even when such knowledge would enable them to adjust behavior to better accommodate their health condition (sharot & sunstein, ) . for example, we see willful ignorance in many people at risk for breast cancer (thompson et al., ) , alzheimer's disease (cutler & hodgson, ) , hiv (hightow et al., ) and huntington's disease (oster et al., ) . the study by ganguly and tasoff ( ) is particularly relevant: they observe people will avoid a costless test for herpesa disease for which there is currently no cure, but for which information is useful in that it helps adjust behavior. people have also been found to willfully ignore health risk information, such as calories in food (thunström et al., ; woolley & risen, ; sunstein, ; thunström, ; nordström et al., ) . willful ignorance of health outcomes is likely to arise when people are torn between what they think they should do and what they want to do (thunström, ; woolley & risen, ) , or when ignorance allows them to form optimal expectations (downplay the probability of a bad health outcome; oster et al., ; nordström et al., ) . for instance, a person may think she should eat healthy, but want to indulge in ice-cream-she might then choose to avoid learning about the exact amount of calories in the ice-cream in order to avoid either her inner pressure to reduce the ice-cream consumption or the guilt from consuming it despite being aware of the calorie content. in this paper, we explore self-selection in covid- testing in the usa. we examine if people willfully avoid getting tested for covid- , and, if so, what individual or household characteristics and circumstances are associated with testing avoidance. given that random voluntary testing is not yet available in the usa, there are no observational data to rely on for our analysis. we therefore design a hypothetical randomized controlled trial (rct). we recruit a nationally representative sample of participants. the study entails two treatments, across which we vary information about the potential emotional cost of testing before asking if participants would agree or disagree to a financially costless covid- test. in the baseline treatment, we inform participants that if they are found to be infected, they are urged to self-isolate at home for days. in the high-cost treatment, we tell participants that those who test positive are strongly urged to self-isolate, which may be in a self-quarantine site away from home. we assume the test itself is costless and that the only cost incurred from a covid- test is the recommended self-isolation for days should the test come back positive. if people are concerned only with their private benefits and costs from taking a covid- test, those with large private benefits and low private costs from knowing that they are infected will be the most likely to get tested. private benefits are significant for people at elevated risk for severe health consequences if they contract the virus or with family members at higher risk, while private costs are low for those who generally live a solitary life, professionally and in private. we expect elderly and those who haveor have a family member that haspre-existing conditions to be more willing to test. furthermore, we expect those at the lowest risk of losing out financially (e.g., risk to labor income or health care costs) or emotionally from self-isolating (i.e., if they are introverts who attach a low value to social interactions) to be the most willing to get tested for covid- . in contrast, if people are concerned only with social benefits and costs, we would expect those most at risk of exposing others to be the most likely to get tested (e.g., potential 'super-spreaders'; i.e., people with jobs that entail mixing with other people, people living in urban areas, young people and people who are extroverts and attach a high value to social interactions). people with the potential to be super-spreaders might be torn about learning whether they are infected by covid- . both private costs and social benefits from being urged to self-isolate for the next days (harvard medical school, ) might be high for this group, and so influence their testing decision in opposite directions. for example, consider the behavior of an extrovert who values social interactions highly. if unsure of being infected, the extrovert behaves just as if she is not infected (e.g., as found for huntington's disease, by oster et al., ) . self-isolation means this person needs to give up highly valued social interactionsa factor that might deter them from a voluntary test for covid- . at the same time, their self-isolation provides particularly meaningful private and social health benefits from reduction in exposure to, and spread of, the disease. these benefits to learning whether they are infected might encourage them to voluntarily test. it is an open question if the benefits outweigh the costs, causing the extrovert to take a costless covid- test. similarly, imagine a store clerk who risks losing income if self-isolating for days. the potential private loss of income would deter them from testing, while the social benefits from reducing disease spread would encourage taking the test. again, the decision to test becomes an open question. previous studies show that willful ignorance arises when prosocial behavior is privately costly (dana et al., ; conrads & irlenbusch, ; onwezen & van der weele, ; gigerenzer & garcia-retamero, ; grossman & van der weele, ) . in this study, we find that around % of people want to take a costless covid- test. as might be expected, people who worry more about their health are particularly likely to want to take the test. we also find that those most likely to want to take the test are those most likely to spread the virus if unaware of their infection, including young people and extroverts with a preference for socializing. extroverts might also be at the highest risk for being infected, but even when we control for personal risks (amount of social interactions and worry about own health), we find they are more willing to test. the ability to afford to self-isolate for days does not seem to affect the willingness to test. our results suggest that there is a significant amount of selflessness in the decision to test; people appear to be highly concerned about the social benefits from testing for covid- and little concerned about private costs. in addition, we do not find the expected treatment effect of our experimental manipulation of the private cost to testing (i.e., the location of self-isolation (at home or in a facility away from home) does not seem to matter to the testing decision). our expectation was that willful ignorance would be higher if selfisolation might take place away from home, since we assume self-isolation away from home is perceived as more costly. one interpretation of the lack of expected treatment effect is that it lends further support to the idea that private costs play a negligible role in the decision to test for covid- . our results matter because they underscore the value of widespread covid- testing, even if such testing cannot be done randomly. our findings suggest that widely available and costless voluntary testing will target rather than scare off those most likely to be 'super-spreaders'. to test people's willingness to take a financially costless covid- test, we designed a hypothetical field experiment. the experiment is a rct with a between-subjects design, consisting of two treatments. in the first treatment (treatment baseline), participants were told they would be urged to selfisolate at home, if having tested positive. in the second treatment (treatment high cost), they were told they might be urged to self-isolate at a special site away from home. participants (n = ) were recruited by the research firm qualtrics, and the sample was required to be nationally representative along the dimensions of gender, age, education, race, income and residential region (east, west, north or south). while the recruitment costs from qualtrics are higher than when recruiting from amazon mechanical turk or turk prime, qualtrics continuously quality checks participants, which enabled us to avoid many issues that may otherwise contaminate online panels (e.g., see chandler & paolacci, ; sharpe wessling et al., ) . participants received standard qualtrics compensation to participate in a survey. testing for the sequence of the experimental study was as follows: step : all participants were asked screening questions at the front end of the survey about their gender, age, education, race, income and region in order to ensure the sample met us national quotas for those characteristics. step : participants were asked whether they had already been tested for the covid- . if 'yes', they were asked why they got tested, the outcome of the test, how many days prior to survey participation they had taken the test and if the test was costly. if 'no', they were randomized into one of the two treatments and asked about their willingness to take a test. specifically, if in treatment baseline, they received the following information: currently, us authorities are working to test more people for the coronavirus. legislators are urging people who test positive, i.e., are found to be infected by the virus, to self-isolate at home for days. if in treatment high cost, they were instead told: currently, us authorities are working to test more people for the coronavirus. legislators are urging people who test positive, i.e., are found to be infected by the virus, to self-isolate for days. some states have started building self-quarantine sitessites where people who have the virus would be isolated for days. if people stay at those sites, it is easier to ensure they comply with the guidelines to self-isolate. thereafter, participants in both treatments were asked: if you were given the opportunity to take a coronavirus test for free within the next days, would you take the test? default alternatives to get or not get information have been shown to affect observed choices of ignorance (grossman, ) . to avoid nudging participants toward any particular answer, there was no default alternative; participants needed to choose either "yes, i would take the test," or "no, i would not take the test." step : all participants were asked about their current level of social distancing (how many people outside their household they had been within feet of in the last days; how many gatherings with more than people they had participated in; and self-assessed level of compliance with social distancing). they were also asked whether they supported the public recommendations for social distancing in general. step : participants were asked questions about factors that might affect the perceived cost of a positive covid- test (implying social isolation for days), as well as the perceived benefits from being able to make behavioral adjustments. they were asked about their job situation, job security and possibility of the main income provider in the household taking sick leave; risk factors for contracting the virus (e.g., living in a urban area, working in a health care facility, working in a grocery store or pharmacy); risk factors (for self or any children) for suffering severe health consequences if contracting the virus (e.g., underlying health conditions that increases the risk, such as cancer, obesity, diabetes, etc.); level of extraversion (francis et al., ) ; and social lifestyle. step : participants were asked about religious belonging, religiosity, political affiliation and social and fiscal conservatism (everett, ) . the full survey can be found in the online supplementary material. of our total sample, participants stated that they had already been tested, while stated that they had not already been tested. we asked those who had been tested for the primary reason they had taken the covid- test. table shows their answers. as expected, given the current prevailing strategy in the usa of focusing the limited testing on people who are symptomatic, most people got tested because they themselves showed symptoms (almost %) or because someone close to them either showed symptoms or was diagnosed with covid- (around %). summary statistics for the participants who had been tested before participating in our study are shown in the online supplementary material. our analysis focuses on the participants who stated that they had not been tested for covid- . due to a coding error in the survey at the beginning of the data collection, seven participants did not respond to the question on whether they were a business owner, employed or unemployed. we dropped these seven participants from our analysis, and we were left with observations. table presents the summary statistics for these participants. unless otherwise stated, all of the remaining analysis focuses on the results for this group of participants. table shows that % of participants who had not yet been tested for covid- are female. the variable age describes a participant's age in years, and the mean age in our sample is years. the variable high-risk age is a dummy variable that takes the value if a person is aged years or older. table shows that % of our participants are aged years or older. the variable rural area takes a value if participants stated that they live in a rural area and if they live in an urban area. table shows that % of our participants live in a rural area. the variables emotional tolerance and financial tolerance are dummy variables that take the value if the participant answered that the maximum time (from the time of taking the survey) he/she would be able to emotionally or financially sustain social distancing was days or longer, given the -day recommended time to self-isolate if you test positive for covid- . these variables take the value if their stated maximum time was days or less. table shows that % of participants stated that they can afford to continue their testing for covid- current level of social distancing for days or more, while % stated that they can emotionally tolerate another days or more of their current level of social distancing. the variable lifestyle impacthealthy is an index that measures the extent to which social distancing has changed participants' behavior in a healthier direction. participants were assigned a value for each of the following: if they stated that social distancing had (a) increased consumption of vegetables, (b) decreased in-between-meals snacking (excluding fruits and vegetables), (c) increased time spent in green spaces, (d) increased time spent doing strenuous or (e) moderate exercising and (f) reduced stress. this variable could take a value between and , where higher values represent healthier changes. the variable lifestyle impactunhealthy is an index that measures the extent to which social distancing has changed behavior in an unhealthy direction. participants were assigned a value for each of the following: if they stated that social distancing had (a) decreased consumption of vegetables, (b) increased in-between-meals snacking (excluding fruits and vegetables), (c) decreased time spent in green spaces, (d) decreased time spent doing strenuous or (e) moderate exercising and (f) increased stress. this variable could also take a value between and , where higher values represent a higher number of unhealthy changes. the summary statistics in table suggest that social distancing has led to more unhealthy behavior than it has healthy behavior, as implied by the lower mean value of lifestyle impacthealthy. we note, however, that these variables are crude measures of the lifestyle impact from social distancing, where each change is given equal weight, although some changes might have a more important health effect than others. the variable business impact takes a value if a participant is a business owner whose business has experienced negative impacts due to covid- , such as their operation losing income, going out of business or being at risk of going out of business. the variable employer impact takes a value if a participant is an employee and his/her employer has experienced a negative impact due to covid- , such as their employer losing income or being at risk for going out of business, if they had experienced pay cuts, reduced working hours or were on unpaid leave as a result of the virus. table shows that of participants who are business owners, or where until a month ago (n = ), % had experienced a negative impact on their business from covid- . of participants who are employees, or were until a month ago (n = ), % had experienced a negative impact on their job security, payment or employer revenues. the variable social distant compliant - feet measures how many people a participant has been close to in the last days. participants could state 'none', person, - people, - people, - people, - people, - people, - people or 'more than people'. we assigned participants the midpoint of the range they picked. for those in the highest range ( and more), we assumed the same size interval as the second to highest interval (i.e., we assumed an endpoint of the last interval equal to people). table shows that the average number of people that participants had been close to during the last days, besides their household members, was . . although not reported in the table , the median was . . the variable social distant compliantgroups measures how many times during the last days a participant has been in a room with or more people. participants could state a value anywhere between zero and ' or more times'. the median of this variable is . table shows that participants on average had been in a room with or more people around . times during the last days. the variable self health risk measures the sum of underlying health conditions that would put the participant at higher risk for developing severe health consequences if becoming infected with covid- . these health conditions include chronic respiratory conditions, heart disease, neurological conditions, diabetes and obesity (cdc, ). the variable child health risk measures the same sum of underlying health conditions for a child in the household. the variable worry about own health is based on the stated extent to which participants worry about their own health due to covid- , where the value indicates 'not at all' and the value indicates 'a lot'. the dummy variable insurance takes a value if a participant states that he/she has private health insurance or is covered by medicare or medicaid and if the participant stated not having any coverage. table shows that % of participants have insurance or medicare or medicaid coverage. the dummy variables republican, democrat and other political party take a value if a participant identifies as republican, democrat or neither, and otherwise. about % of participants identify as republican, % as democrat and % as other. that they had been placed on unpaid leave; and % of workers said that they had had their pay reduced. the variable extrovert is based on the extraversion scale developed by francis et al. ( ) and includes participants' answers to questions such as "are you a talkative person?" and "can you easily get some life into a rather dull party?" in addition to the extraversion scale, we also asked participants to indicate their level of agreement with statements about their general social lifestyle, such as "my social life is very important to me," and "in my spare time, my favorite thing to do is to spend time with friends." if the participant answered yes to three or more of these questions, they were assigned a for the extrovert dummy variable. the answers to these statements were, however, highly correlated with the extraversion scale, so they were excluded from our analysis because they provided little or no additional information. when we pool participants from both treatments who had not been tested prior to participating in our study (n = ), we find that % of participants would be willing to take a costless covid- test. we find no difference in shares of participants willing to test across treatments (pearson χ ( . ); p = . ), suggesting that the location of self-isolation (at home or in a facility away from home), in the event the test comes back positive, is not an important determinant of people's willingness to test for covid- . not only is the treatment effect small, it is also of the unexpected signthe share of people willing to test if self-isolation would happen at home is smaller ( %) than the share of people willing to test if self-isolation might happen at a facility away from home ( %). if anything, people might be slightly more inclined to test if a positive result could lead to isolation away from home (potentially due to this also signaling the greater severity of the covid- situation), but the size of the effect is too small for us to detect with our sample size. we have ruled out participants who stated that they would prefer not to take the test ( / ) were asked for their reasons not to want to take the test. they were given the following alternatives and were asked to mark all that apply: "i would not change my behavior if i learned i had the virus" ( %); "i do not want to self-isolate for days" ( %); "my job prevents me from self-isolating for days" ( %); "i think i have already had the virus" ( %); "it would cause me emotional discomfort if i knew i had the virus" ( %); "it doesn't matter to me if i get tested or not" ( %); other ( %). the numbers in parentheses show the shares of participants who agreed with the statement. as shown, a large share of participants stated that the test would not matter, and that they would not change their behavior anyway. a potential reason for the prominence of these reasons could be that they are already highly complying with social distancing. (table shows that the more people comply with social distancing, the less likely they are to want to take a covid- test.) however, a large share also states 'other', suggesting that the alternatives presented to our participants did not cover the full range of reasons as to why people may refrain from testing. we encourage future research to further explore these reasons. that this absence of identifiable average effect masks any potentially 'rational' heterogeneity in the population (i.e., we have explored whether there exists a treatment effect for subgroups of the population, such as those with children, higher-quality homes (as measured by income) or health anxiety (as measured by underlying health conditions)). one interpretation of the absence of treatment effect is that people assign little weight to the personal cost associated with the location of self-isolating when they decide on whether to take a covid- test. we pool participants from both treatments and examine the determinants of willingness to test. we estimate a probit model. table shows the resulting average marginal effects. concerns about own health are captured by the variable worry about own health. the results in table imply that the more a person worries about their health due to covid- , the more likely they are to take a test. the inclusion of this variable in our model also renders the coefficient for the variable that measures underlying health conditions (i.e., self health risk) small and statistically insignificant (if worry about own health is excluded from the regression, self health risk has the expected positive, and statistically significant, effect on willingness to test). we do not find that people with children who have underlying health conditions are more likely to take the test, perhaps due to the expectation that people of young age are less affected. this result remains robust if we recode the variable child health risk into a dummy variable that takes the value if any child in the household has one or more underlying health conditions. variables that affect a person's financial situation do not seem to matter to the willingness to take a covid- test. in particular, we do not find an effect from business impact or employer impact. we examine the robustness of these findings to alternative measures of business and employer impact. first, we instead include the multitude of variables underlying business impact and employer impact in the regression model (see footnote ), but we do not find an effect from any of those variables that is close to statistically significant at even the % level. furthermore, we do not find an effect on willingness to test from financial tolerance. second, we recode the variables such that they range from little impact to severe impact (ranging from if a business owner or employee has experienced no adverse effects from covid- , to one or multiple effects). again, we find no statistically significant effects from these variables on the willingness to test. taken together, these results suggest that people do not consider their own private costs from a positive test when deciding on taking a covid- test. similarly, we find no effect on the willingness to test from emotional tolerance, implying that the private emotional cost from social isolation in the event of a positive test might not affect the decision to take a covid- test. we find that healthy younger people are more likely to take a test than healthy older people, as implied by the negative parameter estimate for high-risk age. this age effect is consistent with findings in other studies that standard errors in parentheses. *p < . , **p < . , ***p < . . observe older people avoid health-related information more than younger people (thunström et al., ; gigerenzer & garcia-retamero, ) . while this result could imply that older people are more likely to be willfully ignorant, it is also in line with the idea that those with more social interactions (younger people) are more likely to get tested. studies find that people below years old have more social contacts, and therefore are more likely to transmit infectious diseases (mossong et al., ) . furthermore, we find that those who have met more people during the last days are more willing to take the test, as suggested by the negative parameter estimate for social distance compliant - feet. furthermore, the potential 'super-spreaders'the extrovertsare more likely (by %) to take a test compared to the introverts. taken together, this suggests that social benefits weight heavily in people's decisions to test; those most at risk to spread covid- are the most willing to get tested. we find that republicans are % less likely than democrats to get tested. we speculate that this might be due to different information sources and because the risks of covid- might be portrayed differently in liberal and conservative popular and social media. we examined the robustness of this result by including a conservatism scale (everett, ) in the probit regression, and the result remains the same: people who are more conservative are less likely to want to take a covid- test. the conservatism scale is, however, not included in the final model, given its high correlation with the political dummy variables. finally, we find that people with health insurance, or coverage from medicare or medicaid, are around % more likely to take the test. this result might suggest that people who lack health care coverage use willful ignorance as a means to reduce anxiety about how to deal with a diagnosis. this would be in line with previous studies that suggest willful ignorance of health diagnoses may be motivated by the drive to reduce anxiety about the future (e.g., oster et al., ) . our results are robust to the inclusion of other explanatory variables, such as race, education, income and profession with high exposure to infected people (health care worker, store clerk, etc.). but these variables lack explanatory power or are highly correlated with other explanatory variables included in table . the tests conducted prior to participating in our study were neither randomly offered to people (so far, testing for covid- in the usa has been primarily of individuals who showed symptoms), nor costless ( % of those who had tested prior to participating in our study stated the tests were financially costly and % said testing was time consuming). the value of data on observed testing is limited when it comes to helping us understand whether people might purposefully ignore such tests. while acknowledging that, we still compare our identified determinants of testing in table to the determinants of having taken a test before participating in our study (see online supplementary material). while the levels of statistical significance vary, all coefficients are of the same sign as those in table , except for four variables. having taken a test before participating in our study seems to be positively affected by having spent more time in groups with or more people (i.e., social distance compliantgroups), as well as by a child having underlying health conditions (i.e., child health risk). employer impact has a (weakly) statistically significant positive effect on testing prior to participating in our study, while it is not statistically significant in table . insurance is not a statistically significant determinant of having been tested prior to participating in our study, while it does have an effect in table . widespread testing is one of the most important actions that us governments at any level can undertake to help slow down the spread of covid- . given budget and testing supply constraints, it is likely that random, but voluntary, testing will be the most effective policy. we design a survey to examine the risks from self-selection into taking a covid- test. overall, we observe that around % of people would agree to a costless covid- test. we find that people who are more worried about their own health due to covid- are more likely to test, as are young healthy people, relative to older healthy people. ability to afford self-isolation for days does not seem to affect the decision to test. furthermore, people who worry more about their health, and people with health insurance or health coverage through medicare or medicaid, are more likely to take the test, as are people identifying as democrats compared to republicans. contrary to our expectation, we also find that potential 'super-spreaders' are more likely than other individuals to agree to a costless covid- . it could be that extroverts are more willing than expected to take a covid- test because their private cost of doing so is unusually low due to the broadly implemented social distancing at the time of data collection for this study. if extroverts are already relatively isolated (i.e., due to a stay-athome order and mandated closures by the state governor of public spaces, such as gyms, restaurants and bars), the personal cost of testing might be low. furthermore, extroverts might be more likely to get infected if they socialize more, which could be a 'selfish' motivation to get tested. however, we control for the current level of compliance with social distancing, which should address both of these private motivations for increased probability of testing, and we find that people who comply more are less motivated to take the test. we also control for their worry about own health due to covid- . even so, the positive effect on willingness to test from being an extrovert persists. we therefore conclude that the positive effect of being an extrovert on willingness to test for covid- is likely due to social health benefits weighing more heavily in their decision than their private costs from potential self-isolation for days, should the test come back positive. the importance of the prosocial motive in determining covid- testing is consistent with the results of the study by jordan et al. ( ) , who find that prosocial messages are more effective than self-interested messages in promoting behavior that prevent the spread of covid- (e.g., hand washing, hand shaking, hugging). our results suggest that the risks of adverse selection (in terms of failing to target the people most likely to spread the virus) in testing for covid- might be fairly low. this underscores the value of widespread testing, even if it cannot be truly random, and the importance of making such testing available nationwide in the usa as soon as possible. an important shortcoming of our analysis is that it builds on hypothetical survey data. it is well documented that survey answers may be affected by a 'hypothetical bias', meaning that people answer one way in a survey and behave in a different way when faced with real, incentivized decisions. this risk pertains to our study as well, and the hypothetical bias might be particularly pronounced if the choice to test for covid- is regarded as prosocial. several studies suggest that a hypothetical bias is particularly likely when measuring prosocial behaviorpeople often exaggerate the extent to which they engage in such behavior (e.g., murphy et al., ; vossler et al., ; jacquemet et al., ) . furthermore, it is possible that personal costs to the testing decision are less salient in a hypothetical context. once testing is more widespread in the usa, it will be important to examine who actually chooses to get tested, and the extent to which they deviate from the general population. that said, hypothetical and incentivized behavior generally correlate, such that an analysis like ours can provide important insights into the potential pitfalls of voluntary testing, prior to the actual testing. this is useful information to have on hand when designing an efficient and costeffective testing strategy. to view supplementary material for this article, please visit https://doi.org/ . /bpp. . l i n d a t h u n s t r Ö m e t a l . what you can do if you are at higher risk of severe illness from covid- lie for a dime: when most prescreening responses are honest but most study participants are impostors strategic ignorance in ultimatum bargaining most recent data to test or not to test: interest in genetic testing for alzheimer's disease among middle-aged adults exploiting moral wiggle room: experiments demonstrating an illusory preference for fairness the item social and economic conservatism scale (secs)', plos one the development of an abbreviated form of the revised eysenck personality questionnaire (epqr-a): its use among students in england, canada, the usa and australia fantasy and dread: the demand for information and the consumption utility of the future cassandra's regret: the psychology of not wanting to know strategic ignorance and the robustness of social preferences self-image and willful ignorance in social decisions coronavirus resource center failure to return for hiv posttest counseling in an std clinic population preference elicitation under oath don't get it or don't spread it? comparing self-interested versus prosocially framed covid- prevention messaging social contacts and mixing patterns relevant to the spread of infectious diseases a meta-analysis of hypothetical bias in stated preference valuation strategic ignorance of health risk: its causes and policy consequences when indifference is ambivalence: strategic ignorance about meat consumption optimal expectations and limited medical testing: evidence from huntington disease how people decide what they want to know mturk character misrepresentation: assessment and solutions the economics of information random testing is urgently needed ruining popcorn? the welfare effects of information psychosocial predictors of brca counseling and testing decisions among urban african-american women strategic selfignorance welfare effects of nudges: the emotional tax of calorie menu labeling truth in consequentiality: theory and field evidence on discrete choice experiments closing your eyes to follow your heart: avoiding information to protect a strong intuitive preference report of the who-china joint mission on coronavirus disease we thank the stroock fund for financial support. this study was approved by the irb at university of wyoming and was pre-registered in the aea rct registry (rct id: aearctr- ). key: cord- -qdbmpi j authors: sacks, daniel w.; menachemi, nir; embi, peter; wing, coady title: what can we learn about sars-cov- prevalence from testing and hospital data? date: - - journal: nan doi: nan sha: doc_id: cord_uid: qdbmpi j measuring the prevalence of active sars-cov- infections is difficult because tests are conducted on a small and non-random segment of the population. but people admitted to the hospital for non-covid reasons are tested at very high rates, even though they do not appear to be at elevated risk of infection. this sub-population may provide valuable evidence on prevalence in the general population. we estimate upper and lower bounds on the prevalence of the virus in the general population and the population of non-covid hospital patients under weak assumptions on who gets tested, using indiana data on hospital inpatient records linked to sars-cov- virological tests. the non-covid hospital population is tested fifty times as often as the general population. by mid-june, we estimate that prevalence was between . and . percent in the general population and between . to . percent in the non-covid hospital population. we provide and test conditions under which this non-covid hospitalization bound is valid for the general population. the combination of clinical testing data and hospital records may contain much more information about the state of the epidemic than has been previously appreciated. the bounds we calculate for indiana could be constructed at relatively low cost in many other states. constructing credible estimates of the current prevalence of sars-cov- in the united states is challenging. despite growing since the start of the epidemic, testing rates remain low in most of the country: only a small fraction of the population is tested for sars-cov- on any given day. moreover, tests are often allocated to people exhibiting covid- symptoms or who are thought to have come into contact with the virus (abbott and lovett, ) . for example, new york state and texas both use a self-diagnostic tool to screen people for testing. the low rate of testing in the general population means that the number of confirmed sars-cov- cases almost certainly understates the true number of infections in the population. at the same time, statistics like the fraction of tests that are positive likely overstate population prevalence because the tested population is more likely to be infected than the population as a whole. in this paper, we propose a new approach to measuring the point-in-time prevalence of active sars-cov- infections in the overall population using data on patients who are hospitalized for non-covid reasons. there is less uncertainty about sars-cov- prevalence for the non-covid hospital patient population because people in the hospital are tested at much higher rates than the general population, even if they are hospitalized for reasons unrelated to covid- (sutton et al., ) . we combine detailed testing data and hospital data from indiana with a family of weak monotonicity assumptions that seem to have high credibility. the combination of these assumptions with linked testinghospital data leads to relatively tight upper and lower bounds on the prevalence of active sars-cov- infections in the overall population in indiana in each week from mid-march to mid-june. the detailed indiana data allows us to conduct robustness checks that partially validate some of our assumptions. our basic method (without the validation checks) could be implemented using data that many states are already collecting and partially reporting. thus, our approach could help states extract timely prevalence information using existing surveillance data. importantly, our paper is focused on estimates of the fraction of the population that would test positive in each week. these estimates are distinct from recent efforts to estimate the share of the population ever infected with sars-cov- (manski and molinari, ) . the distinction between active prevalence and cumulative prevalence is important because the prevalence of active infections is a key determinant of the spread of the epidemic, given that the level of immunity in the population is thought to be quite low. estimates and forecasts of the prevalence of active sars-cov- infections are crucial for public and private responses to the disease. they have shaped decisions about disruptive non-pharmaceutical interventions such as school closures, non-essential business closures, gathering restrictions, stay-at-home mandates, and temporary increases in the generosity of the unemployment insurance system . reported estimates of prevalence likely also motivate individual precautionary behaviors ranging from wearing a mask to reducing demand for goods and services that require physical interaction allcott et al., ; philipson, philipson, , kremer, ) . finally, estimates of prevalence are a necessary input into efforts to measure other quantities of interest, like the infection fatality rate and the infection hospitalization rate. given its importance, researchers have developed several approaches to measuring sars-cov- prevalence in light of the challenge of non-representative testing. one of the most credible is to conduct a biometric survey in which tests are offered to a representative sample of the population (menachemi et al., ; richard m. fairbanks school of public health, ; gudbjartsson et al., ). other studies have tested a census of smaller populations such as cruise ships (e.g. russell et al. ( ) ). however, it is difficult and costly to regularly implement a survey with accurate coverage and high response rates, especially a new survey that has not been in the field for long. a second approach involves backcalculation methods, which use data on observed hospitalizations or deaths to infer disease prevalence at earlier dates using assumptions about the unobserved parameters that determine the progression of the disease, hospitalization rates, and case fatality rates (brookmeyer and gail, ; egan and hall, ; flaxman et al., ; salje et al., ) . backcalculation may work well if hospitalizations or deaths are well measured, and if previous research has already reached consensus about key parameters related to the disease. however, backcalculation may be less credible for a novel virus because the scientific knowledge base is smaller. and even when backcalculation is based on credible assumptions, it may be of limited value for public health decision making because both hospitalizations and deaths lag current infections (verity et al., ) . an alternative to biometric surveys and backcalculation is to combine non-random clinical testing data with weak distributional assumptions to construct bounds on population prevalence (e.g. manski ( ) ; wing ( ) ). in the covid- epidemic, stock et al. ( ) provide bounds on population prevalence using a testing encouragement design, which is not always available. manski and molinari ( ) bound the share of the population that has ever been infected under a "test monotonicity assumption" that the infection rate is weakly higher among the tested than among the untested. this assumption is appealingly credible, and the bounds can be calculated from widely available test data. however, even when the focus is cumulative prevalence under test monotonicity, the prevalence bounds are often wide because testing is so rare. we pursue a related strategy in this paper. our analysis is based on the insight that test rates are especially high among hospitalized patients, even patients hospitalized for reasons that are apparently unrelated to covid- , such as labor and delivery or vehicle accidents. the upper and lower bounds on prevalence in these populations will tend to be much tighter than similar bounds in the general population. in addition, it is plausible that some types of hospitalizations occur for reasons that are independent of infection risk. for example, people who are hospitalized for injuries sustained in a traffic accident might be expected to have about the same risk of sars-cov- infection as the general population. we build on this insight to estimate more informative upper and lower bounds on weekly sars-cov- prevalence in the population. our paper makes some methodological contributions that may be relevant to the development of more informative public health surveillance systems. we describe the conditions under which upper and lower bounds on active prevalence among non-covid hospitalizations are valid estimates of the upper and lower bounds on prevalence in the general population. we maintain the test monotonicity assumption throughout, and we derive upper and lower bounds on prevalence in the population under two alternative assumptions about the representativeness of non-covid hospitalizations for the broader population. the first assumption is a relatively weak "hospital monotonicity" assumption that prevalence is at least as high among non-covid hospital patients as it is in the general population. this assumption would be satisfied even if hospitalized patients are at greater risk of covid because, for example, people who get into car accidents have more social interactions. the second assumption is a stronger "hospital independence" assumption that prevalence is the same among non-covid hospital patients as it is in the general population. the resulting bounds are informative for prevalence at a point in time, not just cumulative prevalence. this is important because the information required to estimate the bounds is closely related to the simple statistics that many states already report. it appears possible for many states to use our method to report upper and lower bounds on prevalence in near real time using data that they already collect and report. in particular, states already report the covid-hospitalization rate, as well as overall test rates and test positivity rates. to report a version of the upper and lower bounds we describe in this paper, states would simply have to compute testing and positivity rates among non-covid hospitalizations. our first empirical contribution uses this framework to estimate upper and lower bounds on weekly prevalence of sars-cov- in indiana. to operationalize the basic idea, we work with two definitions of non-covid hospitalizations. the first, which we call non-influenza-or covid-like-illness (non-icli) hospitalizations, simply excludes all hospitalizations with diagnosis for icli (center for disease control and prevention, ; armed forces health surveillance center, ) . this definition would be easy to implement in many different hospital data sets and yields a large population of hospital patients. however, we also work with a definition using a narrower set of patients who are hospitalized for six groups of clear non-covid causes: (i) cancer; (ii) appendicitis and vehicle accidents; (iii) labor and delivery; (iv) ami and stroke; (v) fractures, crushes, and open wounds; and (vi) other accidents. the clear-cause analysis is more intuitive and transparent, but it is based on smaller samples and might be harder to implement as part of a public health surveillance system. we show that, in indiana, test rates are much higher among non-covid hospital patients than in the general population. for example, in june, about . percent of the general population was tested in a given week, compared with percent of non-covid hospital patients; test positivity rates are lower among non-covid hospital patients than in the general population. in the general population, . percent of tests were positive. in contrast, among non-covid hospital patients who were tested, only . percent of tests were positive. these testing and positivity rates can be combined to estimate upper and lower bounds on prevalence. under the test monotonicity assumption, between . and . percent of the general population was infected with sars-cov- on june . under the same test monotonicity assumption, the bounds are half as wide for non-covid hospital patients: prevalence was between . and . percent. under the hospital monotonicity assumption, the upper bound on prevalence in the non-covid hospital population is a valid upper bound on population prevalence. and under the stronger hospital independence assumption, the upper and lower bounds on prevalence in the non-covid hospital population are valid upper and lower bounds on population prevalence. the bounds on prevalence based on the non-icli definition are typically very similar to the bounds based on the clear-cause definition. we present bounds under alternative hospital representativeness assumptions (none, monotonicity, independence) to allow readers to make their own judgements about which assumptions are credible, and to better understand how much information about prevalence is derived from the data versus assumptions. we also calculate bounds among icli hospitalizations. we find, of course, much higher prevalence among this group, but our bounds still rule out very high prevalence. specifically, we find that sars-cov- prevalence among icli hospitalizations is no higher than percent at its peak, and no higher than about percent by mid-june. this shows that there is value to testing even highly symptomatic patients, as their sars-cov- rate is far from percent, and testing outcomes would be informative for treatment and quarantine decisions. our second empirical contribution is to assess the credibility of key assumptions that would be difficult to study in other data sets. manski and molinari ( ) point out that the accuracy of sars-cov- virological tests is not well understood. incorporating information about testing errors alters the bounds on prevalence. we use data on people who were tested twice in a two day period to shed some light on the fraction of people who test negative but are actually infected. we tentatively conclude that test errors are have a negligible effect on the upper and lower bounds on prevalence reported in our paper. we also assess the credibility of the hospital representativeness assumptions at the core of the paper. the most restrictive hospital independence condition assumes that sars-cov- prevalence is the same in the non-covid and general populations, and the weaker hospital monotonicity condition assumes that prevalence is at least as high among the hospitalized. although we are not able to directly validate these assumptions, we probe their credibility in two ways. first, we compare the hospitalization bounds to estimates of population prevalence obtained from tests of a random sample of indiana residents in april and june (menachemi et al., ; richard m. fairbanks school of public health, ) . second, we examine the pre-hospitalization test rates of non-covid hospitalized patients. these validity checks are roughly consistent with the the hospital independence assumption, and highly consistent with hospital monotonicity. this suggests that these assumptions might be considered reasonable in other states where it would be easy to estimate the upper and lower bounds but harder to perform elaborate validation exercises. overall, our results indicate that combining testing data and information on non-covid hospitalizations may be a feasible and informative way of measuring sars-cov- prevalence. in the most recent weeks of our data (and under test monotonicity but without hospitalization data), we can only conclude that at most percent of the overall indiana population was actively infected. with hospitalization data and the hospital monotonicity assumption, we can conclude that at most . percent of the indiana population was infected. despite this substantial improvement, the bounds remain wide enough that we cannot conclude whether prevalence has fallen since early april. similar bounds could be constructed in other states using aggregate data on non-covid hospitalizations and their testing and test positivity rates, potentially improving covid surveillance systems across the country. the empirical goal of our study is to bound the fraction of the indiana population that is infected with sars-cov- in each week. to fix ideas, we use i = ...n to index the population of indiana. let c it = indicate that person i is currently infected with sars-cov- on date t. the population prevalence of active sars-cov- infections in indiana at date t is p r(c it = ) = n n i= c it , where we leave conditioning on date t implicit to reduce clutter. we are also interested in prevalence among hospital inpatients with various covid-and non-covid-related diagnoses. this is simply the probability that a person is infected, conditional on being hospitalized for a specified condition or set of conditions. let h it be a binary indicator set to if the person was hospitalized with a non-covid-related diagnosis. then p r(c it = |h it = ) is the prevalence of active sars-cov- infections in the sub-population of people who were admitted with a non-covid-related diagnosis on date t. a key inferential challenge in estimating prevalence is that values of c it are unknown for most people on most days, because testing is rare. let d it = if person i was tested on t and d it = if the person was not tested. let p r(d it = ) represent the proportion of the population tested on date t, where conditioning on t is implicit. continuing with the notation laid out above, p r(c it |d it = ) and p r(c it |d it = ) represent prevalence among people who are tested and not tested, respectively. the value of c it is observed for people where d it = , but unknown for people where d it = , which means that p r(c it |d it = ) is not identified by the data on testing and test outcomes. we define prevalence in the tested and untested hospital populations similarly, but with conditioning on both testing status and hospitalization status. in the absence of any distributional assumptions, the observed clinical tests partially identify prevalence overall, and in any sub-populations that can be defined by observable covariates. use the law of total probability to decompose population prevalence: the only unknown quantity on the right-hand side of the expression is p r(c it |d it = ), which is prevalence among people who were not tested. without any additional assumptions or data, all that is known is that this value lies between and . substituting and for the unknown prevalence yields worst-case lower and upper bounds l w and u w on population prevalence: these bounds define the set of values for unknown population prevalence that are compatible with the observed data and the logical definition of prevalence. the lower bound is the confirmed positive rate, and the upper bound is that rate plus the untested rate. the width of the worst-case bounds on a given day is decreasing in that day's testing rate. testing more people can only increase the confirmed positive rate and decrease the untested rate. however if few people are tested, the bounds can be very wide. to narrow the bounds, manski and molinari ( ) propose the "test monotonicity" condition. this condition requires that the prevalence of sars-cov- is at least as high in the tested population as it is in the untested population. formally, test monotonicity implies that p r(c it |d it = ) ≥ p r(c it |d it = ). this is an appealing condition because virological tests are typically allocated to symptomatic individuals, who have a higher than average likelihood of infection. under test monotonicity, prevalence in the tested sub-population represents an upper bound on the unknown prevalence among the untested sub-population. the lower bound remains the worst-case lower bound. the lower and upper bounds under monotonicity, l m and u m , are: the new upper bound will be lower than the worst-case upper bound as long as prevalence in the tested sub-population is less than . in our data, test rates are less than percent and positivity rates in the population are roughly percent, so this assumption brings the upper bound down from percent to percent or less. a similar assumption could be made for the non-covid hospitalization population, yielding bounds l h m and u h m on prevalence among the non-covid hospitalized population. test monotonicity can be used to narrow the the bounds on prevalence in the population and among non-covid hospitalized patients. because testing rates are much higher in hospitals than in the general population, the bounds on prevalence in hospitalized subpopulations are much narrower. thus, assumptions that link hospital and population prevalence may be a powerful way to reduce uncertainty about population prevalence. we pursue two types of assumptions that enable extrapolation from non-covid hospital populations to the general population: (i) monotone selection into hospitalization and (ii) risk-independent hospitalization. these are both forms of hospital instrumental variable assumptions, and we refer to them collectively as hospital iv assumptions. the hospital monotonicity assumption requires that the prevalence of active sars-cov- infections among non-covid hospital patients is not lower than the prevalence of active infections in the general (non-hospitalized) population. formally, p r(c it |h it = ) ≥ p r(c it ). when prevalence is bounded in the hospitalized and general populations, the hospital monotonicity assumption may further reduce the width of both sets of bounds by ruling out values that would violate it. in particular, under hospital monotonicity, the upper bound on population prevalence cannot be larger than the upper bound on hospital prevalence. when both the hospital monotonicity assumption and the test monotonicity assumption are imposed, the upper bound on sars-cov- prevalence in the population is where u m is the upper bound on prevalence in the population under hospital monotonicity and u h m is the upper bound on prevalence among non-covid hospital patients. in our data, the hospital upper bound is typically lower than the population upper bound, so the hospital monotonicity condition in practice implies that the positivity rate among non-covid hospitalizations is an upper bound population prevalence. a stronger assumption that also facilitates extrapolation from a hospitalized sub-population to the general population is a "hospital independence" assumption, which means that hospitalization for non-covid-related health conditions is mean independent of infection with sars-cov- . independence implies that people infected with sars-cov- have the same probability of being hospitalized for a non-covid condition as people who are not infected with sars-cov- so that p r(h it |c it = ) = p r(h it |c it = ). equivalently, the independence assumption implies that sars-cov- prevalence is the same among people who are hospitalized for non-covid conditions and the general population. that is, under the hospital independence assumption: p r(c it |h j it ) = p r(c it ). the independence assumption implies that non-covid hospitalizations are an instrumental variable for testing. this assumption would be satisfied if non-covid hospitalizations arose randomly in the population, for example because of health conditions (such as pregnancy or heart disease) determined prior to the epidemic. the hospital independence assumption would fail, however, if hospitalization risk was systematically related to covid- risk, for example because essential workers have more social interactions and greater likelihood of hospitalizations. under the hospital independence assumption, the bounds on the common prevalence parameter are defined by the intersection of the hospital and population bounds. the lower and upper bounds under test monotonicity and hospital independence, l m,ind and u m,ind , are: under hospital independence (as well as test monotonicity), the upper bound on prevalence is the same as under hospital monotonicity. what the hospital independence assumption buys us is a tighter lower bound, which is now the greater of the lower bounds on population and hospital prevalence under test monotonicity. in practice we find that the lower bound is always higher in the non-covid hospitalization sub-population than in the general population, so in practice this assumption implies that the lower bound on population prevalence is the confirmed positive rate among non-covid hospitalizations. virological tests for the presence of sars-cov- may not be perfectly accurate, and so far there are no detailed studies of the performance of the pcr tests that indiana is using to test people for sars-cov- . to clarify how error-ridden tests complicate our prevalence estimates, we augment our notation to distinguish between test results and virological status. we continue to use c it to represent a person's true infection status, and we still use d it to indicate whether a person was tested at date t or not. but now we introduce r it , which is a binary measure set to if the person tests positive and if the person tests negative. using this notation, p r(c it = |d it = , r it = ) is called the positive predictive value (ppv) of the test among people who are tested and who test positive. p r(c it = |d it = , r it = ) is called the negative predictive value (npv) among people who are tested and who test negative. −n p v = p r(c it = |d it = , r it = ) is the fraction of people who test negative who are actually infected with sars-cov- . our initial worst case bounds assumed no test errors. relaxing that assumption yields a different set of upper and lower bounds on prevalence. following manski and molinari ( ), we assume that (i) p p v = so that none of the positive tests are false, but (ii) the second condition imposes a bound on −n p v , which is the fraction of people who test negative who are actually infected. under these two restrictions, the new worst case bounds work out to: allowing for test errors in this way increases the worst case lower bound by the best-case fraction of missing positives, and increases the worst case upper bound by the worst-case fraction of missing positives. similar expressions hold for prevalence bounds under test monotonicity and other independence assumptions. the upshot of this analysis is that knowledge of test accuracy is important for efforts to learn about prevalence. in their study of the cumulative prevalence of sars-cov- infections, manski and molinari ( ) computed upper and lower bounds on prevalence under the assumption that λ l = . and λ u = . , citing peci et al. ( ) . manski and molinari ( ) view this choice of . ≤ − n p v ≤ . ] as an expression of scientific uncertainty about test errors, and they refer to the resulting prevalence bounds as "illustrative". however, the structure of the test error bounds makes it clear that assumptions about the numerical magnitude of test errors have inferential consequences. for example, setting λ u = . implies that, regardless of the outcome of the test, at least percent of the people who are tested for sars-cov- are infected. although there is little published evidence on the properties of the sars-cov- pcr test, previous research suggests that pcr test errors are uncommon in other settings. for example, peci et al. ( ) study the performance of rapid influenza tests using pcr-based tests as a gold standard. pcr tests are used as a gold standard because they are expected to have very high ppv and npv. to shed more light on test errors, we constructed a sample of people who were (i) tested on day t, (ii) not tested on day t− , and (iii) were tested again on day t+ . a total of , test pairs met this criteria. using r i and r i to represent the results of a person's first and second test, we found that p r(r i = , r i = ) = . and p r(r i = , r i = ) = . among the people in the twice-tested sample. the two tests were discordant for less than percent of the twice-tested sample. in appendix c, we estimate prevalence and npv in the twice-tested sample under the strong assumptions that the tests have specificity equal to , sensitivity does not depend on initial test result, and retesting is random. using this method, we find that prevalence was percent and n p v = . in the twice-tested sample. with − n p v = . , the estimates imply only about . percent of people who test negative are actually infected. the twice-tested sample is likely not representative of the population, of course. people who are re-tested after a negative test are probably highly symptomatic. this suggests that − n p v = p r(c it |d it , r it = ) is probably higher in the twice-tested sample than in the population. accordingly, we think that a plausible value for λ l is nearly zero, and a plausible value for λ u is . . accounting for test errors in this range would have almost no effect on the upper and lower bounds reported in the paper. our bounds turn out to be fairly simple objects. under test monotonicity, the lower bound on prevalence is the confirmed positive rate, the share of the population that tests positive. the corresponding upper bound under monotonicity is the test positivity rate, the share of tests that are positive. under hospital monotonicity, the upper bound becomes the test positivity rate among non-covid hospitalizations. and under hospital representativeness, the lower bound becomes the confirmed positive rate among non-covid hospitalizations. an appealing feature of these bounds is that they can be calculated with little additional data beyond what public health organizations already report. every state already reports the number of tests and the number of positive tests, and many states report the number of covid-related hospitalizations. states would only have to report test and positivity rates for non-covid-related hospitalizations. this appears possible because many states already report "suspected" or "under investigation" covid hospitalizations, defined as hospitalized patients exhibiting covid-like illness. some states actually report both the number of hospitalizations of patients with covid-or influenza-like illness and, separately, the number of hospitalizations of patients with a positive sars-cov- test (e.g. arizona and illinois (arizona department of health services, ; illinois department of public health, a,b)). thus states have the capacity to identify icli-related hospitalizations and link hospitalization and testing data. our analysis is based on two main data sources managed by the regenstrief institute. first we obtain data on the near universe of clinical virological tests for sars-cov- conducted in indiana between january , and june , . second we obtained data on all inpatient hospital admissions from hospitals that belong to the indiana network for patient care (inpc), which is a health information exchange that centralizes and stores data from health providers across the state of indiana, including all hospitals with emergency departments. the hospital data are derived from the same database that the state uses for reporting hospitalizations on its dashboard (indiana state department of health, ). we link the testing and hospital data using an encrypted common identifier. of see, e.g., the covid tracking project ( ). course, only a subset of hospital patients are tested and only a subset of tested people appear in the inpatient hospital data. for both data sets, we are also able to link the data with basic demographic data collected by the inpc; this information is available only for a subset of patients. the test data contain individual records for nearly all of the sars-cov- tests conducted in indiana during . a small number of tests are excluded from our data because some institutions that conduct tests provide data to inpc but do not allow the data to be used for research purposes. the consequence of these exclusions is that we are missing some tests, which will result in a reduced lower bound in our framework. despite these exclusions, our data set tracks the state's official case counts fairly closely; see appendix figure a. . as an aggregate summary, our data contain , total positive tests, and the state reports , positive tests as of june (indiana state department of health, ). each test record in our testing data includes information on the date the test was run, the outcome of the test (positive, negative, or inconclusive), and a patient identifier that we use to link the test data to demographic files and inpatient hospital files. the hospital inpatient data contain separate observations for each admission. we always observe admission time and a patient identifier that we use to link to the test data and inpatient files. we observe discharge time and diagnosis information only for a subset of admissions. (not all fields are available for all admissions because different institutions contribute different information to the inpc.) because the inpc data come from health care providers and payers, the same hospitalization can appear in the data set multiple times. to de-duplicate these records, we keep one observation per admission time (defined second-by-second), keeping the observation with the most diagnosis codes. in-hospital testing, positivity rate, and confirmed positives the fraction of people who are tested in the hospital is an important quantity of interest in our analysis because hospital patients are tested at a higher rate than the general population, and hospital testing may be less correlated with covid symptoms. our data do not distinguish whether a person was tested in the hospital or whether the test was initiated independently of the hospital visit. we say that a hospitalized patient was tested in-hospital if she had at least one sars-cov- test dated between days prior to admission to days after admission. we chose to focus on this week-long period, rather than strictly between admission and discharge, for three reasons. first, some patients will be tested prior to admission, as part of their preparation for admission. thus it is valuable to look prior to admission. second, we observe the date the test is run, not the the date the sample is collected. backlogs in the testing system may mean that a patient is discharged before the test is run. third, for some admissions, we lack discharge dates, but we can still define in-hospital tests using this measure. we say that a patient tests positive in the hospital if she has at least one positive covid test between days prior to admission and days after admission. we define the positivity rate as the fraction of tests that are positive; the confirmed positive rate is the fraction of the population with a positive test. in some analyses we compare hospital testing and positivity to population testing and positivity. hospital testing and positivity are defined over a week-long span for a given hospitalization. to make the comparison with the general population clean, we examine test rates and positivity in a given week-long period. we say that a person was tested if she was tested at least once in a given week, and we say she was positive if she was positive at least once in that period. throughout, a patient is in the "test sample" if they are tested at least once. we say a patient is in the "inpatient sample" if they are hospitalized at least once. we limit our analysis to admissions with non-missing diagnostic information, and we say a patient is in the "inpatient diagnoses sample" if they meet this restriction. this limitation is important because diagnostic information is necessary for distinguishing covid-related admissions from non-covid-related admissions. we construct three analytic samples from the inpatient data. we start by defining hospitalizations for influenza-and covid-like illness (icli) using icd- codes. we identify admissions with any of a standard set of icd- codes for icli following armed forces health surveillance center ( ). then we identify admissions with any of the additional icd- codes that the cdc recommends using for coding covid hospitalizations (center for disease control and prevention, ). both the influenza-like and covid-like diagnoses include general symptoms such as cough or fever, as well as more specific diagnoses like acute pneumonia, viral influenza, or covid- . we classify hospitalizations as icli-related if they have any influenzaor covid-like illness (icli) diagnoses, and we classify hospitalizations as non-icli if they are not icli-related. appendix b lists the icd- codes used to define the analytic samples. we view the non-icli sample as a useful starting point for our analysis for two reasons. first, our hospital iv assumptions are most plausible for hospitalizations that are not obviously covid-related, and this sample meets that criteria. second, as we have noted, many states already classify hospitalizations as icli-related; thus non-icli hospitalizations are identifiable and measurable in near-real time, so this sample can be studied more broadly. we acknowledge, however, that the non-icli sample may not satisfy the hospital iv assumptions for at least two reasons. first, it may condition on covid itself, since a patient with a reported covid diagnosis would be excluded from it. (in practice we observe many patients with positive covid tests but no covid diagnosis.) second, covid is a new disease with heterogeneous symptoms, so even if a patient is hospitalized because of covid, she may not have one of our flagged diagnoses, and we may incorrectly call her hospitalization non-icli . to avoid these problems, we study a third sample, which we call the "clear cause" sample. these are hospitalizations with a clear cause that is not obviously covid-related. we define clear-cause hospitalizations as hospitalizations with a diagnosis code for labor and delivery, ami, stroke, fractures, crushes, open wounds, appendicitis, vehicle accidents, other accidents, or cancer. for all of these conditions except cancer, we flag hospitalizations with a diagnosis at any priority. for cancer, we flag hospitalizations with a cancer diagnosis code as the admitting diagnosis, the primary final diagnosis, or any chemotherapy diagnosis. appendix b lists the icd- codes used for these classifications. we view the clear-cause sample as important for two reasons. first, we believe the hospital iv assumptions are most plausible for this sample, so we believe the bounds on prevalence are most likely to be valid. second, we view the clear-cause sample as offering a test of the validity of the non-icli sample. to the extent that the two samples generate similar bounds, we can be more confident that the non-icli sample is informative of broader population covid prevalence, despite the problems with the non-icli classification. this would be valuable because classifying hospitalizations as icli-related or not requires less information than ascertaining a clear cause of the hospitalization. we show summary statistics for all of our samples in table , as well as for the state as a whole (from census fact finder and united states census bu-reau ( )). the average tested and hospitalized patient is substantially older than the population as a whole, and also more likely to be female. because the tested and hospitalized samples are not age representative of the general population, we reweight all samples to match the population age distribution. the tested and hospitalized samples are fairly similar to the general population in terms of racial composition. limiting the inpatient sample to admissions with diagnoses reduces our sample size substantially, but it does not appear to change its demographic profile. although our main analysis looks at test rates at the admission level (rather than the person level), the summary statistics show that hospitalized patients are vastly more likely to have ever been tested than the population as a whole -about percent of ever-hospitalized patients, compared to about , out of . million ( . percent) for the general population. icli-related hospitalizations are especially likely to have ever been tested. figure shows the sars-cov- testing rate for each of the sub-populations in our analysis. we report the exact values of each of the test rates and the weekly number of admissions in appendix table a . . because the tested and hospitalized populations have very different age distributions compared to the rest of the population, we reweight the hospital sub-populations to match the coarsened age distribution in the population. specifically, we calculate test rates in week-by-age-group cells, for age groups - , - , - , - , - , and and older. then we average these age-specific testing rates across the age groups, weighting each group by its population share. we report unweighted test rates in appendix table a . . figure shows vastly higher test rates in the hospitalized samples than in the general population. the testing rate in the general population grew from . percent in april to between . and . percent in may and june. so despite tripling, the weekly test in the indiana population rate remained below percent. in contrast, people hospitalized for icli were tested at a very high rate, between and percent in most weeks. testing rates among non-icli hospital patients and among the clear-cause non-covid hospital patients were lower than the icli sample but much higher than the population overall, about percent in april and - percent in may and june. in other words, testing rates among non-covid hospital inpatients are about times higher than testing rates in the general population, but they are typically less than half as high as testing rates in the icli population. these high test rates imply tighter bounds on population prevalence under test monotonicity, as we show in figure and report in appendix table a . . we age-weight the bounds, analogously to our weighting of test rates, and we report unweighted bounds in appendix table a . . several patterns are clear in the figure. first, the icli hospitalized population has higher upper and lower bounds on prevalence than the other groups. for the icli patients, the prevalence bounds are - percent in the first week of our sample, then increase to - percent in the last week of march, before declining steadily to - percent in the final week of the sample. these bounds rule out the possibility that all or nearly all symptomatic patients are infected with sars-cov- . in most weeks the icli bounds lie outside the other groups' bounds, implying (unsurprisingly) unambiguously higher covid prevalence. this separation shows that the data are sensible and that the bounds are informative enough to tell apart these highly distinct populations. the second clear pattern in the figure is that the prevalence bounds are tighter for the non-icli and clear-cause hospitalization samples than for the all-test sample. in fact the bounds for both of these hospitalizations samples are always contained within the all-test bounds. even at their tightest, the bounds for the all-test sample are as wide as . to . percent in the last week of our data. in that week the bounds for non-icli hospitalizations are [ . %, . %] and for clear-cause hospitalizations they are [ . %, . %]. this tight bound implies that the hospitalization data could be informative for population prevalence (under hospital monotonicity or mean independence). the final pattern evident in figure is that the bounds for the non-icli hospitalization sample and for the clear-cause hospitalization sample are nearly indistinguishable. the only noticeable difference is that the upper bound for non-icli hospitalization is perhaps slightly higher. this fact is important because non-icli hospitalizations are potentially easier to measure, but they may be negatively selected in the sense that by construction they may exclude covid-likely cases. the similarity of the non-icli bounds with the bounds for the clear-cause sample (which is not selected based on covid-likelihood) provides some evidence in support of using non-icli hospitalizations to measure general prevalence. our clear-cause hospitalization sample pools many distinct causes, including among others labor and delivery, vehicle accidents, and other accidents, including falls. in principle these hospitalizations may differ in their covid likelihood. one might worry, for example, that pregnant women are especially cautious and careful not to become infected, whereas people getting into vehicle accidents may be less cautious (either because they are not careful drivers, or because they are out of the house at all). we therefore report test rates and bounds for disaggregated causes as well as the overall clear-cause sample. we focus on six sets of causes: cancers, appendicitis and vehicle accidents, injuries (fractures/crush/wounds), non-vehicle accidents, and ami/stroke. these six groups have reasonable sample sizes throughout (they each have , - , admissions per month), and the demographic profiles within each group are roughly similar; see appendix table a . for age profiles of admitted patients by cause of admission. all ages are represented in the cancer sample: appendicitis and vehicle accidents both afflict young people; ami, stroke, and other accidents-primarily falls-afflict older people; and labor and delivery is limited, of course, to women of childbearing age. because not all age groups are represented in every category, we do not age-weight these results. we report the monthly test rates for each of these groups in figure . we also report sample sizes, exact tests rates, and bounds in appendix tables a. and a. , by month and cause. all causes had relatively low test rates in march before rapid increases in april and may. by june there are some differences in the test rates, with higher rates for the injury, accident, and ami/stroke admissions, and less testing for cancer and labor and delivery. we report the bounds on prevalence by cause of admission in figure . in march there is little testing; the bounds are wide and uninformative. the bounds tighten in april, may, and especially june. importantly, we do not see obvious, systematic differences across the groups. typically the bounds overlap, and there is no strong evidence that the upper or lower bounds differ by cause of admission. it is true that in june, cancer patients had zero positive tests, and the upper bound for appendicitis and vehicle accidents was below the lower bounds for injuries, other accidents, and ami/stroke. however in april and may the cancer and appendicitis/vehicle patients had similar or even higher upper bounds than did the injury and other accident patients. this evidence shows that patients admitted to the hospital for different reasons and with different demographic profiles are all nonetheless tested at a high rate and with similar bounds on prevalence. this is perhaps reassuring for the view that pooling many distinct causes of admissions can nonetheless generate meaningful bounds on prevalence. the results so far show that the bounds on prevalence are much tighter for the non-icli hospitalized population than for the population as a whole. this tighter bound is informative for general population prevalence only under assumptions about hospital representativeness, either a monotonicity assumption or an equal prevalence assumption. how valid are these assumptions? assessing them directly is of course impossible because we lack data on prevalence in the population as a whole or in the hospital sample. we have already provided one piece of indirect evidence in support of our hospital representativeness assumptions. the non-icli and clear-cause samples generate similar bounds, and, within the clear-cause sample, there are not large differences in bounds across different causes of admission. this suggests that prevalence does not vary with the exact set of hospitalizations studied, although of course this does not prove monotonicity or representativeness. in this section, we provide two additional pieces of evidence on the hospital iv assumptions. first we show that the hospital bounds are consistent with the estimates of population prevalence from the indiana covid- random sample study (menachemi et al., ; richard m. fairbanks school of public health, ) . second, we compare the hospital sample to the general population in terms of their likelihood of prior testing (prior to the hospital data) and the test rate of their home counties. we take these to be proxies for their concern about covid, although other interpretations are possible. a valuable benchmark for the hospital-based prevalence bounds comes from a largescale study of sars-cov- prevalence in indiana. the study invited a representative sample of indiana residents (aged and older) to obtain a sars-cov- test. the first wave of the study took place april - , and the second wave took place june - . the preliminary results are reported in menachemi et al. ( ) and richard m. fairbanks school of public health ( ). the response rate was roughly percent, and no attempt was made to correct for non-random response. nonetheless this survey appears to be the best benchmark available. we report the point estimates for prevalence (assuming random nonresponse) and their confidence intervals in the top panel of table . the first wave estimates . percent prevalence and the second . percent. we compare our prevalence bound during the same time periods in the bottom panel of the table. we limit our sample to tests of people aged and older, for comparison with the population study. using population testing we obtain very wide bounds that contain the random sample study estimates. this fact provides some support for the test monotonicity assumption. for both the non-covid hospitalization and clear-cause hospitalization samples, the bounds are much tighter. both sets of upper and lower bounds contain the april prevalence estimate, and both sets exclude the june estimate point estimates. however the confidence interval for the june - point estimates overlaps substantially with the non-icli and clear-cause bounds. thus for both dates the prevalence point estimates are consistent with the bounds obtained from the non-covid hospitalizations. as a comparison we also report the bounds from the icli-related hospitalizations, which always exclude the random sample estimates. a standard way of measuring representativeness is to compare the distribution of covariates in a study population to their distribution in the target population. in our case, this approach is most convincing if we have well-measured covariates that proxy for having covid- . two candidate covariates are the community sars-cov- testing rate and the prior testing rate. the idea behind these proxies is that people who come from areas with high test rates, or who have been tested in the past, may themselves have a higher current likelihood of having covid- . to operationalize these measures, we define the community testing rate for person i as the fraction of people in i's county who have ever been tested, as of the end of our sample period. we define the prior test rate of person i as of date t as the probability that i was tested at least once during the week-long period [t − , t − ]. we focus on this window because it is the second week prior to our hospital testing window (which runs from t − to t + for a patient admitted at t). we allow for a week of time to elapse between the hospitalization and the "prior" testing because it is possible that some pre-hospital testing would occur in the window [t − , t − ]. when studying prior tests, we limit the sample to each person's first hospitalization after march , , to avoid picking up the higher testing that mechanically results from the fact that people hospitalized once are more likely than the general population to have been previously hospitalized. as with our bounds, here we weight the data to match the population age distribution. table shows the community testing rate. the average county has a testing rate of . %, with an interquartile range of . % to . %. the average person lives in a county with a test rate of . %. the average non-icli hospitalized patient comes from a county with a test rate of . %: for clear-cause hospitalizations it is . %, and for icli hospitalizations it is . %. these rates are all significantly different from the population average. figure shows the prior testing rate as a function of admission date for the non-icli hospitalization sample, the clear-cause hospitalization sample, and the general population (for which the prior test rate on day t is defined as the fraction tested between t − and t − ). the rates in the hospitalization samples are initially close to the population rate (when testing is low in general), but the lines diverge. by the last week of the sample, the prior testing rate is about . percentage points in the hospitalization samples, relative to approximately . percentage points in the population. although the weekly differences are not individually statistically significant, overall the greater rate of prior testing is consistent with positive selection into hospitalization. however it is also consistent with the possibility that the hospitalization sample simply has more contact with the medical sector, resulting in greater testing at a given sars-cov- prevalence. we have calculated weekly bounds on the prevalence of sars-cov- for the indiana population as a whole and for three hospitalized populations: people hospitalized for influenza-and covid-like illness, people hospitalized for other reasons, and people with clear (and clearly not covid) causes of hospitalization. the bounds are valid under weak monotonicity assumptions. the bounds for the general population are wide but narrow over time. the bounds for the hospitalized population are much tighter, because the hospitalized populations are tested at a much higher rate than the general population. the hospitalized populations are informative for the general population only under additional, stronger assumptions. in particular, if the hospitalized population is representative of the general population in terms of sars-cov- prevalence, then both the upper and lower bounds are valid. if the hospitalized population has a higher prevalence than the general population, then only the upper bound is valid. we assess these assumptions in multiple ways. we find that the non-covid hospitalized population bounds contained the point estimate of prevalence from a random sample in late april. by early june the point estimate from the random sample was below our lower bound, although we cannot reject that it was inside the bound. hospitalized patients also appear to be tested for sars-cov- at somewhat higher rates than the general population, even outside the hospital. this last fact suggests that the representativeness assumption may be violated (although the magnitude may not be too severe), but both are consistent with a weaker monotonicity condition. even under this monotonicity condition, the hospital data are still useful, bringing down the upper bound on population prevalence by a third or more. we believe that the main promise of the non-covid hospitalization population is that it can provide near-real time information about population prevalence. only three numbers are necessary to calculate bounds from the non-covid hospitalizations: the count of non-covid admissions, the number of tests among this group, and the number of positive results. although these numbers are not currently reported, many states already report related numbers, including both the number of covid tests and the count of iclirelated hospitalizations. thus the infrastructure largely exists already to calculate these bounds. the results here help validate this approach for real-time surveillance. notes: column reports characteristics for the set of people appearing in the test data, and columns - for people appearing the hospital data, ever (column ), with at least one diagnosis (column ), at least one non-icli hospitalization for icli (column ), at least one clear cause hospitalization (column , see text for details), or at least one icli hospitalization with a diagnosis and not for icli (column ). notes: the first two rows of the table report the estimated population prevalence and % confidence interval from the indiana covid- random sample study, conducted over the indicated dates, which assumes random nonresponse (menachemi et al., ; richard m. fairbanks school of public health, ) . the remaining rows report the (age-adjusted) bounds on prevalence from our different samples: population testing, non-icli hospitalizations, clear cause hospitalizations, and icli-related hospitalizations. we limit our sample to people aged and older, for consistency with the random sample study. setup and identification here we show how to use data on multiple tests to simultaneously identify prevalence, test error rates, and how to use this information to obtain the negative predictive value, npv. assume in particular that people have been tested exactly twice, with r i the outcome of the first test and r i the outcome of the second test for person i, and c i person i's true infection status, which we assume is fixed between the tests. let p = p r(c i = ) be the prevalence of active sars-cov- infections in this twice tested population. test outcomes may differ from true infection status because of test errors. in general, therefore, there are four possible sequences of test outcomes: ( , ), ( , ), ( , ), ( , ). we let p ab = p r(r i = a, r i = b) for (a, b) ∈ { , } . we make three strong assumptions to simplify the analysis. . the specificity of the test is . that is, β = p r(rj i = |c i = ) = . . the sensitivity of the test, α = p r(rj i = |c i = ), does not depend on the initial test result. . retesting is random, i.e. independent of r i and c i . assumption is the weakest of these assumptions. it implies that there are no false positives, which is consistent with typical practice (ucsf health hospital epidemiology and infection prevention, ). the remaining assumptions are stronger. assumption says that the test errors are independent of the initial test result. it would be violated, for example, if false negatives are more common for patients with high levels of mucus, and mucus levels are correlated across test results. assumption says that retesting rates do not depend on possible testing errors. we would expect this condition to fail if highly symptomatic people with negative tests are especially likely to test negative. we view this assumption as the most suspect. under these assumptions, the probabilities p ab simplify considerable. as the probabilities sum to one, and the assumptions imply that p = p , the only non-redundant probabilities are p = ( − p) + p( − α) p = pα . we can observe p and p . solving for the unknowns p and α, we have p = (p − p − ) p α = p − p + p this shows how to get p and α from two tests and the assumption that specificity equals . our goal is to find the negative predictive value, but we can calculate it given knowledge of α, β and p. in general the npv of a single test is p r(c i = |r i = ). applying bayes rule, n p v = − p p( − α) + ( − p) to implement this approach, we construct a sample of all people who are tested on a given day, not tested the previous day, and then tested again in the next day. there are , such test pairs. we find p = . and p = . . nearly all the mass is on the diagonals; test results switch less than % of the time. this fact, together with the assumption that specificity is equal to , implies very low false negative rates. plugging these values into our formula, we have p = . and α = . , which imply n p v = . . using instead, all people who are retested once within a three day period, we find similar results: p = . , α = . , n p v = . . we emphasize that these estimates are valid for the twice-tested population and under assumptions - , in particular, random retesting. the prevalence estimate is the prevalence among people tested twice, not the population prevalence. and it is only a valid estimate under assumptions - . in reality, it is likely that retests are most common among suspected false negatives (i.e. when a highly symptomatic patient tests negative). we see some evidence for this: p = . and p = . , inconsistent with the random retesting assumption. we therefore do not view our estimates of prevalence and sensitivity as definitive; rather we think of the sensitivity estimate as a lower bound on sensitivity, because we have selected a retest sample which has a disproportionate number of false negatives. as n p v is increasing in sensitivity, α, our implied estimate of − n p v is likely an upper bound on − n p v . covid- test shortages prompt health authorities to narrow access polarization and public health: partisan differences in social distancing during the coronavirus pandemic data dashbaord influenzalike illness. afhsc standard case definitions a method for obtaining short-term projections and lower bounds on the size of the aids epidemic icd- -cm official coding and reporting guidelines april case data a review of back-calculation techniques and their potential to inform mitigation strategies with application to non-transmissible acute infectious diseases estimating the effects of non-pharmaceutical interventions on covid- in europe how disease surveillance systems can serve as practical building blocks for a health information infrastructure: the indiana experience spread of sars-cov- in the icelandic population tracking public and private response to the covid- epidemic: evidence from state and local government actions mandated and voluntary social distancing during the covid- epidemic covid- hospital resource utilization covid- syndromic surveillance gov, last 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tracking project covid- diagnostic testing quick facts: indiana estimates of the severity of coronavirus disease : a model-based analysis. the lancet infectious diseases current activity in vermont three essays on voluntary hiv testing and the hiv epidemic clinical characteristics of patients with coronavirus disease (covid- ) receiving emergency medical services in king county, washington we define icli-related hospitalizations as ones with at least one ili or cli diagnosis code. we define non-icli related hospitalizations as hospitalized with diagnosis codes, but no ili or cli code. we also define "clear cause" hospitalizations. these are hospitalizations for labor and delivery, ami, stroke, fractures and crushes, wounds, vehicle accidents, other accidents, appendicitis, or cancer. with the exception of cancer, we define a hospitalization as belonging to one of these groups if it has any diagnosis codes for that group i . • appendicitis k -k • other accidents w -w • vehicle accident v -v notes: the county test rate is the share of the county population tested at least once in our test data. table reports county-level statistics, as well as the average county test rates for the general population, the non-icli hospitalizations, clear cause hospitalizations, and icli hospitalizations, as well as t-statistic for the null hypothesis that the average person and the average hospitalization have the same county test rate. key: cord- - xoy authors: mahdi, esam; abuzaid, ali h. title: simultaneous diagnostic testing for linear-nonlinear dependence in time series date: - - journal: nan doi: nan sha: doc_id: cord_uid: xoy several goodness-of-fit tests have been proposed to detect linearity in stationary time series based on the autocorrelations of the residuals. others have been developed based on the autocorrelations of the square residuals or based on the cross-correlations between residuals and their squares to test for nonlinearity. in this paper, we propose omnibus portmanteau tests that can be used for detecting, simultaneously, many linear, bilinear, and nonlinear dependence structures in stationary time series based on combining all these correlations. an extensive simulation study is conducted to examine the finite sample performance of the proposed tests. the simulation results show that the proposed tests successfully control the type i error probability and tend to be more powerful than other tests in most cases. the efficacy of the proposed tests is demonstrated through the analysis of amazon.com, inc., daily log-returns. the problem of the analysis of nonlinear time series models has attracted a great deal of interest in finance, business, physics, and other sciences. granger and anderson ( ) and tong and lim ( ) noticed, in many time series modeled by box and jenkins ( ) , that the squared residuals are significantly autocorrelated even though the residual autocorrelations are not. this indicates that the innovation of these models might be uncorrelated but not independent. the authors suggested using the autocorrelation function of the squared values of the series in order to detect the nonlinearity. in this respect, engle ( ) showed that the classical portmanteau tests proposed by box and pierce ( ) and ljung and box ( ) , based on the autocorrelation function of the residuals, fail to detect the presence of the autoregressive conditional heteroscedasticity, arch , in many financial time series models. he introduced a lagrange multiplier statistic, based on the autocorrelations of the squared-residuals, to test for the presence of arch process. mcleod and li ( ) proposed a portmanteau test, which was also based on the squared-residuals autocorrelations, to detect nonlinearity and arch effect. their statistic is similar in spirit to the modified test of box and pierce ( ) proposed by ljung and box ( ) . since then, several authors have developed goodness-of-fit tests based on the autocorrelation function of the squared-residuals to detect nonlinear structures in time series models (e.g., li and mak ( ) ; rodríguez ( , ) ; rodríguez and ruiz ( ) ; fisher and gallagher ( ) ). simulation studies demonstrate the usefulness of using these statistics to test for arch effects but they tend to lack power compared to other types of nonlinear models that do no have such effects. a possible reason for such lack of power could be the fact that none of these tests have considered the cross correlation between the residuals at different powers where the correlations at positive and negative lags might be vary. lewis ( , ) introduced the idea of using the generalized correlations of the residuals to detect nonlinearity without taking into account the distribution of the parameters estimation. recently, psaradakis and vávra ( ) implemented the lewis ( , ) idea and they proposed four goodness-of-fit tests, based on the generalized correlations of the residuals of linear time series model, to test for linearity of stationary time series. two of these tests are similar in spirit to box and pierce ( ) where they replaced the autocorrelations of the residuals in box and pierce ( ) by the cross-correlations of the residuals at different powers getting two tests: one is associated with positive lags; and the other is based on negative lags . similarly, the other two tests were proposed by replacing, respectively, the autocorrelations of the residuals in ljung and box ( ) (or square-residuals in mcleod and li ( ) ) tests by the cross-correlations of the residuals at different powers. their preliminary analysis indicated that the mcleod and li ( ) modification tests control the type i error probability somewhat more successfully than the other tests. hence, they restricted their simulation study focusing on comparing these two tests (where r, s ∈ { , }, r = s) with mcleod and li ( ) test (where r = s = ) and they suggested, in most cases, that at least one of the two cross-correlation tests tends to have more generalized correlation is defined as the autocorrelation between the residuals to the power r at time t and the residuals to the power s at time t + k where r, s are positive s and k is the lag time. the values of autocorrelations of the residuals at positive lags are the same values at negative lags. on the other hand the values of the cross-correlations between the residuals to the power r at lag time t and the residuals to the power s at lag time t + k when k > are not the same when k < . power than the test based on the autocorrelation of the squared-residuals in several time series models. to our knowledge, none of the tests in the time series literature has simultaneously combined the autocorrelations of the residuals and the autocorrelations of their square values with the cross-correlation between them. in this article, we fill this gap by proposing four goodness-of-fit tests. the first part in each of the proposed tests is based on the autocorrelations of the residuals, which is used to test for linearity (adequacy of fitted arma model); the second is based on the autocorrelation of the squared-residuals, which can be used to test for arch , and the third one is based on the cross correlations between the residuals and their squared values, which can be used to test for other types of nonlinear models in which the residuals and their values are crosscorrelated. similar to psaradakis and vávra ( ) , the cross-correlations between the residuals and their squared values propose two different tests. one is based on positive lags and other is based on negative lags. in section we discuss the generalized correlations of residuals and review some test statistics that have been commonly used to detect nonlinearity structure in stationary time series models. in section , we propose new goodness-of-fit (auto-and-cross-correlated) tests that can be used to detect, simultaneously, linear, bilinear, and nonlinear dependency in time series models, and derive their asymptotic distribution as a chi-squared distribution. in section , we provide a monte carlo study comparing the performance of the proposed statistics with those from the literature. we show that the empirical significance level of the proposed tests successfully controls the type i error probability and tends to have higher power than others. an illustrative application is given in section to demonstrate the usefulness of the proposed test for a real world data. we finish this article in section by providing a concluding remarks. auto-and-cross-correlated portmanteau tests let z , z , · · · , z n denote a realization of real-valued stochastic process {z t } where where the polynomials Φ p (b) and Θ q (b) are assumed to have all roots outside the unit circle and to have no common roots and η = (φ , · · · , φ p , θ , · · · , θ q ). in time series literature, the notion of linearity is commonly used when the process {z t } admits the moving-average, ma , representation ( ) where {ε t } are independent and identically distributed, i.i.d., random variables with a zero mean and a constant variance σ . this is the notion considered by mcleod and li ( ) ; lewis ( , ) and psaradakis and vávra ( ) which will also be adopted in this article. on the other hand, there are several time series that do not exhibit a linear behavior. for example, when the innovations {ε t } are uncorrelated but not independent, engle ( ) proposed the autoregressive conditional heteroscedasticity, arch , model that is widely used for analyzing financial time series. this has been generalized by bollerslev ( ) to the generalized autoregressive conditional heteroscedasticity where {ξ t } is a sequence of i.i.d. random variables with a mean value of and a variance value has been proposed to model the dynamic behavior of conditional heteroscedasticity in real time series. e.g.; the exponential garch (egarch ) model proposed by nelson ( ) to allow for asymmetric effects between positive and negative financial time series. tsay ( ) and carmona ( ) provided nice reviews of the garch models. another popular nonlinear model is the threshold autoregressive (tar ) model of (tong, (tong, , (tong, , tsay, ) , which was generalized by chan and tong ( ) and terasvirta ( ) to the smooth transition autoregressive (star ) model. the two regime-switching star model of order ( ; p, p) takes the form i ), i = , , · · · , p are the autoregressive coefficients, ≤ f (.) ≤ is a transition continuous function that allows the dynamics of model to switch between regimes smoothly, and s t is a transition variable. a common formulations for the transition function, which was proposed by terasvirta ( ) , is the first-order logistic function and can represented as: where γ > denotes the smoothness parameter of the transition from one regime to the other, d ≥ is the delay parameter, c is a threshold variable that separates the two-regimes, and σ z is the standard deviation of z t . an alternative choice, which was also proposed by terasvirta ( ) , is the exponential function given by when the value of γ increases, the transition function f (z t ; γ, c) approaches the indicator function in this case, the model in ( ) reduces to the tar model of (tong, ) . arguably the tar models is consider to be the most popular class of nonlinear time series model. therefore, testing for tar and star models have attracted much attention (xia et al., ) . volterra series is another form of the nonlinear stationary process that is widely used in many applications (wiener, , lecture ) . these models have the form where µ is the mean level of z t and {ε t , −∞ < t < ∞} is a strictly stationary process of i.i.d. random variables. let β = (η, µ, σ ) denote the true parameter values in ( ),β = (η,μ,σ ) denote the estimated values, andε i , i = , · · · , n denote the residuals and define the correlation coefficient at lag time k betweenε r t andε s t+k (r, s = , ) aŝ whereγ rs (k) = n − n−k t= f r (ε t )f s (ε t+k ) for k ≥ , γ rs (k) = γ sr (−k) for k < , is the autocovariance (cross-covariance), at lag time k, between the residuals to the power r and the residuals to the power s for r, s = , , and f j ( ( ) of the squared residuals from the linear model given in ( ) have been widely used in several portmanteau statistics to test for nonlinearity. the commonly employed test, which is similar in spirit to box and pierce ( ) , isq where < m < n is the maximum lag considered for a significant autocorrelation . this test is asymptotically distributed as chi-square with m degrees of freedom. mcleod and li ( ) showed that theq test can be improved if the autocorrelation coefficients in ( ) are replaced with their standardized values r rs (k) = n + n − |k|r rs (k), (r = s = , ), k = ± , · · · , ±m. mcleod and li ( ) proposed a portmanteau test, for detecting the presence of the arch effects. their test statistic is given by where the q test is asymptotically distributed as chi-square with m degrees of freedom. simulation studies have showed that theq and q tests respond well to arch models but tend to lack power compared to other types of nonlinear models that do not have the arch effects. the case for absolute residuals is beyond the scope of this article and we focus our attention to the squaredresiduals case. the value of m depends on the sample size, and as a rule of thumb, we consider m ∈ { , , · · · , √ n }, where n denotes the largest integer not exceeding n. a reasonable justification for the lack of powers could be neglecting the cross-correlations between the residuals at different exponent powers (generalized correlations betweenε r t andε s t+k , where k ≥ and r + s > ). in this regard, lewis ( , ) proposed the idea of implementing the sample generalized correlations to detect the nonlinear dependency without considering the distribution of the parameter estimation. recently, psaradakis and vávra ( ) used the idea of lewis ( , ) under the assumption in ( ). they proposed portmanteau tests based on the generalized correlations and demonstrated the usefulness of using the test statistics based on the cross-correlation, between the residuals at different powers, for detecting linearity in time series. their test statistics arê and whereq rs and q rs (r = s) are asymptotically distributed as χ m . psaradakis and vávra ( ) suggested that the tests based on the cross-correlations tend to be more powerful against many types of nonlinearity compared to other statistics based on squared-residual autocorrelations. motivated by the ideas of lewis ( , ) , and psaradakis and vávra ( ), we propose in the next section new test statistics that can be used to detect nonlinearity in time series models. in this section we made some assumptions that are needed to derive the asymptotic distribution of the proposed statistics. in general, the limiting distribution of the portmanteau test statistic required the following assumptions: a . the polynomial Ψ ∞ (b) is differentiable with respect to η in an open neighborhood of the closed disc |b| ≤ . this guarantees that the /Ψ ∞ (b) series is converge and the process {z t } admits the following autoregressive, ar, representation with order ∞ where φ j , j = , , · · · which can be found by solving . hereβ can be estimated by the least squares method or the maximum (or quasi-maximum) likelihood method (see e.g., hannan ( ) ; hosoya and taniguchi ( ) ; kuersteiner ( )). a . ∂γ rs (k)/∂β = o p ( / √ n) for k = , , · · · , n − and r, s ∈ n such that r + s ≥ and if the model in ( ) is correctly identified and the assumptions a -a are held, we propose the portmanteau test statisticsĈ and where the asymptotic distribution ofĈ rs and c rs is chi-square with m − (p − q) degrees of freedom, where r = s ∈ { , }. remark. each of the two test statistics in ( ) can be seen as a linear combination of three existent tests, ljung and box ( ) , mcleod and li ( ) , and psaradakis and vávra ( ), modifying the corresponding tests in ( ). theorem . if {z t } satisfies ( ) and the assumptions a -a are held, then, for any integer m < n, the asymptotic distribution of √ n(r rr ( ), · · · ,r rr (m),r rs ( ), · · · ,r rs (m),r ss ( ), · · · ,r ss (m)) , where r, s = , , r = s, as n → ∞ is gaussian with zero mean vector and the covariance matrix equals to i m . proof. for a fixed m < n, where n is large, the first m sample autocorrelations of the innovations are asymptotically normal with a mean of (ρ ( ), ρ ( ), · · · , ρ (m)) and covariance matrix n − w , where the ( , k)th element of w are given by where ρ (m) is the population autocorrelation of the innovations at lag m. under the assumption a -a , bartlett ( ) showed that ρ (m) = for all m = ; hence the asymptotic distribution of r = √ n(r ( ), · · · ,r (m)) is multivariate normal with mean vector zero and identity covariance matrix (anderson and walker, ) . similarly, under the assumption a -a and from theorem of hannan ( , p. ) and the result c. . of rao ( ) , mcleod and li ( ) showed that the limiting distribution r = √ n(r ( ), · · · ,r (m)) is multivariate normal with mean vector zero and identity covariance matrix. also, under the same assumptions, psaradakis and vávra ( ) showed that the asymptotic distribution of r = √ n(r ( ), · · · ,r (m)) is gaussian with zero mean vector and identity covariance matrix. furthermore, the previous assumptions imply that r , r , and r are independent. therefore, we may conclude that, as n → ∞, the distribution of √ n(r ( ), · · · ,r (m),r ( ), · · · ,r (m),r ( ), · · · ,r (m)) is gaussian with zero mean vector and covariance matrix equals to i m . similarly, it is straightforward to show that √ n(r ( ), · · · ,r (m),r ( ), · · · ,r (m),r ( ), · · · ,r (m)) converges weakly to the standard normal distribution on r m . using the results from theorem , under the adequacy of the fitted arma (p, q) model, and from the theorem on quadratic forms given by box ( ) , it is straightforward to conclude that c rs and c rs will be asymptotically distributed as chi-square with m−(p−q) degrees of freedom. this section presents the simulation results regarding the finite-sample properties of the asymptotic results of the proposed tests. for illustrative purposes, we also consider the three statistics q and (q , q ) given by ( ) and ( ). the comparative study is similar to that provided in psaradakis and vávra ( ) where the data-generating processes (dgp) are based on the following eighteen models: ( )). for each of the m -m models, we use r to simulate , independent trajectories, each is a series of length n + n/ with n ∈ { , , , }, but only the last n data points are used to carry out portmanteau tests to the residuals at different lags m ∈ { , , , , , } (r core team, ). figure illustrates the accuracy of the approximation of the empirical distribution ofĈ rs and c rs , r = s ∈ { , } defined by ( ) and ( ) the sample size), and our preliminary analysis indicate that the portmanteau tests based on the statistics c rs control the type i error probability more successfully than the tests based on the statisticsĈ rs ; hence, we recommend the use of c rs , r = s ∈ { , }. in this section, we calculate the type i error probability (of nominal size % and % ) based on the five test statistics, (c , c ), (q , q ), and q defined by ( ) of fitting a true model, for each n ∈ { , , , }, are averaged across the non-gaussian linear (m -m ) and nonlinear (m -m ) models. in addition, the relative rejection frequencies outside the % significant limits are put in boldface. as shown in table , the simulation results clearly indicate insensitivity to non-gaussianity noise and the empirical level (regardless of the sample size) agrees very well with the corresponding nominal size. the powers of the proposed tests c and c are compared with the powers of q , q , and q statistics for nominal levels α = . , . , and . . similar to the simulation design in section . , we generate artificial series of lengths n ∈ { , , , } from m -m models with innovations having either normal or non-normal distributions. for the non-normal distribution, as seen in figures - , the proposed tests c and c both, substantially, have higher rejection frequencies than the q , q , and q statistics and in all cases, the test c is the more powerful test. in this section, the aforementioned statistics are applied to detect nonlinear dependency in the daily adjusted log-returns of amazon.com, inc., spanning the period january , to decem- estimation. the order of the best of fitted model is selected by minimizing the bayesian information criterion (bic) over the arma (p, q) models, where (p, q) ∈ { , , · · · , (n/ ) / } as suggested by ng and perron ( ) . the bic suggested that no arma process (linear) is detected, in the log-returns of the amazon.com, inc., neither before nor after the spread of the disease. the simulation study suggested the proposed tests, c and c , appeared to be as good as the mcleod and li ( ) statistic in detecting long memory processes and more powerful than psaradakis and vávra ( ). as seen in table , the two tests of psaradakis and vávra ( ) fail to detect the nonlinearity structure in both series. however, when the mcleod and li ( ) and the proposed statistics are used, a clear indication of nonlinear structure appears. in this article, we propose four goodness-of-fit tests to detect various types of linear and nonlinear dependency in stationary time series models. the proposed tests are based on a linear combination of three auto-and-cross-correlation components. the first and the second components are based on the autocorrelations of the residuals and their squares, respectively, whereas the third is based on the cross-correlations between the residuals and their squares. two tests can be seen as an extended modification version to the ljung and box ( ) test, and the others might be considered as an extended modification version to the box and pierce ( ) test. our simulation study recommends to use the former tests as they are insensitive with respect to non-gaussianity assumption of the noise, controlling the type i error probability more successfully than the other tests, and almost always having more power than mcleod and li ( ) and psaradakis and vávra ( ) tests. the idea discussed in this article might be extended to detect seasonality in time series and to identify various types of nonlinearity dependency in multivariate time series. when the underlying process is assumed to be uncorrelated but yet is not independent (weak assumptions), one might be able to propose a new portmanteau test. in such a case, the monte carlo significance test as suggested by lin and mcleod ( ) and mahdi and mcleod ( ) might be used to calculate the p-values based on approximating the sampling distribution of the proposed test. on the asymptotic distribution of the autocorrelations of a 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modeling threshold autoregressive processes analysis of financial time series non-linear problems in random theory coronavirus disease (covid- ) situation reports a portmanteau test for smooth transition autoregressive models key: cord- -jgq dz u authors: busson, l.; bartiaux, m.; brahim, s.; konopnicki, d.; dauby, n.; gérard, m.; de backer, p.; van vaerenbergh, k.; mahadeb, b.; de foor, m.; wautier, m.; vandenberg, o.; mols, p.; levy, j.; hallin, m. title: prospective evaluation of diagnostic tools for respiratory viruses in children and adults date: - - journal: j virol methods doi: . /j.jviromet. . . sha: doc_id: cord_uid: jgq dz u aim: to compare the performances of molecular and non-molecular tests to diagnose respiratory viral infections and to evaluate the pros and contras of each technique. methods: two hundred ninety-nine respiratory samples were prospectively explored using multiplex molecular techniques (filmarray respiratory panel, clart pneumovir), immunological techniques (direct fluorescent assay, lateral flow chromatography) and cell cultures. findings: molecular techniques permitted the recovery of up to % more respiratory pathogens in comparison to non-molecular methods. filmarray detected at least % more pathogens than clart pneumovir which could be explained by the differences in their technical designs. the turnaround time under hours for the filmarray permitted delivery of results when patients were still in the emergency room. since the discovery of viruses in the twentieth century, considerable efforts have been made to improve the technics to detect and identify them. cell cultures were the first diagnostic tool to be used in the mid- s, and since then, new techniques have been developed to decrease the time to a result (immunofluorescence, lateral flow chromatography) or to boost the sensitivity (molecular techniques) (levine, ; ginocchio and harris, ) . many improvements have been made, and techniques combining speed and sensitivity are currently available, such as fully automated 'sample-in, result-out' multiplexed syndromic molecular tools (bluchan and ledeboer, ) . aside from being effective in terms of sensitivity and specificity, these latter diagnostic tools are able to recover non-cultivable viruses. as a consequence, questions regarding the usefulness of 'older' diagnostic methods regularly arise (leland and ginocchio, ; hodinka and kaiser, ) . meanwhile, important questions concerning these 'new' expensive rapid molecular techniques remain unanswered, such as their cost-effectiveness in terms of patient's management, or the clinical significance of detecting nucleic acids of micro-organisms that could be non-infectious at the time the sample is collected. the objective of this work was to compare the performances of antigen detection and cell cultures techniques routinely used since years for the diagnosis of respiratory viral infections in the setting of a tertiary care hospital to those of newer molecular techniques (clart pneumovir, genomica, coslada, spain and filmarray respiratory panel, biofire, biomérieux, marcy l'etoile, france). the study was initiated on the st of february (week ) and ended on the th of march (week ) in the saint-pierre university hospital, a tertiary general hospital with beds located in downtown brussels. this was during the peak of the - influenza season which was moderate in belgium and lasted from week to week . more than % of influenza a isolates collected in belgium were https://doi.org/ . /j.jviromet. . . received june ; received in revised form january ; accepted january a(h n )pdm . regarding influenza b, circulating strains were almost exclusively from the victoria lineage according to the belgian scientific institute of public health (belgian public health institute, ). the enrolment period was chosen in order to be sure to gather positive samples for influenza as it is intended to evaluate, in another article, the impact of the results on antiviral prescription. this choice obviously affects the prevalence of other viruses. adults and children attending the emergency room (er) and presenting with upper or lower respiratory symptoms were prospectively included if either intended to be maintained in the hospital or had any of the following conditions known to expose to a higher rate of complications of viral respiratory infections: chronic respiratory diseases such as cystic fibrosis or asthma, sickle-cell disease, asplenia, neuromuscular diseases, severe neurological affections, hereditary metabolic disorders including diabetes, congenital or acquired immunosuppression, heart defects, chronic nephropathies, chronic liver diseases and pregnancy. children under months of age with a fever without focus of infection were also included. upon inclusion, a respiratory sample was collected. nasopharyngeal aspirate (npa) samples were typically collected from children under years old, and nasopharyngeal swabs (nps) (flocked swab + utm ml, copan, brescia, italy) were collected from older children and adults. the samples were immediately sent to the microbiology laboratory for testing. prior to testing, npa were diluted with ml of viral transport medium composed of veal infusion broth (difco, becton dickinson, sparks, md, usa) supplemented with bovine albumin (sigma aldrich, st. louis, mo, usa). lateral flow chromatography (lfc) tests and the filmarray respiratory panel were used to test samples / , whereas direct fluorescent assays (dfa) and cell cultures were performed during working hours ( : am to : pm) from monday to saturday. the clart pneumovir test was performed once a week. lab results as well as clinical data from patients' chart were recorded and analyzed. antigen detection tests and cell cultures are routine tests performed for patients attending the emergency departments. filmarray and clart pneumovir were performed for the study. because only tests per day are reimbursed by the social welfare, the combination of lfc and dfa tests performed varied during the evaluation based on the most prevalent circulating viruses. from february st to the th , influenza (sofia influenza a + b, quidel, san diego, ca, usa), rsv (binaxnow rsv, alere, waltham, ma, usa) and human metapneumovirus (hmpv) dfa (argene, biomérieux, marcy l'etoile, france) tests were performed. fifty-nine samples were analyzed with this combination. from february th to march th , metapneumovirus detection was replaced by an adenovirus detection test (adenorespi k-set, coris bioconcept, gembloux, belgium). cell cultures were performed as follows: an aliquot of the sample was inoculated on confluent vero (african green monkey kidney), mrc (human lung) and llc-mk (rhesus monkey kidney) cell cultures (vircell, santa-fé, spain) in -well or -well tissue culture plates (greiner-bio one, frickenhausen, germany). cultures were incubated at °c in a % co atmosphere for weeks for the vero cultures plates and llc-mk cells and weeks for the mrc cells. the culture media were replaced weekly. cultures were examined every two to three days using an inverted microscope. hemadsorption was performed on the llc-mk cells at the end of the second week of incubation. the filmarray respiratory panel . is a closed 'sample-in, resultout' multiplex pcr system that integrates sample preparation, amplification, detection and analysis of results in approximately an hour. the panel detects the most common respiratory viruses: adenovirus, coronavirus ( e, hku , nl and oc ), human metapneumovirus, human rhinovirus/enterovirus (without distinction between the two), influenza a (with differentiations of h , h -pdm and h strains), influenza b, parainfluenza - and respiratory syncytial virus (rsv). the panel also detects bacteria; mycoplasma pneumoniae, chlamydophila pneumoniae and bordetella pertussis which were not evaluated in this study. tests were performed according to the manufacturer's instructions. the clart pneumovir test is a microarray technique that targets the same pathogens as the filmarray respiratory panel, with the exception of coronaviruses hku , nl and oc and the aforementioned bacteria. among enteroviruses, this technique only detects echoviruses, but it can differentiate them from rhinoviruses. the extraction of nucleic acids was carried out with the qiasymphony system sp (qiagen) using the qiasymphony virus/bacteria midi kit (input volume μl, output volume μl). the pneumovir assay was performed according to manufacturer's instructions, and detection and interpretation of the results were conducted by a carreader (genomica). as the molecular tests used were presumably more sensitive than the reference standard (viral culture), we constructed a "composite" reference standard to avoid bias in establishing the specificity of the evaluated tests. this "composite" reference standard was constructed as follows: when discrepant results between the molecular techniques were observed, a third molecular technique was performed (argene, biomérieux, marcy l'etoile, france). a sample was considered truly positive for a pathogen if at least molecular techniques were positive for this pathogen. for the targets included in the filmarray test but not in the clart pneumovir panel (coronaviruses hku , nl and oc ), only the specificity of the positive results were evaluated using the argene or laboratory developed tests. data were analyzed using two sided exact chi-square fisher's tests followed in case of statistical significance by chi-square trend tests. the statistical software used were medcalc v . . and ibm spss v . . a total of samples ( npa and nps) from patients were analyzed: samples were obtained from children, of whom were female and were male (mean age: years and months old; median: months old); and samples were obtained from adults, of whom were female and were male (mean age: years old; median: ). for children, % ( / ) of samples were positive for at least one pathogen. the pathogen detected, ranging from most to least, was rhino/enteroviruses ( ), influenza b ( ), influenza a ( ), coronaviruses ( ), adenovirus ( ), metapneumovirus ( ), rsv ( ) and parainfluenza ( ). for adults, % ( / ) of samples were positive, and the detected viruses were influenza a ( ), influenza b ( ), rhino/enteroviruses ( ), coronavirus ( ), adenovirus ( ), metapneumovirus ( ) and rsv ( ). no parainfluenza viruses were detected in the adult patients. all influenza a isolates were a(h n )pdm with the exception of one a(h n ) from one adult patient. influenza b strains were not subtyped. co-detection was more common in children than in adults ( . % vs . %; p < . ). table details the sensitivity and specificity observed for the different techniques, depending on the pathogens. table provides the rate of false negative results, partial agreement (meaning at least one but not all the expected pathogens were detected) and complete agreement (meaning all the expected pathogens were detected) of the non-molecular techniques and molecular techniques compared to the established standard. the filmarray test produced fewer false negative results and partial results compared to non-molecular techniques and the clart pneumovir test (p < . ). false negative results with molecular techniques were significantly more frequent in samples with codetections compared to those with only one pathogen: % vs % for the filmarray test (p = . ) and % vs % for the clart pneumovir test (p < . ). similar result was also observed for cell cultures when limiting the analysis to culturable viruses ( % vs %; p < . ). table reports the mean turnaround time (tat) of the techniques from the reception of the sample in the laboratory to the introduction of the results into the laboratory information system. the lfc and fil-marray techniques have the shortest tat, while cell cultures and the clart pneumovir test have the longest tat. the tat for negative cell cultures is about weeks as they are discarded after this delay. tables and provide the detection rates for different techniques for influenza a and b, depending on the duration of the cough or the age of the patients. there is an effect of cough duration for influenza a with the antigen detection test (p = . ) and cell cultures (p = . ), due to a decrease in diagnostic sensitivity with cough duration (p = . and p = . , respectively). the decrease is observed as soon as the cough duration exceeds days. an age effect was also observed for influenza a with the antigen detection test (p = . ) and cell cultures (p = . ), due to a decrease in sensitivity with age (p = . and p = . , respectively). the decrease is observed from the first age category with the antigen detection and from years for the cell cultures. no effect of cough duration or age was observed with the detection of influenza a for the filmarray and clart pneumovir tests or on the detection of influenza b with any method. as expected, molecular techniques were observed to be the most sensitive. however, the performances of the two evaluated techniques differed; lower sensitivity for the detection of several targets was observed for the clart pneumovir test, notably this technique only detects echoviruses among all enteroviruses. for adenoviruses, metapneumoviruses and rsv, the explanation probably relies more on technical considerations. indeed, false negative results with the filmarray and the clart pneumovir tests were not always for samples with a low viral load, as indicated by the cycle threshold (which correlates with the viral load) of the third molecular technique used to elucidate discrepant results between the first two techniques. as an example, the mean ct value and standard deviation of negative and positive samples for adenoviruses with clart pneumovir were . ( . ) and . ( . ) respectively (p = . ). the choice of primers and probes used to design tests can determine whether a certain strain of virus will be detected. although the filmarray test had a better sensitivity than the clart pneumovir test for the detection of adenoviruses, it may lack sensitivity in detecting certain strains, which could impact the management of immunocompromised patients (song et al., ) . a huge advantage of molecular techniques is that they allow the recovery of those pathogens that are difficult to culture, that will not grow in culture or for which no antigen detection tests are available. in the present study, the rate of complete detection of the pathogens present in the samples was far more important with molecular techniques compared to non-molecular ones. this has already been reported. (weinberg et al., ) viruses with poor detection using non-molecular techniques primarily include adenoviruses, metapneumoviruses and rhino/enteroviruses. there were also positive samples for coronaviruses (mahony, ) which, in our experience, do not commonly grow with routine cell lines, even if coronavirus nl was originally described in llc-mk (van der hoek et al., ) . the rate of co-detection was more important for children, which is a common finding and could be explained by notably increased, longerlasting viral shedding in children under months of age due to less developed mucosal immunity (sharma et al., ) . the co-detection of viruses in children is apparently not linked with a more severe outcome (comerlato scotta et al., ) , and the molecular detection of a virus in a respiratory sample is not always associated with symptoms. the type of detected virus and the age of the patient can be helpful to decide on a care plan (self et al., ) . as previously stated, false negative results with molecular techniques were significantly more frequent in samples with multiple pathogens compared to those with only one pathogen; this finding could be due to possible competition for the reagents when multiple targets are to be detected (bezerra et al., ) . the specificity of all molecular techniques was over %, except that for rhino/enteroviruses with the filmarray test ( . %). the differences observed between molecular techniques could also be due to primer and probe choices. overall, the clart pneumovir is less sensitive than the filmarray except for influenza b and its hands-on time and turnaround time are longer. only positive samples were analyzed for metapneumovirus using an antigen detection test, as it was substituted for adenovirus test during the evaluation. this test nonetheless appeared more sensitive than the cell culture tests, as no metapneumovirus was recovered from cell cultures. this finding was under the expected sensitivity, which is approximately % according to the literature (tang and crowe, ) . the apparent low sensitivity of non-molecular techniques observed for adenoviruses deserves comment. indeed, prolonged shedding after the primary infection is classically described for adenovirus. adenoviruses can also be detected in tonsillar tissue or isolated from a throat sample of up to % of healthy children (song et al., ; kalu et al., ) . these states of prolonged shedding or "latency" are more likely to be detected with molecular techniques. it is also noteworthy that % of adenoviruses detected in this evaluation were associated with one or more other pathogens, supporting the hypothesis that they could be bystanders in some cases. the sensitivity of cell cultures for rhino/enterovirus was also low and could be partially attributed to the fact that group c rhinoviruses do not grow on standard cell cultures (jacobs et al., ) . enteroviruses grow inconsistently on cell cultures, depending on their type, and no cell line enables the detection of all strains (stellrecht et al., ) . unfortunately, rhinoviruses and enteroviruses in this study were not typed. the presence of multiple viruses in a sample also influences cultures because the growth of the fitter or more abundant virus can mask the growth of others (george et al., ) . for example, on the false negative cultures for rhino/enteroviruses, were positive for another virus. likewise, for adenoviruses, for the false negative cell cultures, recovered another virus. molecular techniques supposedly do not suffer from this drawback, although as previously discussed, a higher rate of false negatives was observed when multiple pathogens were present in the sample. cell cultures, however, can enable the detection of unsuspected viruses. this detection was the case in this evaluation for one measles virus, which was not originally suspected, and herpes simplex viruses and cytomegaloviruses (cmv). in one case, cmv could explain the symptoms exhibited by a -month-old patient with a fever without focus of infection. the other cases were more likely to be recurrences or prolonged shedding. regarding the sensitivity of antigen detection tests for influenza, influenza a is more easily detected than influenza b, which has already been reported (busson et al., ) . the decreased sensitivity for influenza a with antigen detection and cell cultures, which depends on the age of patients, can be explained by the higher viral shedding in children, and also because for younger children, npa were preferred to nps. aspirates usually increase the detection rate for viruses over swabs (loens et al., ) . the decreased sensitivity of antigen detection and cell cultures when the duration of the cough increases is expected, because viral shedding is more important in the first days of the disease (aoki and boivin, ). the reason for the lack of similar findings for influenza b is unclear. the absence of sensitivity loss for molecular techniques, depending on the age of the patients and the duration of the cough, can be attributed to the high sensitivity of the techniques. usually, antigen detection tests have a faster turnaround time than cell cultures but a lower sensitivity except for viruses growing poorly, especially metapneumovirus and rsv, for which the sensitivity of antigen detection tests can be better than the one of cell cultures. the specificity of non-molecular tests was above %. false positive results in cell cultures can occur due to cross-contamination between wells on culture plates. antigen detection tests based on lateral flow chromatography are usually the easiest and fastest to perform. techniques based on immunofluorescence are slightly more time-consuming. currently, totally automated techniques with a short hands-on time, such as filmarray, can be realized in a time frame comparable to that of lfc tests. however, only one can be performed at one time, and the analyzer remains occupied for slightly more than an hour. the number of required instruments is based on the test volume at each facility and the desired tat. cell cultures remain the most time-consuming techniques, and results often arrive too late to impact patient management (ginocchio, ) . this was also the case for clart pneumovir in our setting, as it was only performed once a week due to the complexity of the corresponding analytical process. in belgium, non-molecular techniques for the diagnosis of respiratory viruses are reimbursed by the social welfare program, which is not the case for molecular techniques which are charged to the patients. during this evaluation, molecular techniques were free of charge for patients, but they cost approximately euros per patient. the necessity of molecular tests must be seriously considered before prescription. these tests should probably be reserved for the most severely ill patients, for whom rapid and comprehensive microbiological evaluation is most likely to impact patient management. as a comparison, antigen detection tests cost, including workforce, can range between . and euros depending on the test and cell cultures cost about euros. however, non-molecular tests are reimbursed by the social welfare in belgium permitting a broader prescription. the possibilities to implement molecular tests can vary between facilities and countries depending on local policies. using molecular rather than non-molecular techniques could impact patients' isolation strategies (richardson et al., ) , antibiotic/antiviral use or reduce of the length of stay (brendish et al., ; rogers et al., ) , but cost-benefit analyses are difficult to appraise because of many intertwined elements. molecular techniques have considerably increased our capacity to detect respiratory viruses in a timely manner. the main factors limiting a wide utilization of these techniques are cost and the difficulty to absorb the workload in large facilities with numerous samples to analyze per day. another drawback is that latent viruses or traces of genetic material may be detected. the interpretation of a positive result might be difficult, and it must be carefully correlated to the clinical history of the patient as the presence of a virus in the respiratory tract is a factor exposing to bacterial superinfection (vareille et al., ) . it is possible to quantify the viral load in a respiratory sample, but there are conflicting reports regarding correlations between viral load and outcome (granados et al., ; wishaupt et al., ) . technical improvements should be made to prevent variation in quantification caused by sample dilution with saline instilled during aspirates or by the variable quantity of sampled material with swabs. these improvements could render comparisons between studies more reliable and permit the establishment of a threshold, above which detected viruses are indeed involved in an ongoing infectious process. in addition, a positive antigen detection test usually correlates with a high viral load in a sample, and a positive cell culture can only be achieved with infective viral particles. whatever technique is used, fully understanding the benefits and limitations of each is crucial for interpretation. the choice of technique should depend, besides financial considerations, on the necessary sensitivity and speed based on symptoms, comorbidity and risk of a detrimental outcome for each patient. a tertiary care hospital should be able to offer diagnostic tools suitable for each individual case; if testing all patients with molecular techniques is not possible, the use of nonmolecular techniques is preferable over nothing at all. influenza virus shedding -excretion patterns and effects of antiviral treatment viral and atypical bacterial detection in acute respiratory infection in children under five years emerging technologies for the clinical microbiology laboratory routine molecular point-of-care testing for respiratory viruses in adults presenting to hospital with acute respiratory illness (respoc): a pragmatic, open-label, randomised controlled trial evaluation of rapid influenza diagnostic tests during the - epidemic: influences of subtype and viral load ap. duarte de souza et al. respiratory viral coinfection and disease severity in children: a systematic review and meta-analysis rapid and sensitive detection of respiratory virus infections for directed antiviral treatment using r-mix detection of respiratory viruses using non-molecular based methods reagents, stains, media and cell cultures: virology influenza and rhinovirus viral load and disease severity in upper respiratory tract infection is the era of viral culture over in the clinical microbiology laboratory? human rhinoviruses persistence of adenovirus nucleic acids in nasopharyngeal secretions: a diagnostic conundrum role of cell culture for virus detection in the age of technology the origins of virology optimal sampling sites and methods for detection of pathogens possibly causing community-acquired lower respiratory tract infections detection of respiratory viruses by molecular methods comparison of respiratory virus shedding by conventional and molecular testing methods in patients with haematological malignancy impact of a rapid respiratory panel test on patient outcomes respiratory viral detection in children and adults: comparing asymptomatic controls and patients with community-acquired pneumonia the developing human preterm neonatal immune system: a case for more research in this area performances of filmarray respiratory panel v . for detection of adenovirus in a large cohort of pediatric nasopharyngeal samples: one test may not fit all enteroviruses and parechoviruses respiratory syncytial virus and human metapneumovirus identification of a new human coronavirus the airway epithelium: soldier in the fight against respiratory viruses superiority of reverse-transcription polymerase chain reaction to conventional viral culture in the diagnosis of acute respiratory tract infections in children pitfalls in interpretation of ct-values of rt-pcr in children with acute respiratory tract infection the author acknowledges the team of the virology none declared. this study was approved by the ethics committee of university hospital saint pierre (brussels). key: cord- -t pym k authors: dumyati, ghinwa; gaur, swati; nace, david a.; jump, robin l.p. title: does universal testing for covid- work for everyone? date: - - journal: j am med dir assoc doi: . /j.jamda. . . sha: doc_id: cord_uid: t pym k abstract the covid- pandemic has been especially devastating among nursing home residents, with both the health circumstances of individual residents as well as communal living settings contributing to increased morbidity and mortality. preventing the spread of covid- infection requires a multipronged approach that includes early identification of infected residents and healthcare personnel, compliance with infection prevention and control measures, cohorting infected residents, and furlough of infected staff. strategies to address covid- infections among nursing home residents vary based on the availability for sars-cov- tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of covid- by identifying asymptomatic and presymptomatic infections. we review the tests available to diagnose covid- infections, the implications of universal testing for nursing home staff and residents, interpretation of test results, issues around repeat testing, and incorporation of test results as part of a long-term response to the covid- pandemic. we propose a structured approach for facility-wide testing of resident and staff and provide alternatives if testing capacity is limited, emphasizing contact tracing. nursing homes with strong screening protocols for residents and staff, that engage in contact tracing for new cases, and that continue to remain vigilant about infection prevent and control practices, may better serve their residents and staff by thoughtful use of symptom- and risk-based testing strategies. dr. jump reports support for this work in part through the cleveland geriatric research while there is general agreement that increased access to testing is important for personal and public health, the selection and use of diagnostic tests to mitigate covid- infections in post- acute and long-term care settings is complex and should be tailored to individual sites. he responded to antibiotics and his fever resolved within hours. because he met the nursing home's enhanced screening criteria for covid- (table ) , he was placed on transmission- based precautions and a laboratory test for sars-cov- was ordered. the food and drug administration (fda) has authorized several diagnostic and serologic (blood-based) tests as part of the emergency use authorization (eua) process ( table ) . reported that rt-pcr was % sensitive when compared to a computed tomography (ct) scan of the chest. this study was conducted in the early stages of the pandemic on patients. since then, the number of rt-pcr-based tests and availability of those tests, as well as the prevalence and clinical recognition of signs and symptoms of covid- infection, has changed dramatically. all of these factors influence the sensitivity and specificity of diagnostic rt-pcr tests. even if the sensitivity of rt-pcr based testing has increased to an optimistic % to %, it still means that out of every to negative results will be a false negative and miss a covid- infection. a lower level of sensitivity may not be an issue in settings or regions where the disease prevalence is low. where the disease is prevalent however, such as during a facility outbreak, negative results must be viewed with caution. the sensitivity of the test also depends on when testing is done during the course of illness, with the peak of viral shedding occurring around the time of symptom onset. a bayesian hierarchical model, fit to previously published studies describing the performance of sars-cov- rt-pcr tests, reported the probability of a false negative rt-pcr test over time. from exposure (day ) to the typical time of symptom manifestation (day ), the probability of a false negative results changes from % on day , to % on day , reaching a nadir of % three days after symptom onset on day . in some individuals, rt-pcr tests will remain positive for weeks after symptom resolution. staff, particularly in areas with mandates for serial testing of healthcare workers. this also offers the possibility that staff may effectively collect their own samples. self-collected samples have the advantage of decreasing staff exposure and their use of ppe. antigen tests on may th , , the fda provided the first eua for a test designed to detect an antigen specific to sars-cov- ; a second antigen-based test received an eua on july nd , . , antigen tests target markers on the outer surface of the viral capsule and do not require extraction of rna. viral structures that represent good candidates for antigen-based testing include nucleocapsid phosphoproteins and spike glycopeptide proteins. advantages to antigen-based tests are the relatively lower cost compared to rt-pcr tests, the ease of collection samples from the anterior nares, the potential to scale the number of tests, and the rapid turn- around-time, providing answers within minutes. a disadvantage to antigen-based tests, however, is lower sensitivity, which can lead to false negative results. this is a particular issue in the setting of outbreaks or in regions with increased prevalence rates of sars-cov- . the j o u r n a l p r e -p r o o f fda recommends that a second pcr-based test should be used to confirm negative results for individuals likely to have covid- . given that only of the diagnostic tests given euas are antigen-based, the role for these tests is still evolving and may be best suited for diagnosing symptomatic individuals seeking medical care, rather than screening asymptomatic individuals or healthcare workers. . regardless, cms recently announced a plan to deploy the two available antigen test kits to all u.s. nursing homes to assist in universal screening efforts, though noting caution in interpreting negative results. facilities using antigen tests need to make sure they have obtained the required federal and/or state clinical laboratory improvement amendments (clia) waivers, competency trained staff, a recording system to document and track results, and are able to report results to state and/or federal agencies as required. unfortunately, many nursing homes may not be able to implement universal testing for a multitude of reasons, including lack of access to testing, inadequate supplies of ppe, limited personnel, and insufficient resources to pay for testing. - as they attempt to respond to federal and state recommendations and requirements, many nursing homes will need to consider other approaches to testing such as unit-based testing and/or risk-based testing. regardless of how they proceed, it is essential that nursing homes work with their laboratory provider to prioritize residents and staff tests and ensure rapid turnaround times ( hours or less). unit-based strategies, while not desirable, would be most suitable for situations in which testing capacity is limited. for this approach, the building focuses testing on residents and staff members who had close contact with the index case. testing can also be extended to include high risk individuals such as those leaving the facility frequently (e.g., for hemodialysis, radiation therapy, or off-site chemotherapy) and those recently admitted. determination of whom to test first is inherently complex and may be best approached by a multi-disciplinary team that includes the infection preventionist, medical director, director of nursing, and administrator. the need and frequency of staff and resident testing in that particular facility. as mentioned above, however, insufficient access to rapid diagnostic testing, ppe, staff, and resources may render seemingly insurmountable challenges. even under these dire circumstances, nursing homes will continue to strive to provide the best care they can offer for residents entrusted to their care ( table ) . the prospect of reopening nursing homes, which includes permitting visitors, presents additional complexities. efforts by states to relax stay-at-home orders, reopen businesses, and even encourage tourism contribute to increased spread of sars-cov- in the community which in turn means increased risk for nursing home staff to acquire and transmit the virus to their residents. as part of plans to reopen nursing homes, cms recommended "baseline" testing for all nursing residents and staff, along with the capacity to continue weekly tests for staff. after the initial response to the cms recommendation, most, if not all, nursing homes should continue surveillance testing. older adults often manifest atypical signs and symptoms of infection. while it may be tempting to attribute a change in condition to exacerbation of known heart failure or sinus congestion to allergies or a "summer cold", the severity of the illness experienced by some if testing many residents, consider using two teams with staff not assigned to frontline care -one to prepare each resident and room, and one to obtain the specimen. identify the ordering provider for the laboratory requisition, which can be the medical director. ensure that ppe is available for the staff obtaining np swab. ideally, ppe worn during sample collection includes a respirator, eye protection, a gown, and gloves. in settings without respirators, a surgical mask and face shield may be used instead. testing of staff identify the list of staff that will need to be tested. decide on the source of the sars-cov- specimen (np, nasal, oropharyngeal, oral). if using pcr, identify and train staff to perform testing including need to change ppe between staff members. chose a room for testing and ensure that staff are able to social distance while waiting for testing. if testing is done in the facility, identify the ordering provider, which might be the medical director or an employee health provider. if testing is done outside the facility, evaluate the process of obtaining the results. identify and communicate with the laboratory to ensure that the testing supplies are available and the laboratory can run the some states do not need a provider order for the staff testing but this is requested by the laboratory. some insurance providers are not covering testing of asymptomatic nursing home staff. when possible, sample collection should be in a well-ventilated area, which includes outdoors and, weather permitting, may be feasible to accomplish with staff members. j o u r n a l p r e -p r o o f large number of tests and provide the results within - hours. dealing with sars-cov- testing results from residents create a process to communicate the test results with residents and their families or responsible party. identify how information is shared with the local or state health department. ensure that a cohorting plan is in place before testing. assess the availability of personal protective equipment (ppe). ensure that shared equipment is available to dedicate to the covid- cohort develop a policy for when covid- positive residents should be transferred to an outside covid- facility, another nursing home or hospital. one option is to communicate with resident's family that they will only be informed of positive test results. plan for use of multiple means of communication to residents, family members, and/or responsible parties. this may include use of recorded phone systems, email, website updates, town-hall updates, and direct phone communication. communication about resident results should ensure individual privacy. prepare for the additional works of moving residents and their belongings to a covid- cohorting area. dealing with sars-cov- results from staff create a process to communicate the test results with staff, respecting employee privacy. create a process to communicate with residents and their families or responsible party that the facility has staff that tested positive. identify a process to communicate results with the local or state health department, including plans for monitoring of isolation, return to work and contact tracing for quarantine. for staff that test positive and work at multiple facilities, inform the health department so the information can be communicated to other facilities. assign a staff member the role of monitoring staff furloughs and review of criteria to return to work. they also should monitor adverse effects such as hospitalization and death establish a process to deal with staff shortages: ) train non-medical staff at your facility to assist with resident related tasks, ) establish relationship with nursing agencies, ) collaborate with hospital systems and evaluate if they can assist with staffing needs, ) evaluate other staffing options such as reaching out to nursing schools. unprecedented solutions for extraordinary times: helping long-term care settings deal with the covid- pandemic the food and drug administration comparison of four molecular in vitro diagnostic assays for the detection of sars-cov- in nasopharyngeal specimens correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases interpreting diagnostic tests for sars-cov- variation in false-negative rate of reverse transcriptase polymerase chain reaction-based sars-cov- tests by time since annals of internal medicine duration of isolation and precautions for adults with covid- . centers for disease control and prevention detection of sars-cov- in different types of clinical specimens a combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of sars-cov- swabs collected by patients or health care workers for sars-cov- testing the food and drug administration. coronavirus (covid- ) update: fda authorizes first antigen test to help in the rapid detection of the virus that causes covid- in patients commissioner o of the. coronavirus (covid- ) update: daily roundup molecular targets for the testing of covid- trump administration announces initiative for more and faster more-faster-covid- -testing-nursing-homes.html . centers for medicare and medicaid services. frequently asked questions: covid- testing at skilled nursing facilities/ nursing homes american health care association. point-of-care antigen test devices -ahca information for laboratories about coronavirus (covid- ). centers for disease control and prevention the food and drug administration duration of antibody responses after severe acute respiratory syndrome persistence of antibodies against middle east respiratory syndrome coronavirus performing facility-wide sars-cov- testing in nursing homes. centers for disease control and prevention covid- ): interim clinical guidance for management of patients with confirmed coronavirus disease (covid- ). centers for disease control and prevention the incubation period of coronavirus disease from publicly reported confirmed cases: estimation and application asymptomatic and presymptomatic sars-cov- infections in residents of a long-term care skilled nursing facility -king county evidence supporting transmission of severe acute respiratory syndrome coronavirus while presymptomatic or asymptomatic nursing homes continue to face critical supply and staff shortages as covid- toll has mounted nursing home care in crisis in the wake of covid- centers for medicare & medicaid services. toolkit on state actions to mitigate covid- prevalence in nursing homes new state by state breakdown: covid- testing for nursing homes and assisted living american health care association/national center for assisted living the centers for medicare & medicaid services. nursing home reopening recommendations for state and local officials | cms continuing temporary suspension and modification of laws relating to the disaster emergency guidance for infection control and prevention of coronavirus disease (covid- ) in nursing homes (revised) | cms discontinuation of transmission-based precautions and disposition of patients with covid- in healthcare settings (interim guidance). centers for disease control and prevention guidance for use of certain industrial respirators by health care personnel | cms how not to wear a mask. the new york times taking action to protect america's nursing home residents against covid- . your valley medicare administrative contractor (mac) covid- test pricing . r som.pdf. accessed key: cord- -qhlo l authors: axell-house, dierdre b.; lavingia, richa; rafferty, megan; clark, eva; amirian, e. susan; chiao, elizabeth y. title: the estimation of diagnostic accuracy of tests for covid- : a scoping review date: - - journal: j infect doi: . /j.jinf. . . sha: doc_id: cord_uid: qhlo l objectives: to assess the methodologies used in the estimation of diagnostic accuracy of sars-cov- real-time reverse transcription polymerase chain reaction (rrt-pcr) and other nucleic acid amplification tests (naats) and to evaluate the quality and reliability of the studies employing those methods. methods: we conducted a systematic search of english-language articles published december , -june , . studies of any design that performed tests on ≥ patients and reported or inferred correlative statistics were included. studies were evaluated using elements of the quality assessment of diagnostic accuracy studies (quadas- ) guidelines. results: we conducted a narrative and tabular synthesis of studies organized by their reference standard strategy or comparative agreement method, resulting in six categorizations. critical study details were frequently unreported, including the mechanism for patient/sample selection and researcher blinding to results, which lead to concern for bias. conclusions: current studies estimating test performance characteristics have imperfect study design and statistical methods for the estimation of test performance characteristics of sars-cov- tests. the included studies employ heterogeneous methods and overall have an increased risk of bias. employing standardized guidelines for study designs and statistical methods will improve the process for developing and validating rrt-pcr and naat for the diagnosis of covid- . after its emergence in december , the virus now known as sars-cov- was identified and sequenced in early january , allowing for the rapid development of diagnostic testing based on the detection of viral nucleic acid (i.e., real-time reverse transcription polymerase chain reaction [rrt-pcr]). because infected patients can present with non-specific symptoms or be asymptomatic, the development of accurate diagnostic tests for both clinical and epidemiological purposes was a crucial step in the response to the covid- pandemic. in the united states, the spread of sars-cov- rapidly outpaced the capacity to test for it, resulting in the food and drug administration (fda) relaxing regulatory requirements to increase testing availability. the fda granted the first emergency use authorization (eua) for a sars-cov- rrt-pcr diagnostic test on february , . consequently, hundreds of tests for sars-cov- , among them rrt-pcrs, other types of nucleic acid amplification tests (naats), and automated and/or multiplex methods based on proprietary platforms, obtained fda emergency use authorization (eua). as of august th , , the fda has granted euas to diagnostic tests, including molecular tests, antibody assays, and antigen tests. although the fda began requiring the submission of validation methods and results as part of eua application for sars-cov- diagnostic tests, these tests were not initially required to undergo the rigorous assessment that would normally be part of the fda approval process. researchers also began developing alternative nucleic-acid based methodologies to detect sars-cov- , including reverse-transcription loop-mediated isothermal amplification (rt-lamp), and others. concurrently with rapid test production, publications emerged reporting clinical diagnostic test performance characteristics, such as "sensitivity" and "specificity", though some lacked the rigorous methodologies usually required to formally estimate diagnostic accuracy. here we present a scoping review of the literature with two main objectives: ) to assess the methodologies used in the estimation of diagnostic accuracy of sars-cov- tests and ) to evaluate the quality and reliability of the studies employing those methods. searches were performed through medline (ovid), embase (elsevier), scopus, web of science, cinahl, and pubmed following the preferred reporting items for systematic reviews and meta-analyses (prisma) guidelines between december , and june , . the following search string was used: ( -ncov or sars-cov- or sars-cov or covid- or covid or covid) and ("positive agreement" or "negative agreement" or "overall agreement" or "diagnostic accuracy" or "positive rate" or "positivity rate" or "test performance" or "reference standard" or "gold standard" or sensitivity or specificity or "percent agreement" or "concordance" or "test agreement" or "predictive value" or "false negative" or "false positive") and ("polymerase chain reaction" or pcr or "reverse transcriptase" or "nucleic acid amplification test" or naat or isothermal or "rt-lamp" or "rt-pcr" or "molecular test"). the literature hub litcovid's "diagnosis" section was screened in its entirety once and then daily for relevant titles. we liberally screened articles by title and abstract for further evaluation. articles were included if they met the following criteria on screening: ) peer-reviewed publication, ) study evaluated diagnostic test accuracy of naat, ) diagnostic test performed on ≥ patients, ) diagnostic/clinical sensitivity, specificity, other correlative statistics, or test positive rate were either identified by name or were included in the publication as a numerical value and we could reproduce the calculations. exclusion criteria included: ) pre-print status, ) guidelines, consensus, review, opinion, and other summary articles ) entirely pregnant or pediatric populations, ) overlap of study population with another included publication. four authors independently extracted data and two authors reviewed data for accuracy. for study characteristics, we extracted: first author name, country, study design, patient population, total number of patients or samples included in test performance calculations, and number of cases according to rrt-pcr (tables - ) or total number of cases based on positive result of any platform tested (table ) . for patient characteristics, we extracted age and sex. for index test and reference standard characteristics, we extracted: test type (naat) or definition (clinical diagnosis, composite reference standards), specimen (naat), specimen dry/collection liquid status (for studies evaluating abbott id now), proprietary automated and/or multiplex systems -henceforth called "platforms" (naat), and target genes of primers (naat). for outcomes, we extracted the values of test performance characteristics with their designation according to the original authors, without our interpretation. for this reason, we indicate these outcomes as "reported" (r): reported sensitivity (rsn), specificity (rsp), positive predictive value (rppv), negative predictive value (rnpv), accuracy (racc), positive percent agreement (rppa), negative percent agreement (rnpa), overall agreement (roa), and kappa coefficient. additionally, we extracted "positive rate," a non-standard term used by the included studies to refer to the number of positive naats in a population of patients suspected to have covid- (table ) , or to the number of positive samples in a total population of positive samples after repeat testing (table ) . we constructed x contingency tables and reproduced test performance characteristic calculations to demonstrate the methods of how the original authors obtained the values (supplementary table ) . we report additional pertinent study data in supplementary table : enrollment dates, number of sites of enrollment, symptomatic status, and chest radiology status. no articles were excluded on the basis of quality in order to present the most comprehensive summary of the currently available evidence. we presented the extracted data in tabular form mirrored by a descriptive synthesis in two broad categories: diagnostic accuracy studies for rrt-pcr (tables - ) , and diagnostic accuracy or comparative agreement studies of two naats (tables - ). tables are thematically divided based on the reference standard strategy, or approach to obtaining comparative agreement measures. diagnostic accuracy studies for rrt-pcr were arranged alphabetically in tables by first author last name (tables - ) . diagnostic accuracy and comparative agreement studies for two naats were arranged by decreasing order of studies per methodology, then alphabetically by methodology or platform (tables - ) for easy comparison. due to significant diversity in methods and reporting of results, we reported grouped summary data for study characteristics, patient characteristics, and outcomes. we used the framework of the quality assessment of diagnostic accuracy studies (quadas- ) to evaluate our selected articles (supplementary table ). we collected data, or noted their absence, for a narrative description of risk of bias and concerns of applicability based on the quadas domains. for assessment of bias in patient selection, we evaluated author conflicts of interest, study design type, inclusion/exclusion criteria, method of patient enrollment, and reporting of patient demographics and characteristics (i.e. symptomatic status). for assessment of bias in reference standard and index test, we evaluated the accuracy of the reference standard, the description of duration of symptoms at time of testing, whether the threshold to determine a positive test was prespecified, and researcher blinding to reference standard and index test results. for assessment of bias in flow and timing, we evaluated whether the reference standard was the same for all patients, the sequence and timing of the performance of the reference standard and index test, whether test performance characteristics were calculated based on sample numbers or patient numbers, and whether indeterminate or invalid results were included in test performance calculations. our search yielded articles, with unique articles after deduplication. after screening title and abstract, articles underwent full text evaluation. ultimately, articles were included in our review ( figure ). three studies, with to patients, report a "positive rate" as the number of positive rrt-pcr out of the number of suspected cases of covid- , with a range of . % to % (table ) . [ ] [ ] [ ] the studies do not report these values as "sensitivity" directly, however these concern that their low calculated positive rates ( . % and . %, respectively) were indicative of a failure of rrt-pcr to diagnose covid- . , in terms of quality assessment, the studies lack specific details as to how patients were classified as having suspected covid- infection. the accuracy of clinical diagnosis based on case definitions is unclear but is likely not ideal for diagnosis. additionally, duration of symptoms at the time of clinical diagnosis or rrt-pcr testing was not provided (supplementary table ). eight studies, with a range of to , patients per study, attempted to determine the accuracy of rrt-pcr by comparing the initial rrt-pcr result to the result after multiple repeated samples from the patient submitted for rrt-pcr testing, which was called the reference standard (table ) . [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] three studies reported this value as a "positive rate," ranging from . % to %, , , and five reported sensitivity, with a range of . % to . %. [ ] [ ] [ ] , of these studies, only he et al included an rsp of %, calculated from patients who remained negative for sars-cov- after repeated sample testing (supplementary table ). green et al. included patients in their study regardless of whether they were tested once or multiple times, using data from these subsets of patients to make assumptions for estimating clinical test characteristics. in addition, this study also conducted multiple different naats and rrt-pcrs on patients, whereas other studies employing this strategy used only one type of naat. additionally, the authors do not clarify whether patients who had repeat sars-cov- test were consistently tested with the same naat/rrt-pcr test or a different one. they also calculated test performance characteristics differently from other studies: two estimates of sensitivity were calculated, one in which the rate of false negatives for single-tested patients was %, and one in which the "false negative" rate was the same as in repeat-tested patients in their study of approximately . %. however, the details of how they calculated test characteristics were not presented. to clarify the two assumptions made in the calculations, we in terms of quality assessment, most of the studies were performed with non-cohort design, and six consisted of only patients who were determined to have covid- by rrt-pcr, i.e. cases only (table ) . , , [ ] [ ] [ ] five of the studies had inclusion criteria which caused pertinent patients to be excluded by necessitating patients to have had a well-performed ct chest or x-ray (supplementary table ). this excluded several patients who would otherwise have been pertinent to the study of test diagnostic accuracy. , , , , the studies involved repeating rrt-pcr several times for a reference standard, but each patient received a different number of repeat tests over a different time period, resulting in each patient receiving a different reference standard. one study tracked negative-to-positive conversion over to days, and another tracked over to days, leading to concern that potentially a patient could have been infected in the time between the initial test and the final test and confounding results. one study counted invalid results as negative results and indeterminate results as positive results when calculating test performance characteristics, otherwise the rationale and ways invalid and indeterminate results were handled were not reported in these studies. three studies determined the accuracy or agreement of rrt-pcr or automated rrt-pcr platforms/instruments compared to a reference standard based on the results of several tests as a "composite reference standard" (table ) . [ ] [ ] [ ] there were between and patients per study. suo et al considered a positive result of either repeated measurements of rrt-pcr or serology to indicate a positive test according to the reference standard; reported sensitivity of initial rrt-pcr result was %, rsp %, rppv %, and rnpv %. zhen et al compared rrt-pcr performed according to the us cdc protocol to a composite reference standard in which the consensus result of or more out of molecular assays was considered the correct result. the rrt-pcr had an rppa of %, an rnpa of %, and cohen's kappa coefficient of . . cradic et al did not study rrt-pcr but studied three automated molecular assays and used a composite reference standard of the consensus result of two or more of the three assays. while abbott id now had a rppa of %, the roche cobas and diasorin simplexa assays had a rppa of %. these studies either did not report how samples were selected for evaluation (supplementary table ), , or reported that only samples which had sufficient residual volume and had been properly stored were selected. days after the initial test, after the patient had been discharged from the hospital, leading to potential exposure for initial infection or reinfection. the performance other nucleic acid amplification test methods compared to standard rrt-pcr fourteen studies compared other nucleic acid amplification test methods to detect sars-cov- to rrt-pcr (table ) suo et al evaluated digital droplet polymerase chain reaction (ddpcr), with rsn %, rsp %, rppv %, rnpv of %, and racc %. bulterys et al study evaluated an isothermal amplification method with rsn . % and cohen's kappa . . wang, cai, and zhang et al evaluated one-step single-tube nested quantitative polymerase chain reaction (osn-qrt-pcr) with cohen's kappa of . . regarding evaluation of quality (supplementary table ) , the majority of studies did not report how patient samples were selected for evaluation. , , , , [ ] [ ] [ ] [ ] in the study conducted by bulterys et al, sample selection was a convenience selection of samples with residual volume that had been stored correctly. most studies did not report symptomatic status of the patient - , - or patient demographics. [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] problematically, many of the studies did not report when the reference standard was conducted on the patient samples compared to the index test, or whether actions that could potentially alter test results (such as freeze/thaw cycles) occurred between reference standard or index test. [ ] [ ] [ ] [ ] , , four studies calculated test performance characteristics based on number of samples rather than number of patients. , , , the management of indeterminate and invalid test results went largely unreported. [ ] [ ] [ ] [ ] [ ] , the performance of naat platforms compared to rrt-pcr as the reference standard fifteen studies compared automated naat platforms to various rrt-pcr assays to determine test performance characteristics ( other studies evaluated ausdiagnostics (rsn %, rsp . %), hologic panther fusion (rppa . %, rnpa . %), luminex nxtag (rsn . %, rsp %), mesa biotech accula (rppa . %, rnpa %), or qiastat-dx (rsn %, rsp %) compared to rrt-pcr. with regards to quality evaluation (supplementary table ), most studies did not report method of sample collection/patient recruitment, , , , [ ] [ ] [ ] [ ] [ ] [ ] [ ] and four studies conducted a convenience selection of samples, including enrichment for positive samples. [ ] [ ] [ ] eight studies conducted test performance calculations on sample numbers instead of patient numbers. , , , , , [ ] [ ] [ ] four studies conducted calculation of test performance characteristics with indeterminate or inconclusive results as "positive," , , , and the management of indeterminate/inconclusive as well as invalid results went unreported in an additional three studies. , , no study reported the blinding of researchers to the reference standard or index test results. ten studies, containing between and patients per study, evaluated the agreement between two different types of naat platforms ( in the studies, some platforms were identified as the "comparator" or "reference" platforms, including cepheid xpert xpress, abbott realtime, , hologic panther fusion, , and roche cobas , , and these were listed as "platform # " in table . three studies did not identify any studied platform as the "comparator" or "reference standard," and instead only reported general, non-directional measures of agreement such as overall agreement, cohen's kappa, or alternatively, the calculations of ppa and npa were identical no matter their method of calculation (supplementary table ) . , , regarding quality evaluation (supplementary table ), the samples used for calculating test performance characteristics were reported to be selected for enrichment of positive samples, , for diversity of viral load, , otherwise curated, or the method of selecting samples was unreported. , , , symptomatic status of the patients was largely unreported. , [ ] [ ] [ ] [ ] [ ] [ ] [ ] five studies included samples where one test was conducted, then interim freezing, cooling, or other storage, before performance of the second test. , [ ] [ ] [ ] two studies did not report the sequence of testing of the two platforms or interim handling or storage of the samples. , the status of researcher blinding to either platform result was not reported in any study. in our scoping review of articles concerning test performance characteristics of rrt-pcr and other naat used for the diagnosis of covid- , we were able to observe several overarching themes. clinical diagnosis by the case definition for covid- used in the early period of the pandemic does not correlate well with positive rates of covid- rrt-pcr ( table ). the result of the initial rrt-pcr performed on a patient, if negative, may not be reflective of the result after multiple repeated rrt-pcrs for that patient ( table ) . several alternative naat methods, many of which are easier or faster to perform, may be comparable to standard rrt-pcr (table ). proprietary multiplex, automated, and/or point-of-care methods are comparable to in accuracy to rrt-pcr (table ) and to each other (table ), although the abbott id now sars-cov- test appears to have lower comparative agreement to other platforms. , [ ] [ ] [ ] [ ] [ ] these findings should be viewed cautiously as the sars-cov- tests in these studies have not undergone rigorous evaluation necessary for fda approval due to the emergency state generated by the covid- pandemic. in addition, during our scoping review, we found substantial heterogeneity among available studies in terms of test types, reference standards, metrics, and details of study design and methodology. we categorized the included studies by four different reference standard strategies: clinical diagnosis/case definitions (table ) , repeated index testing (table ) , composite reference standard (table ) , and rrt-pcr (table and ) . additionally, we identified a fifth category, where instead of using a reference standard, comparative agreement between two naat platforms was calculated (table and ). the main limitation of the first group of studies (table ) was the use of a "case definition" as the reference standard to report a "positive rate" of rrt-pcr. during novel disease outbreaks, standard case definitions are often developed to assist clinicians in case identification before a diagnostic test is available. unfortunately, the studies included in this group were unable to use a clear case definition; instead they refer to a population of "suspected cases," for which the definition is not reported. [ ] [ ] [ ] because this group enrolled patients prior to february , in china, during the time in which the chinese national guideline for diagnosis and treatment of covid- (ngdtc) published five different versions of the covid- case definition, the case definitions in use at the time of these studies varied. a recent study estimated that if a single guideline (specifically, version of the ngdtc) had been used to identify cases from the beginning of the outbreak to february , , there would have been more than three times as many identified cases in hubei province. this is relevant to our review because the two largest studies that evaluated the rrt-pcr positive rate of patients with a clinical diagnosis of covid- took place in wuhan, hubei province, and included patients evaluated before february , , (supplementary table ). this increased case estimate due to diagnosis of covid- based on case definition complicates the legitimacy and reported accuracy of the "positive rate" of rrt-pcr referred to in these studies. the second group assessed rrt-pcr test performance characteristics via repeated index rrt-pcr testing ( table ). most studies in this group reported "sensitivity" by dividing the number of participants with positive baseline rrt-pcrs by the total number of participants who eventually had a positive rrt-pcr after repeated measurements. while such an approach may have some advantages over the use of a case definition alone as a reference standard, this strategy is, nonetheless, an imperfect solution with its own set of inherent limitations. sars-cov- infection is transient and the associated viral loads are time-varying because of the natural pathophysiology of the infection. therefore, the time interval between each repeated test becomes crucially important, and even relatively small time differences (and/or lack of uniformly used intervals) could complicate the interpretation of re-test results and their quality as reference standards. furthermore, repeated use of the same test as a reference standard for itself does not eliminate the inaccuracies or limitations of the test. such comparisons ultimately reflect the reliability of the test (assuming a short, uniform time interval between tests), rather than providing a true view of test accuracy. the third group of three studies calculated test performance characteristics of rrt-pcr according to a composite reference standard (table ). using arbitrary rules to combine multiple different and imperfect tests inevitably creates a reference standard with some degree of bias. furthermore, all three studies in this group included the test under evaluation as part of the composite reference standard, which leads to additional bias, described below. use of a biased composite standard is likely to lead to reduced sensitivity, among other errors affecting true test performance characteristics. the fourth group of studies evaluated sars-cov- diagnostic tests that are under development as well as proprietary testing platforms (most of which are based on standard rrt-pcr methods). these studies used traditional rrt-pcr as a reference standard; results are summarized in tables and , respectively. importantly, while these studies were not designed to estimate the accuracy of rrt-pcr, their results indicate that the index tests did not identify significantly more positive samples than rrt-pcr. finally, the last group of studies compared sars-cov- naat platforms (table ) . these comparative accuracy studies examined the agreement between two non-reference standard tests. although most of the testing platforms evaluated in these studies were based on standard rrt-pcr, the agreement between two non-reference standard tests is not equivalent to test accuracy, as mentioned previously. this scoping review is limited by the lack of reporting of several key study features in the majority of the articles evaluated, which is an important indicator of quality and potential bias. based on the quadas- criteria, most of the included studies had concern for bias (supplementary table ). the most prominent concerns were unclear inclusion/exclusion criteria, unclear method of enrollment/selection of patients and samples, and unclear handling of indeterminate/inconclusive and invalid results. additionally, many of the studies were conducted in a so-called "two gate" (case-control) design, in which cases and controls were known and selected ahead of time, rather than performing the test on a group of patients or samples with suspected covid- . these factors likely incorporate bias that significantly confounds the results of the studies, thus, the accuracy of the tests in other settings with different prevalences (such as asymptomatic screening, other age groups) may not be truly generalizable. furthermore, few studies were able to evaluate both the index and reference tests simultaneously or within a short period of time, which is key to avoiding biases caused by changes in the patient's true disease status; this bias can also affect the diagnostic accuracy of the index test. the best approach to determining diagnostic test performance characteristics in the absence of a "gold" standard is an open question in diagnostic accuracy methodology. while many methods have been described, there are only a few well-defined statistical approaches that use a reference standard in lieu of a gold standard, reviewed elsewhere. latent class analysis is one commonly used approach in situations in which neither the true error rates of the reference standard nor the true prevalence of the disease are known. this approach uses the results of a set of imperfect tests to estimate parameters related to sensitivity, specificity, and prevalence often using maximum likelihood methods. however, this is not the only method available and every method has its own strengths and limitations. therefore, careful interpretation by studies that attempt to estimate test characteristics is warranted to account for and clarify the inherent limitations of assessing accuracy-related metrics when a gold standard is unavailable. evaluation of the performance characteristics of sars-cov- diagnostic tests is vital to control of the ongoing covid- pandemic. while more than sars-cov- molecular diagnostic tests have received fda euas, we have described in this scoping review that the performance of few of these tests has been assessed appropriately. the lack of robust test performance that we noted in many studies published to date is undoubtably due in part to the critical need for tests, which resulted in accelerated test development. however, our scoping review also uncovered imperfect methods for estimating diagnostic test performance in the absence of a gold standard and demonstrate that the accuracy of these tests should be interpreted with caution. future studies would benefit from employing statistical methods such as latent class analysis and other methods referenced above to accurately analyze their data. indeed, instituting national requirements for test performance analysis and reporting, perhaps based on the existing fda guidelines on diagnostic tests, would advance the goal of standardizing the evaluation sars-cov- diagnostic test performance. such an initiative would lead to statistically robust conclusions regarding the accuracy of the index test, which will in turn support hospitals and clinicians as they determine the optimal test to use for covid- diagnosis. table . abbreviations-aigs: automatic integrated gene detection system, bal: bronchoalveolar lavage, ci: confidence interval, ddpcr: digital droplet polymerase chain reaction, e: envelope, iamp: isothermal amplification, iqr: interquartile range, κ: kappa statistic, n/a: not applicable, n: nucleocapsid, no.: number, nps: nasopharyngeal swab, nr: not reported, ops: oropharyngeal swab, orf ab: open reading frame ab, osn-qrt-pcr: one-step single-tube nested quantitative real-time polymerase chain reaction, racc: reported accuracy, rdrp: rna-dependent rna polymerase, ref stnd: reference standard, rnpa: reported negative percent agreement, rnpv: reported negative predictive value, roa: reported overall agreement, rppa: reported positive percent agreement, rppv: reported positive predictive value, rrt-pcr: real-time reverse transcription polymerase chain reaction, rsn: reported sensitivity, rsp: reported specificity, rt-lamp: reverse transcription loop-mediated isothermal amplification, rt-raa: reverse-transcription recombinase-aided amplification, s: spike, y: years. a novel coronavirus from patients with pneumonia in china genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding presymptomatic transmission of sars-cov- -singapore preferred reporting items for systematic reviews and meta-analyses: the prisma statement synthesis without meta-analysis (swim) in systematic reviews: reporting guideline quadas- : a revised tool for the quality assessment of diagnostic accuracy studies correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases positive rate of rt-pcr detection of sars-cov- infection in cases from one hospital in comparison of different samples for novel coronavirus detection by nucleic acid amplification tests chest ct findings in coronavirus disease- (covid- ): relationship to duration of infection sensitivity of chest ct for covid- : comparison to rt-pcr clinical performance of sars-cov- molecular testing diagnostic performance between ct and initial real-time rt-pcr for clinically suspected coronavirus disease (covid- ) patients outside wuhan, china testing for sars-cov- : can we stop at two? clin infect dis diagnosis of the coronavirus disease (covid- ): rrt-pcr or ct? frequency and distribution of chest radiographic findings in covid- positive patients detection and analysis of nucleic acid in various biological samples of covid- patients clinical evaluation and utilization of multiple molecular in vitro diagnostic assays for the detection of sars-cov- ddpcr: a more accurate tool for sars-cov- detection in low viral load specimens comparison of four molecular in vitro diagnostic assays for the detection of sars-cov- in nasopharyngeal specimens development of a reverse transcription-loop-mediated isothermal amplification as a rapid early-detection method for novel sars-cov- evaluation of rapid diagnosis of novel coronavirus disease (covid- ) using loop-mediated isothermal amplification real-time reverse transcription loop-mediated isothermal amplification for rapid detection of sars-cov- a novel reverse transcription loop-mediated isothermal amplification method for rapid detection of sars-cov- rapid and visual detection of novel coronavirus (sars-cov- ) by a reverse transcription loop-mediated isothermal amplification assay multiple-centre clinical evaluation of an ultrafast single-tube assay for sars-cov- rna a reverse-transcription recombinase-aided amplification assay for rapid detection of the novel coronavirus (sars-cov- ) multiplexing primer/probe sets for detection of sars-cov- by qrt-pcr triplex real-time rt-pcr for severe acute respiratory syndrome coronavirus development of an automatic integrated gene detection system for novel severe acute respiratory syndrome-related coronavirus (sars-cov ) comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of sars-cov- novel one-step single-tube nested quantitative real-time pcr assay for highly sensitive detection of sars-cov- evaluation of the covid id now eua assay comparison of two commercial molecular tests and a laboratory-developed modification of the cdc -ncov rt-pcr assay for the detection of sars-cov- comparison of abbott id now, diasorin simplexa, and cdc fda eua methods for the detection of sars-cov- from nasopharyngeal and nasal swabs from individuals diagnosed with covid- validation and verification of the abbott realtime sars-cov- assay analytical and clinical performance multi-center evaluation of the cepheid xpert xpress sars-cov- assay for the detection of sars-cov- in oropharyngeal swab specimens comparison of commercially available and laboratory developed assays for in vitro detection of sars-cov- in clinical laboratories multicenter evaluation of the cepheid xpert xpress sars-cov- test rapid and sensitive detection of sars-cov- rna using the simplexa tm covid- direct assay clinical evaluation of the cobas sars-cov- test and a diagnostic platform switch during hours in the midst of the covid- pandemic comparison of sars-cov- detection from nasopharyngeal swab samples by the roche cobas sars-cov- test and a laboratory-developed real-time rt-pcr test interpret with caution: an evaluation of the commercial ausdiagnostics versus in-house developed assays for the detection of sars-cov- virus comparison of the panther fusion and a laboratory-developed test targeting the envelope gene for detection of sars-cov- clinical performance of the luminex nxtag cov extended panel for sars-cov- detection in nasopharyngeal specimens of covid- patients in hong kong comparison of the accula sars-cov- test with a laboratory-developed assay for detection of sars-cov- rna in clinical nasopharyngeal specimens evaluation of the qiastat-dx respiratory sars-cov- panel, the first rapid multiplex pcr commercial assay for sars-cov- detection comparison of abbott id now and abbott m methods for the detection of sars-cov- from nasopharyngeal and nasal swabs from symptomatic patients performance of abbott id now covid- rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a new york city academic institution five-minute point-of-care testing for sars-cov- : not there yet clinical evaluation of three sample-to-answer platforms for the detection of sars-cov- comparison of cepheid xpert xpress and abbott id now to roche cobas for the rapid detection of sars-cov- the detection of sars-cov- using the cepheid xpert xpress sars-cov- and roche cobas sars-cov- assays comparison of two high-throughput reverse transcription-polymerase chain reaction systems for the detection of severe acute respiratory syndrome coronavirus clinical evaluation of a sars-cov- rt-pcr assay on a fully automated system for rapid ondemand testing in the hospital setting effect of changing case definitions for covid- on the epidemic curve and transmission parameters in mainland china: a modelling study evaluation of diagnostic tests when there is no gold standard. a review of methods using a combination of reference tests to assess the accuracy of a new diagnostic test value of composite reference standards in diagnostic research diagnostic test evaluation methodology: a systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard -an update food and drug administration cfdarh. statistical guidance on reporting results from studies evaluating diagnostic tests key: cord- -lrg s n authors: stoye, jorg title: a critical assessment of some recent work on covid- date: - - journal: nan doi: nan sha: doc_id: cord_uid: lrg s n i tentatively re-analyze data from two well-publicized studies on covid- , namely the charit'{e}"viral load in children"and the bonn"seroprevalence in heinsberg/gangelt"study, from information available in the preprints. the studies have the following in common: - they received worldwide attention and arguably had policy impact. - the thrusts of their findings align with the respective lead authors' (different) public stances on appropriate response to covid- . - tentatively, my reading of the gangelt study neutralizes its thrust, and my reading of the charit'{e} study reverses it. the exercise may aid in placing these studies in the literature. with all caveats that apply to n= quickfire analyses based off preprints, one also wonders whether it illustrates inadvertent effects of"researcher degrees of freedom." this note takes a second look at two recent papers on covid- released by leading german research groups. both received widespread attention and arguably had policy impact. the first, by christian drosten's research group, was cited as evidence against opening schools; the second one, by hendrick streeck with coauthors, was cited as evidence in favor of a partial reopening of germany. both made important data collection efforts and then interpreted those data. i limit my analysis exclusively to this last step of interpretation, which is also the only aspect on which i can claim expertise. i find that, based on information available in the preprints, my own analysis would plausibly have had a neutral or even the opposite tendency in each case. i next elaborate this somewhat formally and then discuss implications. the charité study: viral load in children . background jones, mühlemann, veith, zuchowski, hofmann, stein, edelmann, corman, and drosten ( , henceforth " the charité study") analyze viral load by age in a convenience sample of covid-positive patients in berlin. the aim of the investigation was to see whether epidemiological and anecdotal evidence of children being less contagious could be corroborated. the study received massive media coverage in germany and abroad. its data are visualized in figure . the seemingly strong association between age and viral load is corroborated by a nonparametric omnibus test of association. however, the paper next tests for significant differences across all pairwise combinations of age bins (and repeats the analysis with different binning). after adjustment for multiple hypothesis testing, no specific comparison is significant. this is reported in the abstract as follows: " [t] hese data indicate that viral loads in the very young do not differ significantly from those of adults." some disagreements with the analysis may come down to taste. the authors focus on a hypothesis test as deliverable of their analysis; i would have recommended a nonparametric mean regression with error bands, resulting in some estimated age effect. the main reason is that substantive significance does not equal statistical significance -if we found a minuscule but highly significant effect, we would not care either. next, the core finding is that a certain hypothesis does not get rejected. thus, the analysis suggests absence of evidence, table , panel , in the charité study. error bars display ± . standard errors. from the study's abstract: " [t] hese data indicate that viral loads in the very young do not differ significantly from those of adults." (inspired by the image accompanying textor ( ) .) which is of course not evidence of absence. although this distinction is central to how we teach hypothesis tests, including in medicine (altman and bland, ) , it is at most barely maintained in the paper (see the aforecited sentence) and completely lost in its perception. as a result, the data that are visualized in figure fueled headlines like "covid patients found to have similar virus levels across ages" (gale and mulier, ) and "children are just as contagious as adults" (kieselbach, ) . more troublingly, i am not convinced that the evidence is absent. to the statistically educated reader, the above headlines may suggest that the study tests, and fails to reject, h : "children have the same viral load as adults." it does not. it rather splits the sample into age bins and then simultaneously tests whether any of the possible pairwise combinations of age groups exhibit a significant difference in load. with proper adjustment for the possibility of false discoveries from tests, not one comparison shows up as significant. this is reported as main conclusion, even though it is at tension with a test reported elsewhere in the preprint that indicates some difference across age bins (kruskal-wallis test, table a , p = . % for [ ] the bins in figure ). that is, the analysis finds a significant age effect -it is merely that post-hoc comparison does not single out a specific one of pairs as culprit. if one's take-home message is a finding of nonsignificance, one should make a good faith effort to apply a powerful test. that did not seem to happen here. on the contrary, artificially coarsening the age variable and, especially, pooling the comparison of interest with comparisons that nobody inquired about is bound to sacrifice power. what would the result have been without these choices? to take an educated guess, i will now try to recover from the paper a test of h : "children have the same viral load as adults." to this purpose, i combine the first two and the remaining age bins of figure to find means of . and . with % confidence intervals of [ . , . ] and [ . , . ], respectively. a simple t-test rejects the null of equal means at a two-sided p-value of . %. it would seem that the lower viral load in the youngest age groups is highly significant. what gives? i reiterate that this simple test would not be my preferred analysis of the raw data. however, i am willing to defend it vis a vis the preprint's multiple nonparametric hypothesis tests. specifically: • the test only considers one rather than hypotheses. i consider this a feature and not a bug. the data were collected specifically to investigate the relative viral load of children, and the methodological justification for pooling this comparison with others is not elaborated. indeed, one could arguably conduct a one-sided test and report a p-value of . %. • the test is influenced by the authors' choice of bins and by my inspection of the visualization, so it strictly speaking involved an informal specification search. however, given the study's purpose, my own pre-data plan (conditionally on involving a simple hypothesis test to begin with) would have proposed more or less the same comparison. hence, this should not a major concern. that said, taking the above p-value entirely at face value is not recommended, but it is also not necessary for my point. • the test is exact only if relevant true distributions are normal. this is clearly not the case, neither exactly (negative values are impossible) nor approximately (the paper reports corresponding tests). however, i compare means across two samples of size and , and the empirical distributions appear slightly skewed but well-behaved (see figure in the charité study). an appeal to the central limit theorem would seem innocuous. in fact, this consideration is more pressing for the charité study itself. they perform simultaneous tests on relatively small bins and therefore encounter the one-two punch of (i) looking at the further-out-in-the-tails quantiles of sampling distributions that become relevant with bonferroni-type adjustments and (ii) rather small sample cells. indeed, of the tests involve the " - " age bin, which contains observations. this makes it harder to appeal to normal approximations, yet two of the three multiple hypothesis tests reported in the paper do so anyway and essentially differ from my test only through adjusting for multiplicity of hypotheses. this simple analysis is not meant to be conclusive. my only point is that the paper's nonsignificance result seems to be driven by researcher choices. for any conclusions beyond that, i would want to see the results of a nonparametric regression analysis that undoes the age binning of data. the closest approximation to this that i am aware of is the insightful renalysis by held ( ) , which qualitatively agrees with mine. the ideal solution here would be publication of the data; while this might not be legally easy, i note that a lot could be done with literally only age and viral load. streeck, schulte, kümmerer, richter, höller, fuhrmann, bartok, dolscheid, berger, wessendorf, eschbach-bludau, kellings, schwaiger, coenen, hoffmann, stoffel-wagner, nöthen, eis-hübinger, exner, schmithausen, schmid, and hartmann ( , henceforth "the gangelt study") is an early seroprevalence study conducted in the small german town of gangelt, which had witnessed a superspreader event. the study made headlines for estimating a local prevalence of % and especially an ifr of . %, which was perceived as surprisingly low (and would certainly be considered on the very low end now). from the latter number, the authors also informally extrapolate to . million infected germans, an extrapolation that was correspondingly perceived as high, therefore arguably reassuring, but also implausible. the study received considerable attention that was apparently seeked out by the lead author, who vocally advocated for partial reopening of north rhine-westphalia. reanalysis. it has been widely remarked that, even if one feels confidence extrapolating gangelt's ifr, one cannot extrapolate the ci to either nationwide ifr or nationwide prevalence. the reason is that gangelt's fatality count was considered nonstochastic, but for the purpose of extrapolating results to germany, it is a realization of "successes" (scare quotes very much intended) in a large trial. for illustration, a simplistic % confidence interval for gangelt's expected fatality count covers all integers from to . but the point estimator itself may not be the only plausible choice either. it implies that only % of cases were detected nationwide, an implication that was picked up by the media (burger, ) but also frequently called out as implausible. indeed, the discovery rate in gangelt was estimated to be %. extrapolating from this number to germany would imply an ifr of . % rather than . %. what gives? the discrepancy stems from the fact that, if we believe gangelt to be representative of germany, we have overdetermined but not quite consistent estimating equations. for sake of argument, say we have fatalities, officially confirmed cases, and true infections in gangelt, while we have fatalities, confirmed cases, and an unknown true prevalence in germany. by the rule of proportions, we could back out an estimate of nationwide prevalence either as × / = (an update of the study's preferred estimate) or as × / = (extrapolating the undercount). the numbers differ by so much because the crude case fatality rate (cfr) equals / = . % for gangelt and / = . % for germany. thus, assuming that the ifr (interpreted as population-level expectation) is actually the same, gangelt either tested more or got really lucky. by extrapolating the local ifr, the study assumes the former but without discussing this assumption. at the same time, proponents of extrapolating the undercount could point out that the underlying binomial samples of / versus / are of vastly different size. should we really prioritize the former over the latter in extrapolation? or was gangelt indeed just lucky? this is marginally implausible in that the (exact binomial) two-sided p-value for the former sample being drawn from the latter urn is . %. but modest demographic difference between gangelt and germany, or accounting for clustered sampling of both numerator and denominator (the sample units were households; the superspreading event apparently spared local nursing homes), could easily compensate for that. what's more, the fatality count meanwhile increased to . while it is not clear that this fatality was among the infected during the study's time frame, adding it would change the aforementioned p-value to . %. also, it would mean that the local and nationwide numbers are consistent up to sampling error according to the more sophisticated analysis in rothe ( , numerical claim verified in personal communication). again, my point is not that the study's implicit argument is necessarily false. gangelt's undercount might indeed be atypically low: being a hotspot, the town saw much more testing than other places. however, that does not logically imply that gangelt had more testing relative to true prevalence. my complaint is that this case was not made, and a this ci just inverts the poisson distribution. it is reported to illustrate that the issue is not negligible. see rothe ( ) for a sophisticated analysis of the multilayered inference problem. note also that i use the higher (= ) of two fatality counts offered in the preprint. the nationwide numbers were reported by johns hopkins university on / . they implied a slightly lower case fatality rate at the time of the study. [ ] different extrapolation that would align the study with other recent seroprevalence studies (and have shorter confidence intervals to boot) was not discussed. a balanced analysis might well provide both and also some form of interpolation. partial identification would be one framework close to my heart, but the primary concern is transparency about how different identifying assumptions would interact with the data at hand. this is not a "gotcha" paper. both aforecited studies are carefully and competently executed, especially considering the extreme time pressure. they are transparent about computations, the computations appear correct, and i have no doubt that they were executed in good faith. compared to some concurrent work by prominent u.s. researchers (e.g., as discussed by gelman ( )), both studies are models of good science. also, there are obvious limitations to quickfire reanalysis without raw data, and everything i have to say is accordingly tentative. with that said, i stand by the following assessments: there are many good arguments against a quick reopening of schools, but the charité study does not add to them. neither does the gangelt study paint a substantially more optimistic picture on ifr than other recent seroprevalence studies. with the due caution warranted by a sample size of n = , it is of note that both studies were perceived as having a certain policy thrust; in both cases, this thrust correlated with public perception of some authors' stand on covid- policy; and in neither case was it corroborated by my reading. that is my methodological point. specific, reasonable but not objectively forced choices of statistical analysis -what is sometimes referred to as "researcher degrees of freedom"-informed results that align with researchers' public stands. i emphasize that i do not suggest any intent. however, even at the very top of the discipline, the effects of, for example, deciding when an analysis is complete cannot be assumed to just go away. while i think that my comments on the specific studies are of interest, an important message to you -the reader-and me is to redouble consideration for such effects in our next study. on an immediately practical note, it illustrates that a data repository for covid- related research would be invaluable. finally, it is a reminder of the importance of professional peer review. while both of the above studies were controversially discussed by experts right away, my impression is that critical voices gained any traction with the public only for the gangelt one. in sum, this may be the rare case where rapid peer review of an academic paper would plausibly have affected the news cycle. statistics notes: absence of evidence is not evidence of absence german study suggests infections are times the number of confirmed cases fatal flaws in stanford study of coronavirus prevalence a discussion and reanalysis of the results an analysis of sars-cov- viral load by patient age kinder sind genauso ansteckend wie erwachsene (children are just as contagious as adults) open review of the manuscript: 'an analysis of sars-cov- viral load combining population and study data for inference on event rates infection fatality rate of sars-cov- infection in a german community with a super-spreading event here's a replot of their own data. means +/- *se from their table . their conclusion: no sig. viral load difference between children and adult. media: children just as infectious as adults, study shows key: cord- - w l q authors: lombardi, andrea; consonni, dario; carugno, michele; bozzi, giorgio; mangioni, davide; muscatello, antonio; castelli, valeria; palomba, emanuele; cantù, anna paola; ceriotti, ferruccio; tiso, basilio; pesatori, angela cecilia; riboldi, luciano; bandera, alessandra; lunghi, giovanna; gori, andrea title: characteristics of , healthcare workers who underwent nasopharyngeal swab for sars-cov- in milano, lombardy, italy date: - - journal: clin microbiol infect doi: . /j.cmi. . . sha: doc_id: cord_uid: w l q objectives: the management of healthcare workers (hcws) exposed to confirmed cases of covid- is still a matter of debate. we aimed to assess in this group the attack rate of asymptomatic carriers and the symptoms most frequently associated with the infection. methods: occupational and clinical characteristics of hcws who performed a nasopharyngeal swab for the detection of sars-cov- in a university hospital from february , to march , , were collected. for those who tested positive and for the asymptomatic positives we checked laboratory and clinical data as of may to calculate the time necessary to become test-negative and to verify whether symptoms developed thereafter. frequencies of positive tests were compared according to selected variables using multivariable logistic regression models. results: positive tests were among , hcws ( . %, % confidence interval [ci]: . - . ), with a marked difference between symptomatic ( / , . %) and asymptomatic ( / , , . %) workers (p< . ). physicians were the group with the highest frequency of positive tests ( / , . %), whereas clerical workers and technicians displayed the lowest frequency ( / , . %). the likelihood of being positive increased with the number of reported symptoms and the strongest predictors were taste and smell alterations (odds ratio [or]= . ) and fever (or = . ). the median time from first positive test to a negative test was days ( % ci: - ). conclusions: a relevant number of hcws can be infected by sars-cov- without displaying any symptom. among symptomatic workers, the key symptoms to guide diagnosis are taste and smell alterations and fever. in median, almost four weeks are necessary to achieve negativity of nasopharyngeal swab. severe acute respiratory syndrome coronavirus (sars-cov- ) is a previously unknown virus which recently jumped from a not yet identified animal host to humans and it is responsible of coronavirus disease . the virus has now spread worldwide from china, causing the first pandemic of the xxi century, disrupting health-care services in the affected countries and exacting a terrific toll of human lives. - healthcare workers (hcws) are a crucial actor in the pandemic. indeed, they are acting in an emergency situation and are continuously at risk of being infected. at the same time, they are in contact with the most fragile elements of our society, those who need health assistance. it is therefore mandatory to avoid that infected hcws act as spreaders of the disease. unfortunately, it is still unclear which microbiologic investigations and procedures should be adopted toward hcws in covid- settings, especially to those exposed to confirmed cases of covid- and at risk for infection. to answer this question, we reviewed all the nasopharyngeal swab performed in hcws exposed to confirmed cases of covid- at the foundation irccs ca' granda ospedale maggiore policlinico located in milan, the capital of lombardy, by large the italian region mostly affected by we assessed frequency of positive tests among symptomatic and asymptomatic hcws and evaluated the association between occupation, symptoms (type and number), and presence of the infection. furthermore, we also calculated the median time between the day of diagnosis (first positive test) and the day in which the hcw became test-negative. we collected occupational and clinical characteristics of all the consecutive hcws who we tested hcws at risk for infection, which is defined as a contact with a patient or another hcw with (or later diagnosed with) sars-cov- infection. all those at risk were, according to the internal protocol, identified and contacted by the hospital infection prevention unit, isolated at home and tested. hcws were subdivided into physicians (including residents), nurses and midwives, healthcare assistants, health technicians, and clerical workers and technicians. all the information was collected by the infectious disease notification form associated to each test. workers were defined as symptomatic if presented any of the following in the days preceding the test: fever, cough, dyspnoea, asthenia, myalgia, coryza, sore throat, headache, ageusia or dysgeusia, anosmia or parosmia, ocular symptoms, men (three physicians and two nurses) and three women (two physicians and a clerical worker) were hospitalized. a minority of the hcws ( / , , . %) reported to have had a contact with an infected person outside the hospital (relatives, colleague, or friends). of these, / ( / , . %) were found to be positive. in this italian group of hcws exposed to confirmed cases of covid- , the presence of symptoms, and particularly taste and smell alterations and fever, was associated with interestingly, the auc of a model considering six groups of symptoms (fever, myalgia, asthenia, ocular symptoms, dyspnoea, and taste and smell alterations) was . . based on these results, it seems reasonable to tailor the screening approach of hcws at risk based on the resources available. in low-resource settings we suggest focusing to test those with symptoms to maximize efficacy, especially considering the continuous exposure of hcws to at risk situations, thus requiring repeated testing sessions. nevertheless, it should be underlined that in our study a non-negligible number of workers were infected but displayed no symptoms, meaning that a fraction of those infected can be lost with a symptoms-based screening strategy. therefore, in middle-and high-resource settings a mass screening for all hcws exposed to confirmed covid- cases appears the best approach to limit the spread when stratified according to occupation, test-positive frequencies were clearly higher among subsets with direct contact with patients (physicians including residents, nurses and midwives, healthcare assistants and health technicians) than those without (clerical works and technicians). consequently, careful screening of these groups of workers should be mandatory. no differences in terms of infection attack rate were seen between different age groups nor between men and women, suggesting that risk factors for acquiring covid- among hcws are unrelated to age and sex. another relevant point is the significant number of hcws who were negative at the first test but resulted positive when tested a second time. this might represent a serious concern, as a discrete fraction of those can further spread the virus unnoticed, thus hampering the efficacy of the screening strategy. it should be noted, however, that the second test was performed on a small number of operators and not on a routine basis, making these considerations subject to several potential biases. in addition, in a relevant proportion of our population we could not retrieve information about the most likely date of exposure to a documented case. thus, we cannot exclude a recent contact in which case the first test may have been performed too early (i.e. still in the incubation period which has been estimated to be five days), before a sufficient amount of viral particles is detectable in the nasopharynx. moreover, it has to be considered that hcws employed in covid- units/hospitals are at risk of sars-cov- exposure on a daily basis and therefore repeated exposures, even unnoticed, can occur also after the first one who motivated the test. moreover, technical limitation can be responsible of falsely negative test, considering that the sensitivity of nasopharyngeal swab for sars-cov- detection has been estimated to be around %. finally, we observed a median time from first positive test to a negative test of days. this our study has some limitations. first, the surveillance system was quickly set-up in a few days due the virus spread in our region since february , when the first italian case was identified in the south-east part of lombardy. therefore, data quality was imperfect and extensive time-consuming data editing (through review of electronical records and, when necessary, of paper forms) was required to retrieve and complete the relevant information. for the same reason, and because we wanted to provide a rapid response to concerns about virus spread in the hospital, we were forced to limit the analyses to only a part of the work- world health organization (who), covid- definitions key: cord- -e imc r authors: shevachman, m.; mandal, a.; mitragotri, s.; joshi, n. title: a long-lasting sanitizing skin protectant based on cage, a choline and geranic acid eutectic date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: e imc r the recent outbreak and rapid spread of coronavirus disease (covid- ) is a global pandemic and a massive public health crisis. covid- has also had a severe impact on the quality of life and mental health. while different health authorities such as who and cdc are encouraging adoption of strategies including hand washing and use of facemasks to reduce the spread of the pathogens and infections, adoption of these approaches requires substantial commitment. current hand sanitizers based on ethanol provide immediate protection, however, the protection rendered by such sanitizers is very short-lived due to their rapid evaporation. a long-lasting sanitizing skin protectant that can effectively inactivate sars-cov- and provide persistent efficacy over several hours will provide people the freedom to carry on with their activities without constant concerns about the cleanliness of their hands. herein, we describe a skin protectant, ionlasttm, based on an ionic liquid/deep eutectic solvent, formed by gras materials, choline and geranic acid (cage, cg- ), that provides protection for at least h after a single application. ionlasttm was formulated as a gel that facilitates easy application on the skin. tolerance of cg- was substantiated through a study in human volunteers. in vitro studies confirmed that ionlasttm effectively inactivates a human coronavirus hcov e. a second human clinical study established that a single application of ionlasttm imparts protection against microbes that lasts up to several hours. severe acute respiratory syndrome coronavirus (sars-cov- ) has emerged as a global pandemic that has infected > million people worldwide with , deaths reported as of july , [ ]. the zoonotic virus, sars-cov- is responsible for the coronavirus disease (covid- ) , which is associated with severe respiratory distress, fever or chills, cough, sore throat, congestion, nausea, and diarrhea [ ] . older adults and individuals with underlying health conditions such as heart or lung diseases and diabetes patients are at a higher risk of experiencing mortality from the infection [ , ] . the world health organization (who) declared covid- outbreak as a pandemic on march , and since then, the number of confirmed cases, deaths, and economic losses arising fromsars-cov- have amassed to an alarming level [ ] . sars-cov- pandemic is not only a significant public concern in terms of human health, but its impact on the economy is also far-reaching [ ] . apart from disproportionately affecting the vulnerable, especially the elderly and minorities, it has ravaged the economic wellbeing of many, and has placed an incalculable burden on local governments. in a mere few months, it has had an impact of greater than $ t on the economy, causing the largest global recession in history [ ] . in fact, covid- is expected to result in long-term health issues straining the healthcare system more than ever before [ ] . even as the number of new cases seem to plateau in certain parts of the us, the recent uptick in number of new cases in other parts of the country suggests that this is not merely an issue to be managed by the healthcare system, but a call for everyone in the society to play their part to minimize the risk of transmission [ ] . sars-cov- is highly contagious and can be easily transmitted from human-to-human even when the subjects are asymptomatic, presymptomatic or have mild symptoms [ ] . while vaccines and antiviral drug discovery remain paramount to curb this deadly pandemic, virus containment is of utmost importance and will require behavioral changes from each individual [ , ] . regulatory agencies including the center for disease control (cdc) and who have issued guidance for behavioral changes including handwashing for seconds, wearing masks when in public and social distancing [ , ] . whilst these are simple in principle, strict compliance with these requirements is difficult to sustain. since it is neither practical nor viable to completely lockdown all aspects of the economy or daily lives, methods that can improve compliance will contribute significantly towards the outcome. since , the us food and drug administration proposed ethanol at concentrations between % and % as safe and effective for hand sanitizers [ ] . who recommends using formulations containing %v/v ethyl alcohol or %v/v isopropyl alcohol to inactivate pathogens effectively, including acute respiratory syndrome coronavirus (sars-cov), middle east respiratory syndrome coronavirus (mers-cov) and most recently, sars-cov- [ ] . however, the biggest shortcoming of such alcohol-based formulations is that their protective effect lasts only till the alcohol evaporates i.e. seconds- minutes. once the alcohol evaporates there is no protection remaining on the hands leaving the person vulnerable to the very same risks of infection and transmission. hence, development of an effective hand sanitizer that can generate long-lasting protective effects can offer significant benefits in minimizing rampant viral transmissions and maximize virus inactivation in a pandemic situation like sars-cov- outbreak [ , [ ] [ ] [ ] . . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint there has been no significant innovation in hand santizers from the s when alcoholbased sanitizers were first introduced [ ] . here, we report a sanitizing skin protectant, ionlast tm that contains an ionic liquid/deep eutectic solvent, choline geranate (cg- , % w/w) formulated in ethanol. cg- is non-volatile and is hypothesized to remain on the skin long after ethanol evaporates thus protecting the skin for several hours. cg- has already been confirmed to demonstrate broad-spectrum antimicrobial properties against atcc strains of bacteria, virus, and fungi [ ] [ ] [ ] [ ] . the mechanism of antimicrobial action is mediated through lipid extraction and membrane disruption [ ] . we anticipated that the same properties of cg- may support its efficacy against sars-cov- . safety of cg- in human volunteers. safety of cg- ( % concentration) was tested in a -week human repeat insult patch test (hript) in adult human volunteers. the concentration of cg- was times higher than that used in ionlast tm . cg- was applied to the back of the subjects over a marked x cm area and covered with an occlusive hypoallergenic patch to maximize penetration. distilled water was used as a negative control. the patches were removed by the subjects after h and a new one was applied by the site staff at the same exact site at the next visit. the subjects reported to the site for a total of visits, each week. during each visit the application area was observed by the study investigator and a new patch was applied. none of the subjects showed any skin reactions in the first visits ( -days). subjects did not display any irritation throughout the entire -day study. between visits through , subjects experienced some skin irritation. however, there was no follow-up treatment required for any of these subjects that showed irritation. there were no other adverse events reported in the study. furthermore, upon completion of the -day study period, and a rest period of two weeks, cg- application with occlusion to a different part of the body, did not create any sensitization response at and h. superior antibacterial efficacy of ionlast tm . in order to determine the prolonged protective effects of ionlast tm in contrast to the currently marketed products containing % ethyl alcohol, an in-vitro efficacy study was conducted using e. coli following modified astm e methodologies. one milliliter of the test and comparator products were applied onto the precleaned glass surfaces and dried for min. glass slides were inoculated with µl of bacterial suspension at various timepoints ( min, h, and h). the test compound was chemically neutralized after an exposure duration of min before transferring the samples to agar plates. the agar plates were visually compared for microbial growth after incubation for h at °c. no e. coli growth was observed for the ionlast tm -treated groups for min, h as well as h which clearly indicated the persistent antimicrobial activity of ionlast tm . in contrast, almost similar e. coli growth was observed for the saline-treated group and the comparator, ethyl alcohol % hand sanitizer treated group (fig. ) . this indicates that alcohol-based products might have limited ability to provide long lasting protective effects against microbes. on the contrary, ionlast tm provided clear indication of long-lasting protection against pathogens and thus potentially reducing disease transmission during a pandemic. . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint protection against hcov e. based on the previously demonstrated broad-spectrum antimicrobial properties of cg- [ ] , we anticipated that cg- and the skin sanitizer containing cg- (ionlast tm ) would effectively deactivate coronavirus likely through disruption of the phospholipid bilayer glycoproteinaceous envelope. we evaluated the virucidal effects of ionlast tm gel and the active cg- ( % w/w in purified water) against human coronavirus strain e (hcov e) using a virucidal suspension test (in-vitro time-kill method) based on industry/regulatory-relevant global standardized methodologies (astm e - ). the log reductions from the initial population of the hcov e following s and s exposure to ionlast tm was found to be > . . in fact, the percent reduction for both the time points was > . . similarly, we evaluated the virucidal activity of cg- ( % w/w) using the quantitative suspension test for exposure times, min and min. the percent and log reductions from the initial population of the hcov e following min and min exposure to cg- ( % w/w) was found to be > . and > . respectively ( fig. and tables s and ). clinical studies approved by an irb were performed at bioscience laboratories, inc. (testing facility) in compliance with good clinical practice regulations to test the effectiveness of ionlast tm to provide extended protection against microbes. specifically, ionlast tm was applied to the forearms of human volunteers and the randomly assigned test sites on each forearm were challenged by application of staphylococcus aureus (s. aureus) at various times after the application of ionlast tm . the residual antimicrobial efficacy of ionlast tm was tested using a modification of the standardized test method described in astm e - ( ) in healthy subjects. a significant (≥ . ) log reduction in s. aureus from the control was observed following min., h and h post-ionlast tm application. immediately following application and -min air-dry of the ionlast tm , the mean log microbial recovery for the treated subjects was found to be . ± . in contrast to . ± . for the untreated subjects. furthermore, the log microbial recovery, h following application of the ionlast tm , was found to be . ± . for the treated subjects vs . ± . for untreated subjects. interestingly, post h application of ionlast tm , the log microbial recovery for treated subjects was also . ± . in comparison to . ± . for untreated subjects. note that the lowest detectable limit of the study was . log cfu/cm . ionlast tm thus demonstrated prolonged microbial protection for up to h after a single application ( fig. and table s ). these data and the lack of any trend from . h, h and h suggest that the effectiveness of ionlast tm could persist beyond h. sar-cov- , the virus that causes the covid- disease has evolved into a global pandemic and is highly contagious affecting > million people worldwide over a span of just months. while the development of effective vaccines and antiviral therapies remain at the forefront of the global efforts to curb this deadly infection, the immediate response plan to control covid- should include breaking the chain of transmission of the virus and preventing associated illness and death [ ] . current evidence suggests that sars-cov- predominantly spreads through person-. cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint to-person via saliva and respiratory secretions or droplets [ ] . other modes of transmission could be contaminated objects or surfaces (fomite transmission), fecal-oral, bloodborne, mother-to-child, and animal-to-human transmission [ ] . the relative roles of various routes are unclear and will require additional epidemiological data as well as mechanistic information about the virus entry. for example, angiotensin-converting enzyme (ace ), the cell receptor for sars-cov- entry is abundantly present in blood vessels/capillaries of the skin, the basal layer of the epidermis, and hair follicles [ , ] . hand hygiene is widely recognized for playing a major role in limiting the spread and transmission of such infectious diseases [ ] . in fact, in order to cope with such a pandemic situation, cdc has specifically recommended washing of hands with soap and water whenever possible. however, it has been reported that frequent washing hands with water and soap may damage skin potentially leading to dermatitis [ ] . while alcohol-based hand sanitizers with at least % alcohol can help in avoiding sickness and spreading germs to others, unfortunately the protective effect of alcohol lasts only till the alcohol evaporates i.e. less than a couple of minutes. frequent handwashing is also burdensome and disruptive in many situations, and in some cases just not practical [ ] . inspired by the fact, that cg- exhibits broad-spectrum antimicrobial properties against a range of bacteria, virus, and fungi, we developed an alcohol-based sanitizing skin protectant containing cg- as a countermeasure to restrict the rampant spread of the covid- infection. cg- inactivates pathogens by extracting lipids and disrupting the cell membrane [ ] . more importantly, unlike ethanol, which is highly volatile, cg- , being an ionic liquid/deep eutectic solvent, has a very low vapor pressure and can remain on the skin long after ethanol evaporates. this long-lasting residence of cg- is expected to be responsible for long-lasting protection against sars-cov- thus limiting the need for frequent hand washing. human volunteer studies confirmed the safety of the active, cg- (~ % concentration). hript, an industry standard test for evaluating the potential of a test material to induce sensitization in humans after repeated exposure was adopted [ ] . among adult human volunteers who were treated with x higher cg- than that used in the ionlast tm , subjects did not display any irritation throughout the entire -day study. there were no other adverse events reported in the study. furthermore, following completion of the study and a rest period of two weeks, cg- application to a different part of the body, did not create any sensitization response at and h which indicates the potential of cg- as a safe additive for topical products. in-vitro bactericidal assay was conducted to compare the longevity of antibacterial efficacy of ionlast tm in contrast to currently marketed alcohol-based products against e. coli. the visual difference in the number of viable test microorganisms for the alcohol-based product and ionlast tm was striking for all the time points including min, h and h. no notable difference in the microbial growth was observed between the untreated and alcohol-based hand sanitizer treated groups (fig. ) indicating the short duration of protection rendered by ethanol. this signifies the persistence of protective effects of ionlast tm against e. coli and possibly other pathogens for up to h. . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint the encouraging results obtained from the bactericidal efficacy studies, motivated us to test ionlast tm against hcov e. as theorized, cg- was able to deactivate the virus, generating excellent virucidal efficacy against hcov e. ionlast tm generated > . log reductions in viral titers following s and s exposure. moreover, virucidal activity of the active, cg- ( % w/w) for exposure times, min and min generated similar log reductions (> . ) from the initial population of the hcov e as ionlast tm (fig. ) indicating hcov e is highly susceptible to ionlast tm . residual antimicrobial efficacy study was undertaken to measure the relative persistence of antibacterial activity under controlled clinical test conditions. the results demonstrated a significant (≥ . ) log reduction in s. aureus following immediate, h and h post-ionlast tm application (fig. ) . these results further support persistent pathogen inactivation efficacy of ionlast tm . upon further clinical studies demonstrating the prolonged protection rendered against hcov e, ionlast tm may open new opportunities in the recommended hand hygiene protocols for preventing disease transmission. with its long-lasting effect, ionlast offers a promising complement to the existing cdc/who guidelines for good hand hygiene. clinical safety study of cg- . for the hript, skin irritation and sensitization potential of cg- was evaluated in a -day human repeat insult patch test in volunteers. this cosmetic study was approved by an irb and conducted by ama laboratories inc. in new york. cg- ( %, liquid) was applied on the back of volunteers over a x cm area on each of visits over a period of weeks. the application area was occluded with hypoallergenic tape. the subjects were required to keep the tape for h. at each visit, the application site was evaluated for skin irritation on a -point scale ( - ). any subjects that showed irritation rated at or higher were withdrawn from the study and monitored for changes. after completion of the -week test period the subjects were given a to -day rest, after which cg- solution was applied to a previously unexposed site. the subjects were then evaluated for any skin reactions after and h. in-vitro bactericidal efficacy. in order to determine the relative bactericidal efficacy of ionlast tm in contrast to an alcohol-based product, astm e , standard test method for efficacy of sanitizers recommended for inanimate non-food contact surfaces was modified and employed accordingly. briefly, pre-cleaned surfaces were transferred into sterile petri plates using sterile forceps and covered with ml of the test substances and held for min at ambient temperature to dry. the inoculation with µl of e. coli suspension was performed at min, h and at h. after each inoculation, the exposure time was min. after min, the test compound was neutralized, and the viable bacteria were resuspended. a neutralization study was conducted to assure that the neutralizers used for the study quench the antimicrobial activity of each test material and were not toxic to the challenge species. after neutralization, the samples were plated on agar plates and transferred into the incubator set at °c for h. an average of at least ≥ cfu of bacteria were recovered from the negative and neutralization controls. the number of viable organisms on the agar plates treated with ionlast tm were then compared visually to a . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint negative control (untreated) and the comparator (ethyl alcohol % hand sanitizer) following h incubation. virucidal suspension test. the virucidal test was based upon astm e - , standard practice to assess the activity of microbicides against viruses in suspension. all testing was performed in accordance with good laboratory practices (glp), as specified in cfr part at bioscience laboratories, inc. (bsl), bozeman, montana. the characterization of the identity, strength, purity, composition, stability, and solubility of the test product(s) was performed by cage bio inc. the percent and log reductions from the initial population of the viral strain(s) was determined following exposure to the test product, ionlast tm , for s and s, and to the test product, cg- ( % w/w), for minand min. testing was performed in replicate. plating was performed in four replicates. coronavirus (alphacoronavirus) strain e (atcc #vr- ) and mrc- (atcc #ccl- ; human lung fibroblast cells) were used for the study. residual antimicrobial efficacy test. the residual antimicrobial efficacy testing was carried out using a modification of the standardized test method described in astm e - ( ), standard guide for evaluation of residual effectiveness of antibacterial personal cleansing products. the study was conducted in compliance with good clinical practice regulations, good laboratory practice regulations, the standard operating procedures of bioscience laboratories, inc., the study protocol, and any protocol amendments. bacterial recoveries were assayed after application of test material, using the forearms as a substrate. at least twelve test subjects (aged - years), with healthy skin were used in this study, and the test product was applied on one arm, and had the other arm untreated as the negative control. the test sites on both forearms were inoculated with suspensions containing s. aureus (atcc # ), immediately after the -minute product drying time, and at approximately h and h following test material applications. the test sites were sampled using the cup scrub procedure approximately min following each inoculation. the log microbial recoveries of treated versus untreated sites were the basis for assessing the residual antimicrobial effectiveness of the test product. a neutralization study was also performed to assure that the neutralizers used in the recovery medium quench the antimicrobial activity of each test material and were not toxic to the challenge species. study procedures were based on astm e - ( ), standard test methods for evaluation of inactivators of antimicrobial agents. s. aureus (atcc # ) was used as the challenge species in the neutralization study. . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . table s . log reduction and percent reduction from control of hcov e (atcc #vr- ) following -and s by the test product: ionlast tm table s . log reduction and percent reduction from control of hcov e (atcc #vr- ) following -and min by the test product: cg- ( % w/w) table s . log microbial recoveries and log microbial reductions from control of s. aureus (atcc # ), by subject; immediately ( min), h, and h following application of the test product: ionlast tm author contributions: ms led characterization, formulation development; ms, am and nj designed the glp antibacterial and vircucidal studies, and data analysis; ms and nj participated in characterization, design of clinical safety study and data analysis; am performed data summary, am and sm summarized findings and wrote the manuscript with the help of all authors. funding: this study was funded by cage bio. competing interests: cage bio has a license to and ownership of patents pertaining to ionic liquids. am, ms, and nj are employees and shareholders of cage bio. sm is a shareholder and board member/consultant to liquideon, cage bio, and i o therapeutics. data and materials availability: any data associated with this study are available from the authors upon reasonable request. . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint figures fig. . in-vitro antibacterial efficacy against e. coli. number of viable test microorganisms treated with the test substances, ethyl alcohol % hand sanitizer (comparator) and ionlast tm in comparison to the saline-treated group (negative control) the treated groups were incubated with the test substances for min, h and h and subsequently exposed to e coli for min and then neutralized. bacterial growth was assessed on agar plates after a -hour incubation period. . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint virucidal infectivity to mrc- cells for (a) ionlast tm and (b) cg- ( % w/w) treated viral suspensions in comparison to virus control (untreated) for different exposure times. log reduction are included above the bar. viral titers are displayed as tcid /ml values (n= ). lloq, lower limit of quantification; tcid /ml, % tissue culture infectious dose. . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint fig. . residual antimicrobial efficacy against s. aureus. the means of log microbial recovery in comparison to untreated subjects (a) immediately ( min), (b) h, and (c) h following application of the test product: ionlast tm . data are averages ± sem, statistics by two-way anova with bonferroni's multiple comparison-test. ****p < . (n= ). . cc-by-nc-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted august , . . https://doi.org/ . / . . . doi: medrxiv preprint a new coronavirus associated with human respiratory disease in china covid- : a novel zoonotic disease caused by a coronavirus from china: what we know and what we don't sars-cov- and covid- : a genetic, epidemiological, and evolutionary perspective the proximal origin of sars-cov- transmission of sars-cov- , required developments in research and associated public health concerns covid- : in the absence of vaccination -'mask-the-nation the socio-economic implications of the coronavirus pandemic (covid- ): a review review of the novel coronavirus (sars-cov- ) based on current evidence from sars to covid- : a previously unknown sars-related coronavirus (sars-cov- ) of pandemic potential infecting humans -call for a one health approach. one health airborne transmission of sars-cov- : the world should face the reality broad-spectrum coronavirus antiviral drug discovery decoding sars-cov- transmission and evolution and ramifications for covid- diagnosis, vaccine, and medicine hand hygiene and the novel coronavirus pandemic: the role of healthcare workers universal use of face masks for success against covid- : evidence and implications for prevention policies hand sanitisers amid covid- : a critical review of alcohol-based products on the market and formulation approaches to respond to increasing demand inactivation of severe acute respiratory syndrome coronavirus by who-recommended hand rub formulations and alcohols. emerg infect dis hand sanitizers: a review on formulation aspects, adverse effects, and regulations rational hand hygiene during the coronavirus (covid- ) pandemic efficacy of various disinfectants against sars coronavirus hand sanitizers: a review of ingredients, mechanisms of action, modes of delivery, and efficacy against coronaviruses mechanism of antibacterial activity of choline-based ionic liquids (cage) choline and geranate deep eutectic solvent as a broad-spectrum antiseptic agent for preventive and therapeutic applications ionic liquids as a class of materials for transdermal delivery and pathogen neutralization scope and efficacy of the broad-spectrum topical antiseptic choline geranate current knowledge of covid- and infection prevention and control strategies in healthcare settings: a global analysis transmission of covid- virus by droplets and aerosols: a critical review on the unresolved dichotomy risk of sars-cov- transmission by aerosols, the rational use of masks, and protection of healthcare workers from covid- high expression of ace on keratinocytes reveals skin as a potential target for sars-cov- sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor frequent hand washing for covid- prevention can cause hand dermatitis: management tips. cureus overzealous hand hygiene during the covid pandemic causing an increased incidence of hand eczema among general population in vivo studies of substances used in the cosmetic industry . cc-by-nc-nd . international license it is made available under a key: cord- - sr djft authors: mentus, cassidy; romeo, martin; dipaola, christian title: analysis and applications of adaptive group testing methods for covid- date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: sr djft abstract testing strategies for covid- to maximize number of people tested is urgently needed. recently, it has been demonstrated that rt-pcr has the sensitivity to detect one positive case in a mixed sample cases [ ]. in this paper we propose non-adaptive and adaptive group testing strategies based on generalized binary splitting (gbs) [ ] where we restrict the group test to the largest group that can be used. the method starts by choosing a group from the population to be tested, performing a test on the combined sample from the entire group and progressively splitting the group further into subgroups. compared to individual testing at % prevalence we save % at % we save % and at % we save % of tests. we analyze the number of times each sample is used and show the method is still efficient if we resort to testing a case individually if the sample is running low. abstract in addition we recommend clinical screening to filter out individuals with symptoms and show this leaves us with a population with lower prevalence. our approach is particularly applicable to vulnerable confined populations such as nursing homes, prisons, military ships and cruise ships. testing capacity for covid- is still too scarce to meet the needs to meet global health needs. conned are at particular risk for rapid contagion. they may include those who reside in facilities such as prisons, ships, military units and nursing homes. the goal of this paper is to increase the capacity to identify asymptomatic carriers of covid- by applying group testing methods. current practice typically involves a one-patient-one-test strategy. recently the potential to detect covid- rna in a mixture of samples from individuals has been validated [ ] using rt-pcr. the method was rst devised in during world war ii to test large groups of us servicemen for syphillis prior to deployment [ ] . now, just as in the wwii era, large scale testing is necessary. covid- is a highly contagious disease that can lead to pneumonia, acute respiratory distress syndrome (ards) and death. clinical symptoms and phyiscal exam features may include fever, cough, shortness of breath, malaise, lethargy, ageusia, anosmia and gastrointestinal (gi) symptoms. besides this diseases potential lethality, it is highly contagious. with the demonstrated success of group testing using rt-pcr for nding sars-cov- rna [ ] , there is a renewed interest in the practical applications of mathematical group testing algorithms. in [ ] a nonadaptive group testing method and practical applications are explored. we describe both non-adaptive and adaptive group testing based on generalized binary splitting (gsb) [ ] . the adaptive approach optimizes group size according to the prevalence. we provide an algorithmic specication for subdividing groups and account for the limited test accuracy and the possibility that the an individual's sample size constrains the number of tests. we explain how prescreening symptomatic cases and separately testing them ca dramatically improves the performance. pre-screening reduces the prevalence in the test groups, this approach is relevant for large scale populations and particularly for conned groups. figure . : (image credit: matthew heidemann) our group testing method consists of rst clinically screening out symptomatic individuals. this will lower the prevalence in the test population. our group testing is especially eective when we can assume the prevalence is uniform over the whole population. therefore, it is especially applicable to conned or cohesive populations. we split the asymptomatic individuals up into groups for which we mix the samples from each individual and test them. a negative result will conrm many negative cases. we subsequently divide groups and test the mixtures of samples for positive results. this we show, conserves the number of tests and, as a result, the time spent testing. using numerical experiments, we also show that our methods can be performed without running out of samples from passing through too many rounds. this application utilizes a primary clinical screening step to ensure that the tested population is composed of asymptomatic covid- (-) and (+) patients. this ensures the lowest prevalence of disease in the population and enhances the ecacy of the method. clinical screening should rst take place in the selected population to screen out as many potential positive patients as possible before administering the test. all patients with history of cough, shortness of breath, nausea, gastrointestinal symptoms, fever, malaise, lethargy, recent contact with positive covid- patients, have physical exam consistent with those ndings should be segregated out of the population. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint clinical screening will decrease the prevalence of covid- carriers in the test population if the probability of being asymptomatic given covid- (+) is less than the proportion of the population that is asymptomatic (regardless of covid- (+) or (-)). we demonstrate this by proving the following claim. claim. the sub-population not showing any symptoms will have a lower proportion of symptomatic carriers when the proportion of people not showing any symptoms in our group is less than the estimated proportion of covid- carriers who are asymptomatic. we can prove this through a couple of applications of bayes' theorem. we refer to the event that an individual does not show symptoms as no symptoms. the event that an individual has symptoms that are signs of covid- is referred to as symptoms regardless of whether they carry the disease. we denote the event of carrying the covid- virus as covid- . then an asymptomatic carrier is referred to as no symptoms and covid- . let p (a) denote the probability of an event a occuring. written in terms of probabilities, screening will help when p (covid- |no symptoms) < p (covid- ). re-writing the left side of the inequality, we get p (covid- |no symptoms) = p (covid- and no symptoms) p (no symptoms) = p (no symptoms|covid- ) p (no symptoms) p (covid- ). . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint therefore it is necessary and sucient for p (no p (no symptoms) < , which is the same as p (no symptoms|covid- ) < p (no symptoms). this is the probability of being asymptomatic given that they have covid- for the population we are testing. if a population has a low prevalence of covid- then it is likely for groups of individuals to not have any positive cases. therefore it is often the case that one test of the mixture of their samples is all that is needed to determine that they are all negative. in this example cases are conrmed either (+) or (-) using tests. some cases are left un-determined for future rounds of testing. otherwise, a positive result on the combined samples indicates that there are some positive cases. we are therefore able to design a strategy to use less tests to determine whether each individual is positive or negative for the disease by testing mixtures of samples from groups. to suciently identify negative cases and positve cases the groups must be large enough to balance nding many negative cases with one test, and locating some positive cases. step one of the group test method is: . a group size is chosen so that the frequency that a group has only (-) cases (gure . ) is roughly equal to the probability we nd at least one (+) case in the group. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint table . : group size specied for the divide and test method. by dtg we mean to apply divide and test, using the minimum of g and the group size for divide and test (e.g. dt will use a group of size if dt uses a group of size ). we study limited group sizes to explore how many tests can be saved depending on the limitations of the instruments. if the test of the group's combined samples is positive, indicating that one of the individuals in the group is positive, apply a routine of repeatedly dividing the group into subgroups applying tests to the subgroups until a positive individual is identied. this is step two of the group test method. . if the rst test is (+), divide the group into two subgroups of equal size. test the combined sample from individuals in one subgroup to determine which halve contains some positive individuals. repeat this step on the subgroup that contains the positive cases. this routine is referred to as binary search. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint when the test result of the group's samples is (+) we split the group into two equally sized subgroups testing one of them to decide if it contains some positive cases or if it consists entirely of negative cases. in the second situation, the second half must contain positive cases. continue the search on the subgroup with positive cases in the same way dividing it into two halves test- . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint ing the mixed samples from one of the half-subgroups. repeating this step we are able to nd one positive case. along the way many groups of several individual are likely to be conrmed negative with a relatively small number of tests. any subgroup that was not tested retains its undetermined status and is returned to the general set of samples to be conrmed positive or negative. . repeat the procedure starting with . on the individuals in the population for which whether they carry the disease has yet to be determined. in this paper we consider group testing methods that follow two dierent interpretations of step in the procedure above: methods with a xed group size and methods where the group size changes based on the results of previous tests. each type of method uses a slightly dierent denition of prevalence. prevalence is dened as the probability p an individual in the population has covid- . for each level of prevalence we specify a xed number of individuals to test their combined samples, performing binary search if it is positive. the xed group size method we analyze in this paper is divide and test (dt). we also consider dorfman's method as a method to compare the methods against, as well as a simpler alternative that only ever uses an individuals samples for a maximum of two tets. prevalence is dened as the count of positive cases in the test population. as testing is carried out, the conrmed positive and negative cases are set aside are both removed from the undetermined test population. therefore, the population and the prevalence changes during the testing process. the group size depends on both the population and the prevalence. the adaptive group testing method presented in this paper is generalized binary splitting (gbs). in addition to studying these two classes of methods, we make modications to the methods to take into account limitations of the devices and techniques used to test samples for covid- rna. specically, we study methods with limited group sizes. these are dt and gbs with maximum group g (dtg and gbsg). they are dened so that any time either dt or gbs species a group size over the capped limit g we take the group size to be g. to cover a wide range of limits of detection we consider groups of sizes , , , and . non-adaptive group testing method: divide and test (dt) this method is can be thought of as a xed group size version of the generalized binary splitting method [ ] . . if p > . then test each member of the population individually. otherwise, let α = log p − . select a group of individuals g with |g| = α and apply one test to g. if it is negative, then we conclude that the result of each case in g is negative. . if g is positive we use binary search to nd exactly one case that we can deduce is positive. . repeat the method starting with step . on the yet to be conrmed portion of the population. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint adaptive testing method: hwang's generalized binary splitting (gbs) the group testing methods suggested in this paper are based on hwang's generalized binary splitting method. in [ ] gsb is designed to nd up to d (+) cases in a population containing n individuals. it is described as follows: take g a group of cases such that |g| = α and apply one test to g. if it is negative, then we conclude that the result of each case in g is negative. . if g is positive we use binary search to nd exactly one case that we can deduce is positive. . set the population to the set of individuals not determined (+) or (-). we set n to be the new population size. if we have found a positive case in the last two steps, we take d − to be the new number of positives in the un-tested population. this method is extended to populations with a random number of (+) cases by setting the upper limit on positive cases according a chosen condence level (i.e. the probability that the number of (+) exceeds this is very small). in probability terms, if the number of positive cases d is generated acccording to a probability distribution, and we assume probability c that will identify every positive case, then let d c be such that p (d ≤ d c ) < c. generalized binary splitting is then applied to nd at most d c positive cases in the population. the setting of hwang's paper is group testing for general purposes, including identifying defective parts or products in addition to determining individuals with a disease. it is an ethical requirement to determine if each person is (+) or (-) if they are tested for covid- . therefore gsb is appplied for an upper bound d c of positive cases at a xed level of condence c. if exactly d c positive cases are found, then there with non-zero probability there are some cases that have not been determined. otherwise if < d c positives are identied, then we are certain we have found them all and it will also happen that a positive or negative conrmation was given to each individual by the end of the testing process. in the case where there could be more positive cases, we repeat gsb with the same level of condence c on the remaining population. rather than considering the application of a level of condence as an idiosyncracy of the method, it is actually a fundamental property of identifying asymptomatic covid- carriers. asymptomatic positives cannot be identied without testing them, we can only pick an upper bound on the cases with a high level of certainty. it might seem preferable to then choose a method that instead prescribes a group-size for each level of prevalence, such as dorfman's method or divide and test, but for those methods the possibility that we have misjudged the prevalence still needs to be factored in! condence bounds on group testing methods we will apply dt and gbs with groups capped at , , , and samples using two dierent levels of condence. • gbsg with d . (i.e. p (d ≤ d . ) = . ). we repeat gbsg at this level of condence if there are undetermined cases remaining. • we apply dtg with the group size log( p − ) . • gbsg with d . . for a population generated by a prevalence level p, this will perform worse on average than the application with d . , but level of eciency theoretically guarenteed for gsb [ ] will hold with % condence. therefore, we can be more condent of the algorithms performance. • for populations of size n generated with prevalence p, we apply dtg at the actual prevalence level of the population with % condence. that is, we apply dtg with the group size (with ceiling g) corresponding to p . = d. n . . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint for small to medium sized populations, the % condence upper bound is very dierent from the mean. the dierent condence levels are very close for large n for a constant probability of having covid- . how condent we are needs to be taken into account in this scenario as well because assuming a uniform probability of having the disease is likely to be too broad of an assumption. there are many dierent factors that lead to sub-populations having distinct frequencies of carrying covid- and the certainty about the prevalence varies as well. dorfman's method [ ] we compare the results from dt and gbs methods to dorfman's method. dorfman's method is as follows: . for a the optimal group size b (dened below), apply one test to a group of b cases. if the result is negative, then conclude that every case in the group is negative. if the test result is negative then one test was used for b cases. if it is positive, then b+ tests were used. the quantity b is chosen to minimize the expected number of tests used to determine the result of one individual case, we will use this formulat to compute the expected proportion of tests saved for several dierent levels of prevalence to compare to the successor binary search based methods we choose study. to evaluate and analyze the performance we assume that the populations are sequences of randomly generated i.i.d. variables representing cases with the probability of having the disease p. the population is then modeled by probability distribution with the following parameters. • n -the size of the population/number of cases • pthe probability that a case is positive. we refer to this as the prevalence. • a case is then a bernoulli random variable that is positive with probability p and negative with probability − p. • the number of positive cases is then a binomial random variable with n samples and probability p of a success, we write this as binomial(n, p). in the section we analyze the performance of the group testing methods at a selection of prevalences for populations of size and . in section we analyze the performance at the . condence upper bound. this can be thought of as overestimating the prevalence by a large enough amount so that we are % sure that the actual number of positive cases falls at or below this level. in section we analyze the number of rounds of testing each sample goes through. our results suggest that not only do group testing methods save tests and time, but they can be done within the realistically expected amount of usage for each test. an analysis of the histograms of the number of tests per case from which we compute the average performances is in the numerical results section after the bibliography (section ). please visit https://github.com/cmentus/group-testing/ to nd the jupyter notebook for all numerical experiments. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint performance of group testing methods at dierent prevalences for our performance analysis, we sample populations of sizes n = , at prevelance levels p = . , . , . , . , . , . , . , . , . , and . . we present the mean of samples and present them in the table below. for dtg results, some of the entries are left empty. this is because the xed group size is less than the capped group size so it would be redundant to list it, and for the performance refer to the nearest entry to the left. we do not do this for gbs because the group size is adaptive and there is nothing restricting it from becoming small. in each table we list the percentage of tests saved from employing the group test methods. . we analyze the eect of picking the prescribed method for a conservatively large estimate on the prevalence. a larger estimate on the prevalence will still take advantage of the frequent occurence of many consecutive negative cases. the overestimate we use corresponds to a probability of having less positive cases of . . we sample the populations at least times and take the mean of the proportion of tests saved over all samples. specically for dtg applied to populations of and we generated samples. for gsbg we applied to populations of size we sampled times except for gsb . for gsbg applied to populations of size we sampled times except for gsb we sampled times. the dierences in number of samples . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint are due to the overall computational expensiveness of simulating gsb and dt. the mean savings of each numerical experiment are presented in the following and various prevalences at the . condence level d . . note that d . is closer to d . for higher populations (that is d. d. is closer to ). therefore the performance is closer to the results depicted in the previous section. although demonstrated to be more ecient in test usage, generalized binary splitting requires some samples to be used at least as many times as the logarithm of initial group size. for maximum group sizes of and this implies that positive cases will be tested at least or times. as is demonstrated by gures . and . it is possible for tests to be used more than twice as many times. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint figure . : for gbs we sample a population of size , and record the number of times each case is tested. note that for prevalence of p = . % a case at most times in the population. in gure . where we perform the same experiment we nd cases that are tested up to times. we apply gbs to nd at most d . (see section ??) we see in gure . that the proportion of cases that are tested many times (more than ) is very low. this is evidence that testing the cases indivually when we are running low (if we are limited to uses) adds up to less than % extra tests. if we are able to test a sample more than this many times, individually testing when we are about to run out eects the eciency negligibly. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint we plot the histograms of the number of times postive results and negative results are tested given that they are tested more than once. interestingly, sometimes the number of times negative cases are tested seems to have a larger maximum. gaining knowledge of covid positive status in asymptomatic carriers is of prime importance in the ght to contain and eliminate the disease. the group testing strategy will generate certainty and a margin of safety in conned populations and may be useful in detection of disease burden in geographically dispersed populations as a mode of surveillance. a key factor in our strategy is the two phase approach that we propose. clinical screening of symptomatic patients cuts down the prevalence of covid- in the chosen asymptomatic test populations. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint rapid, large scale testing is urgently needed for naval ships and military bases. a recent outbreak upon the uss roosevelt has brought this concern to the forefront of military proporities [ ] . recently italian prisoners have rioted rioting due to lack of testing [ ] . prisoners have been released from nyc prisons due to concern for spread of coronavirus [ ] . nursing homes have been sites of extensive outbreaks [ ] . screening an asymptomatic population is challenging but important. sensitivity of tests is paramount but also utilization of resources must be ecient. this study proposes a statistically valid mathematical model to optimize number of tests performed on chosen populations. the future direction of our work will require clinical validation with real world application of this group testing strategy. the clinical screening of symptomatic patients out of our population is helpful but it will also make detecting virus in asymptomatic people potentially tougher because of the chosen viral load. current rt-pcr methods are standard but have a concerning false negative rate in symptomatic patients [ ] . this may be further exacerbated in asymptomatic patients. future studies may explore or consider the use of more sensitive techniques including ddpcr and addition of other sampling techniques such as fecal specimens and perhaps advanced imaging such as chest ct scan. based on the above evidence it is clear that a comprehensive strategy is necessary to test all asymptomatic people. this strategy will uncover the hidden silent carriers of disease. group testing has the chance for saving tests, while giving an exit to revert to individual testing if there are more cases than estimated. these strategies are not necessarily the theoretical optimums. nevertheless, by our calculation and numerical simulations they have the power to cut down the number of tests used. the group testing method is applicable to conned populations from both a clinical and mathematical stand point. we can clinically screen conned groups to decrease the prevalence in a predictable way. this method allows each patient in the population to get a test result. we explore adaptive and non-adaptive strategies for group testing for covid- , therefore we add adaptive and binary search based non-adaptive strategies. both perform well even when we restrict the size of the group based on the sensitivity of rt-pcr. we test the performance of two algorithms: divide and test and generalized binary splitting. for populations of size and with each case being positive independent of one another with probability p, we nd that both methods save many tests. in fact, even when we restrict the size of the groups they make substantial savings. for example at prevalence . and group sizes capped at , both dt and gsb are capable of outperforming dorfman's method, that requires a group size of for optimal performance. for a population of and condence level . , the dt and gbs also have a similar performance to dorfman's method at . where dorfman's method is chosen as if we knew the exact prevalence. we nd that dt outperforms gsb on average even though gsb in theory uses close to optimal number of tests for a known xed number of (+) cases (bounded above by #tests − + information lower bound). this indicates that non-adaptive binary search methods have the potential to save many tests. it is possible that gsb is more generally applicable to populations that cannot be thought of as being generated since samples can be divided frozen and stored for continuous use we mathematically analyze how many divisions we have to use for each sample. we nd that testing individually when the sample is about to run out does not subtract substantially from the savings. we demonstrate that for a group size of the generalized binary search on cases uses the same sample more than times for < % of all cases. therefore, applying a test individually to samples when they are running low is a viable way to save many tests while not depleting material from one person's sample. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint for both gbs and dt. the maximum group size is . for gsb we sampled populations, for dt we sampled populations. note that the spread of the dt algorithm is much wider and has many cases that need a much lower number of tests than gsb. the small bars in gsb are caused by the % chance of not identifying all of the cases in one run and so repeating the process on the rest of the population. . cc-by-nc-nd . international license it is made available under a author/funder, who has granted medrxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) the copyright holder for this preprint . https://doi.org/ . / . . . doi: medrxiv preprint correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases the detection of defective members of large populations a method for detecting all defective members in a population by group testing evaluation of group testing for sars-cov- rna. medrxiv italian coronavirus prison riot six dead coronavirus new york update: mayor announces immediate release of prisoners convicted for non-violent oenses all residents of new jersey nursing home presumed positive for coronavirus evaluation of covid- rt-qpcr test in multi-sample pools. medrxiv we thank martin douglas for interesting and useful discussions about group testing methods using binary search. we are also grateful to matthew heidemann, blake elias, kevin schallert, gary chizever, michael wells, olga buchel and patrick o'neill for contributing ideas and useful feedback.we are indebted to yaneer bar-yam for important recommendations that greatly improved the ideas, clarity and organization of the paper. we thank matthew heidemann for the diagram at the beginning of the paper that skillfully explains our process. thank you to david f. schaeer, marcel dvorak, julia naso and marthe kenny charles for discussions about the limit of detection for sars-cov- rna by rt-pcr and recommendations that lead us to simulate group tests with maximum sizes , and .we thank endcoronavirus.org and the new england complexity institute for giving us the platform to meet and collaborate as a team and meet great people with diverse backgrounds and skillsets united in the cause to ght the current pandemic. key: cord- - dzkgt w authors: carpenter, christopher r.; mudd, philip; west, colin p.; wilber, erin; wilber, scott t. title: diagnosing covid‐ in the emergency department: a scoping review of clinical exam, labs, imaging accuracy and biases date: - - journal: acad emerg med doi: . /acem. sha: doc_id: cord_uid: dzkgt w in december a novel viral respiratory pathogen emerged in china, ultimately named severe acute respiratory syndrome coronavirus (sars‐co‐v‐ ) with the clinical illness dubbed coronavirus disease (covid‐ ). covid‐ became a global pandemic in early forcing governments worldwide to enact social isolation policies with dire economic ramifications. emergency departments (ed) encountered decreased patient volumes before some in seattle, new york city, new orleans, and detroit experienced waves of covid‐ patients mixed with asymptomatic patients or those concerned about potential exposures. diagnosing covid‐ was hampered by inadequate supplies of reagents and kits, which was compounded by clinical and radiographic features that overlap with numerous seasonal viral respiratory infections. dr. christopher r. carpenter (orcid id : - - - ) article type : evidence-based diagnostics in december a novel viral respiratory pathogen emerged in china, ultimately named severe acute respiratory syndrome coronavirus (sars-co-v- ) with the clinical illness dubbed coronavirus disease . covid- became a global pandemic in early forcing governments worldwide to enact social isolation policies with dire economic ramifications. emergency departments (ed) encountered decreased patient volumes before some in seattle, new york city, new orleans, and detroit experienced waves of covid- patients mixed with asymptomatic patients or those concerned about potential exposures. diagnosing was hampered by inadequate supplies of reagents and kits, which was compounded by clinical and radiographic features that overlap with numerous seasonal viral respiratory infections. the united states (us) food and drug administration (fda) issued an emergency use authorization on february , to enable centers for disease control (cdc)-qualified laboratories to perform covid- testing. as of june , the fda provided emergency use authorization for commercial assays, including polymerase chain reaction tests and immunoglobulin assays. early real-time reverse transcription polymerase chain reaction (rrt-pcr) tests had false-negative ( -sensitivity) rates as high as %. as waves of covid- patients present to ed's in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of covid- diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared this article is protected by copyright. all rights reserved decision-making choices ( figure ). this review provides a narrative overview of published research with the primary objective to describe the frequency, causes, and implications of falsenegative rrt-pcr for diagnosis and surveillance. secondary objectives include describing potential diagnostic biases in current rapid cycle covid- diagnostic research reports, while providing recommendations for clinicians for interpreting results with knowledge of these design and reporting limitations. a final objective is to add context to rrt-pcr ordering and interpretation by understanding the diagnostic accuracy and additive value of history, physical exam, routine hematology and chemistry tests, computed tomography (ct), and serology for covid- immunoglobulins. this is a scoping review that adheres to prisma-scr reporting recommendations. the published literature was searched using strategies created by a medical librarian for covid - and diagnostic accuracy. the search was implemented in pubmed -and embase with a date limit from january , until present with an english language limit. the search strategy used a combination of standardized terms and key words, including but not limited to (covid- or novel coronavirus or sars-cov- ) and (diagnosis or polymerase chain reaction or serology or crispr-cas or sensitivity/specificity) (appendix). the testing search was based on cheng et al., adding to this prior publication by incorporating clinical exam, imaging, and serology into the synthesis of current diagnostic research. the searches were run on april and may , . one author (crc) reviewed the title and abstracts for all identified citations. other authors reviewed the manuscripts identified and added pertinent references. original research studies describing the frequency of history/physical exam findings or diagnostic accuracy (sensitivity, specificity, likelihood ratios) of history/physical exam, labs or imaging for covid- were included. exclusion criteria included non-english, animal research, study protocols, prevention, pathophysiology, lab processing, or policy manuscripts. two authors (crc, sw) abstracted this article is protected by copyright. all rights reserved diagnostic accuracy data and reported adherence to the standards for reporting of diagnostic accuracy (stard) guidelines. compliance with stard was used as a measure of research quality. the same two authors synthesized the results into summary conclusions. a total of , citations were screened (figure ) . none of the studies cite or adhere completely to either the standards for reporting of diagnostic accuracy (stard) or the updated reporting framework for history and physical examination. many of these early publications are letters or case reports with uncertain editorial rigor judging by the turnaround time from initial submission to publication. many studies rely upon rrt-pcr as the criterion standard for covid- , but few contemplate the possibility or likelihood of false-negative or false-positive rrt-pcr results. none of the studies discuss the possibility of various diagnostic biases (spectrum, incorporation, partial verification, differential verification, or imperfect gold standard), nor the potential skew of these biases in observed estimates of sensitivity or specificity. fever is the most commonly reported finding in %- % of covid- cases, - but fever alone does not distinguish this virus from other infections. therefore, absence of fever is inadequate for travel screening and likely for other decision thresholds such as whether ed staff can work shifts. hyposmia (diminished sense of smell) and hypogeusia (diminished taste) have also emerged as covid- symptoms. both hyposmia (positive likelihood ratio [lr+] . , negative likelihood ratio [lr-] . ) and hypogeusia (lr+ . , lr- . ) are better to rule-in than to rule-out covid- , but neither may be fully adequate for either purpose. although multiple covid- studies report acute smell or taste disorders as a distinguishing symptom, no other studies report diagnostic accuracy or sufficient details to compute likelihood ratios for hyposmia or hypogeusia. [ ] [ ] [ ] [ ] [ ] [ ] loss of smell is not necessarily associated with nasal obstruction or rhinorrhea. in one case-control study, new onset smell and taste disorders are more common with covid- than with influenza ( % vs. %). consequently, influenza decision this article is protected by copyright. all rights reserved aids or diagnostic algorithms do not incorporate hyposmia or hypogeusia. , anosmia, which may be the only complaint in some covid patients, is noted by %- % of covid- patients and is the initial symptom in %. [ ] [ ] [ ] additionally, % recall an acute onset of symptoms associated with taste and smell. anosmia is more common in women and may persist for two weeks. predictive models incorporating a change in taste or smell to distinguish covid- from viral mimics appear most sensitive. cough is only present in % patients. , neither cough, dyspnea, sore throat, nor fatigue distinguish covid- from other illnesses, but current studies do not quantify accuracy. , lymphopenia occurs in over % of covid- patients. , , neutrophil to lymphocyte and platelet to lymphocyte ratios do not distinguish elevated ldh is also frequently described. , , , none of these lab findings are commonly utilized in the diagnosis of influenza, but their prevalence and accuracy to distinguish covid- from other viral mimics merit further evaluation. , elevated prothrombin time (pt), ferritin, d-dimer or il- are associated with severe covid- . - existing studies do not report sensitivity or specificity of these labs. most studies use rrt-pcr as the criterion standard for diagnosing covid- . this test as used in current assays provides a qualitative detection of nucleic acid from the sars-cov- virus. this article is protected by copyright. all rights reserved capacity and time-to-diagnosis in many settings, , prompting laboratory researchers to explore the concept of specimen pooling in which multiple patients' samples are tested simultaneously with further individual testing only if the pooled specimen is positive. the optimal pool specimen when covid- community prevalence is less than % is four patients, which improves testing efficiency by %. there is limited information on the diagnostic accuracy of the rrt-pcr test. although an increasing number of studies provide head-to-head comparisons, - systematic reviews provide little quantitative accuracy data and no meta-analysis or assessment of individual study quality. no rrt-pcr test is clearly superior to others in terms of diagnostic accuracy, but some provide faster results and commercial tests may be less sensitive than hospital-developed tests. , it is known, however, that false negatives are frequent, so current recommendations advise incorporating patient's exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) ct results into real-time determination of covid- status. repeat or even serial rrt-pcr testing is required to confidently exclude covid- . multiple studies report initially negative rrt-pcr results becoming positive with subsequent rrt-pcr tests in the following days or weeks. , others report hospitalized covid- patients with initially positive rrt-pcr tests becoming negative prior to discharge with subsequent readmission for positive tests in the ensuing days. ren et al. noted rrt-pcr sensitivity with one test was % and increased to % with a second test. a strategy of three negative rrt-pcr results is superior to two negative rrt-pcr followed by bronchoalveolar lavage. repeating initially negative rrt-pcr up to five times increases sensitivity to %. covid- patients identified on first rrt-pcr often have more severe disease associated with higher mortality, likely due to higher quantities of virus in those individuals. older patients are more likely to remain rrt-pcr positive for an extended period, but whether this means they are contagious has yet to be determined. potential reasons for false negative rrt-pcr results are summarized in table . - emergency physicians will rely upon the rrt-pcr assay selected by their hospital laboratory, which may this article is protected by copyright. all rights reserved balance the limit of detection and sensitivity against turn-around-time, complexity, cost, workflow, availability of reagents and kits, specimen type, and lab personnel risk handling those specimens. patients under investigation for covid- who ultimately rule-out are rarely reported in currently available studies, so specificity and false positives are generally not reported in the literature. however, false positives appear rare. in cdc testing, there was no significant cross-reactivity with other common respiratory viruses or seasonal coronaviruses. contamination of the specimen or reagents used in the rrt-pcr is therefore the main mechanism for false positives results. the cdc recommends protocols to prevent and detect potential contamination in order to minimize false positive results. , nasopharyngeal (np) samples are most commonly obtained and studied, but oropharyngeal (op), saliva, sputum, stool, blood, and/or urine specimens can also be evaluated. obtaining np samples requires time and appropriate training, increases exposure to staff secondary to coughing and gagging, and is uncomfortable for patients. methodologically, few rrt-pcr accuracy studies describe how research or clinical staff were trained to collect np specimens, so fidelity and reproducibility remain in question. wang et al provide videos describing np and op collection methods, note poor agreement between the two sampling methods (kappa = . ), and a higher yield with np. saliva can be collected outside the hospital without training, perhaps as part of a telemedicine evaluation for covid- . , one small italian study indicated that saliva specimens demonstrate detectable sars-co-v- virus and the limit of detection is not affected by patient age. sputum samples exhibit higher viral load than op sites. - however, as already noted many patients under investigation lack a cough and fewer still have sputum production. expectoration of sputum may also expose health care workers collecting the sample to aerosols that would not have been generated without a sample collection attempt. furthermore, a bayesian analysis of prevalence-dependent positive and negative predictive values by ghosal and sinha demonstrates that even when the covid- prevalence is high ( %) the positive predictive value (ppv) of sputum rrt-pcr is only . % and the negative predictive value (npv) is %. ppv and npv vary with disease prevalence. specifically, ppv increases with higher disease prevalence and npv increases with lower disease accepted article prevalence making extrapolation to clinical populations challenging if the study prevalence does not match the patients to whom the test is applied. for this reason, diagnosticians prefer likelihood ratios. blood and urine are inadequate specimens for rrt-pcr as most patients do not exhibit virus in these body fluid compartments. in addition to the cdc developed rrt-pcr test, manufacturers have developed molecular tests that target different portions of the sars-cov- viral genome and run on rapid testing platforms. for example, reverse transcription loop mediated isothermal amplification (rt-lamp) can detect sars-cov- within minutes. [ ] [ ] [ ] other laboratories are exploring highthroughput sequencing as for inconclusive fluorescence quantitative polymerase chain reaction specimens as a rapid mediator for the presence or absence of sars-cov- . the diagnostic accuracy of these tests is similarly not reported, but these tests have not shown cross-reactivity to other respiratory viruses and bacteria. on may , , the us fda issued an eua for a sars-cov- antigen test. this test detects sars-co-v or savs-cov- nucleocapsid protein antigens in np or nasal specimens using a lateral flow immunofluorescent sandwich assay. this assay is run on a point-of-care device in laboratories that are able to perform high, moderate, or waived complexity tests, and can provide tests within minutes. while the diagnostic accuracy of this test is not available at this time, the fda reports high specificity but sensitivity that is less than rrt-pcr. the fda and the manufacturer recommend negative results "be treated as presumptive and confirmed with a molecular assay, if necessary for patient management". chest x-ray chest x-ray is essential to evaluate for covid- mimics such as pneumonia, pleural effusion, or pulmonary edema. typical covid- findings include hazy opacities that are often bilateral and peripheral. with the exception of one outlier, the reported sensitivity of single view chest xray for covid- ranges from % to %. this article is protected by copyright. all rights reserved accuracy of chest x-ray early in the covid- pandemic. currently available covid- chest x-ray studies do not report specificity or reliability. computed tomography (ct) findings suggesting covid- include ground glass opacity (often bilateral) and peripheral predominant lesions without mediastinal adenopathy or pleural effusions, though these findings represent non-specific manifestations of acute lung injury associated with numerous infectious and non-infectious etiologies. , incidental findings consistent with covid- are observed on ct of the chest in patients without respiratory symptoms. multiple studies report covid- identified by ct after one or more negative rrt-pcr tests. [ ] [ ] [ ] [ ] when the covid- epidemic erupted in china, clinicians lacked access to rrt-pcr kits and then as rrt-pcr became available, low rrt-pcr sensitivity reinforced belief in the additive value of ct for many. these observations and scenarios prompted some to advocate for ct as a first-line supplement to the diagnostic evaluation for covid- , combining rrt-pcr with ct. , if ct alone or in combination with rrt-pcr reduced false-negative rates, the positive public health implications for case identification and control of disease transmission could be substantial. however, these benefits must be balanced against the cost of ct, medical radiation dangers, or practical limitations in busy hospitals with hourly trauma and stroke arrivals and potentially time-dependent emergencies juxtaposed against advised ct shutdowns for covid- cleaning requiring or more minutes. , this cleaning time would also delay access to ct for every patient in the ed, thereby prolonging potential exposure to those in the ed to other patients with covid- . some propose covid- patients wear n- masks and plastic bags over their heads to eliminate or reduce these cleaning times. pragmatically, among those detected by ct no defined benefit, such as reduced mortality or faster resolution of covid- symptoms has been described. in addition, radiologists' sensitivity for diagnosing covid- by ct findings ranges from % to % with specificity from % to %. preliminary artificial intelligence studies report radiologists' sensitivity improves from % to % and specificity this article is protected by copyright. all rights reserved from % to % with this artificial intelligence image augmentation, while others hypothesize that the most valuable role for this technology may be quantify the proportion of lung affected by covid- . despite these issues, multiple studies highlight that the sensitivity of ct is substantially higher than that of the first rrt-pcr, while combining ct and rrt-pcr provides maximal sensitivity (~ %). , , theoretically, the sensitivity of ct would decline when testing populations outside of an epidemic (low prevalence rates), while specificity would be reduced when mimics like influenza are more common. , the british society of thoracic imaging recommends against ct when rrt-pcr is positive, but to consider ct when the initial rrt-pcr is negative in order to identify co-existing disease or potential covid- complications such as pulmonary embolism. tavare et al. developed a single-center protocol to prioritize inpatient ct decision-making for initial covid- negative rrt-pcr patients based upon initial clinical suspicion and chest x-ray findings. the us fda has also issued an eua for the development of sars-cov- antibody tests. these antibody tests detect circulating igm, igg or both that are reactive against sars-cov- virus using lateral flow assays (lfa) or enzyme-linked immunosorbent assay (elisa). however, unlike rrt-pcr tests, there is data regarding the diagnostic accuracy of these serologic tests. whitman and colleagues evaluated lfa and elisa tests for sars-cov antibodies. they used plasma or serum samples from patients with symptomatic, rrt-pcr-confirmed positive patients as the gold standard for disease, and pre-covid- specimens from the american red cross as negative controls. sensitivity of both igm and igg varied by days since symptoms onset, with sensitivities for either igm or igg at > days ranging from % to %. specificity for either igm or igg also varied by test, ranging from % to %. similarly, benavid and colleagues used a commercially available lfa test to perform a seroprevalence study in santa clara county, california and reported a sensitivity of % and a specificity of . %. true positive serologic tests for sars-cov- antibodies indicate prior infection with sars-cov and the development of an immune response. this may be helpful in identifying those who this article is protected by copyright. all rights reserved were asymptomatic or minimally symptomatic at the time of infection, as well as those who were unable to receive a molecular test when symptomatic. while some experts believe that the presence of igm or igg reactive against sars-cov- will confer immunity, this has not yet been shown. if the presence of antibodies on a true positive serologic test does confer immunity, the titer of antibodies required to confer immunity remains unknown, as does the duration of that immunity. false positive results may be due to cross-reactivity with other coronavirus strains which cause the common cold. the fda recommends the following information be included in the instructions for use and patient test reports: knowledge of the diagnostic characteristics, including sensitivity, specificity, and likelihood ratios of tests for sars-cov , the virus that causes covid- , is important to understand how to best apply these tests for patient care and disease surveillance. because this novel virus emerged as a significant pathogen in humans only a few months ago, diagnostic tests have been developed rapidly under fda euas in the us. consequently, we have less information about the diagnostic accuracy of these tests than we would under normal circumstances, but we do know that both false negatives and false positives may occur. an illustration of the false positive and false negative rate as a function of prevalence for two serologic tests for sars-cov- is provided in figure . false negative tests commonly occur with rrt-pcr tests for several reasons (table ). there are a number of potential implications of a false negative rrt-pcr test for sars-cov- . from the this article is protected by copyright. all rights reserved patient's standpoint, a patient with a negative test may lead to an assumption that they are not infected and subsequently diminished adherence to instructions to isolate and take other infection control measures, increasing the risk of infecting others. in the hospital setting, precautions may be relaxed in the presence of a negative test, increasing the risk of transmission to healthcare workers and other patients. in patients with moderate or high pretest probability of disease, a negative test may not reduce the posttest probability of disease below a level where precautions to prevent spread of disease become less necessary. in patients with a low pretest probability of disease, the likelihood of disease given a negative test will be low. however, even low individual likelihoods of disease can cumulatively contribute to substantial risk of outbreaks across larger groups for more contagious infectious diseases, such as covid- . false negative tests are also a consideration with serological testing. however, since these tests should generally not be used to assess an active infection, the risks of a false negative are less significant for disease transmission. a false negative serological test would incorrectly classify a person as not having an immune response to sars-cov- . if "immunity passports" became a reality, this could incorrectly and adversely affect a person's ability to travel or work. the increased sensitivity of ct for covid- might provide a net public health benefit if falsenegative rrt-pcr patients with higher clinical suspicion were accurately identified during the initial ed evaluation. mathematical models provide a theoretical basis for the concept that increasing diagnostic efficiencies (for example, by improving sensitivity with addition of ct) will decrease the risk of covid- transmission. pending the availability of rapid, reliable, and sufficiently accurate covid- tests in ed settings, the identify-isolate-inform ( i) approach to decrease spread might be improved with more liberal ct use. one italian hospital reported liberal ct screening for respiratory patients with possible false-negative chest x-ray results, but thus far has not reported on the positive or negative impact of that approach on individual patient care or public health. in the early stages of covid- , as many as % of patients this article is protected by copyright. all rights reserved with respiratory symptoms may have normal imaging. radiologists have also noted that the quality of early ct accuracy studies is questionable because the rrt-pcr assay used as the criterion standard is either not described or the accuracy of that standard undefined. in addition, ct findings are not pathognomonic for covid- as influenza, cytomegalovirus, and atypical pneumonia have similar findings. , as a consequence of these ct limitations in addition to the costs, radiation exposure, and downstream effect on other patients in terms of diagnostic delays and cross-contamination, multiple groups, including the fleischner society and the british society of thoracic imaging discourage ct as a routine screening approach. , nonetheless, ct likely plays a role when rrt-pcr tests are either too inaccurate, unavailable or suffer unacceptably slow turnaround times in patients with higher levels of covid- concern based on exposure history or other clinical findings. the public health benefits of a more liberal ct screening approach from the ed merit additional research. false positive tests associated with rrt-pcr for sars-cov are believed to be rare and would most commonly occur due to contamination. false positive tests may occur more commonly with serological tests, which have reported specificities ranging from - %. the positive predictive value is a function of both test sensitivity and specificity as well as the pretest probability of disease. this implies that positive test results are more likely to represent false positive results when the pretest probability of disease is low. the instability of positive predictive value is especially important as we apply imperfect diagnostic tests to low risk patient populations, such as asymptomatic patients in low prevalence communities. as an example, the antibody test used in a california community study has a reported sensitivity of this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved society with a false positive serologic test for sars-cov antibodies. patients may assume that they have developed immunity to covid- , leading to a reduction in risk-mitigating activities such as physical distancing. healthcare workers with false positive tests may similarly reduce their vigilance and use of precautions due to an incorrect assumption that they have immunity. this could place these individuals and their close contacts at increased risk of contracting covid- . multiple forms of diagnostic bias exist and each skew measured estimates of sensitivity and specificity in different directions. incorporation bias is possible when the criterion standard includes the index test (for example, rrt-pcr) in ultimately determining whether the disease is present or absent. incorporation bias increases measured sensitivity and specificity. this is pertinent to covid- because most early studies incorporate rrt-pcr into the criterion standard. , differential verification bias is possible when patients with a positive or concerning index test (e.g., ct findings associated with covid- ) are more likely to receive an immediate invasive gold standard such as repeat rrt-pcr testing or bronchoalveolar lavage specimens. , differential verification bias raises specificity in diseases that resolve spontaneously or lowers specificity for diseases that only become detectable during follow-up. imperfect gold standard bias is possible when the standard used to classify the presence or absence of disease misclassifies some patients. imperfect gold standard bias raises observed specificity if errors on the index test and "copper standard" are correlated with true disease status and lowers observed specificity if errors on the index test and the copper standard are independent. this is pertinent to covid- because no well-accepted criterion standard yet exists. a better criterion standard for covid- will certainly emerge and we propose some ideas in table . , temporal bias reflects variation in observed accuracy based on the period of time or stage of disease when index testing occurred. in covid- viral shedding is highest in the early stages of disease with the highest positive rates noted within the first week. , spectrum bias is possible when the spectrum of disease severity differs between the study and clinical application (example, critically ill covid- patients in the intensive care unit versus this article is protected by copyright. all rights reserved asymptomatic patients evaluated in ambulatory clinics). spectrum bias skews observed sensitivity upwards in sicker populations and skews specificity upward in healthier patients. , spectrum bias is worth considering when applying diagnostic accuracy results from patients with varying severity of illness to dissimilar populations. for example, among covid- patients from cruise ships evaluated with ct, those with symptoms more commonly had covid- ct findings than those without symptoms ( % vs. %). the rapidly expanding evidence base around covid- diagnostic accuracy for clinical exam, routine labs, imaging, and advanced testing provides important lessons moving forward for clinicians, researchers, and journal reviewers. covid- researchers need to contemplate myriad biases carefully in reporting observed diagnostic accuracy. if a bias is likely and the anticipated skew in observed sensitivity or specificity is upwards and the observed accuracy is already too low, further studies of that diagnostic test may not be warranted. the stard reporting guidelines provide manuscript protocols to ensure adequate description of methods and results so that diagnostic biases are easier to identify. , unfortunately, none of the early covid- diagnostic research cites stard or adheres to these reporting standards, which is not uncommon in emergency medicine. , clinical decision aids consist of three or more findings on history, physical exam, routine labs, or imaging that, in combination, more accurately identify patients at lower or higher risk of a disease or outcome. diagnostic and prognostic decision aids are commonly developed and employed in emergency medicine to reduce practice variability without compromising patient outcomes. efforts to develop covid- decision aids might include something like the pulmonary embolism rule-out criteria (perc) rule to identify subsets of ed patients at lower risk of covid- pending definitive testing. alternatively, a decision aid might serve prognostic purposes to identify covid- patients more likely to decompensate in response to the viral infection. [ ] [ ] [ ] [ ] when decision aid investigators attempt to derive and validate these this article is protected by copyright. all rights reserved instruments, higher quality emergency medicine research quantifying accuracy and reliability (or the elements of history, physical exam, labs, and imaging that become predictor variables of the decision aid) will be required as the basis for selecting variables likely to improve model performance. most laboratory tests are quantitative rather than qualitative, including covid- rrt-pcr and serological assays. when sensitivity and specificity are reported, the quantitative labs have been dichotomized at some level. another approach to evaluating diagnostic accuracy for quantitative data is interval likelihood ratios (ilr). one advantage of ilr's is that indeterminant results are more readily interpreted. as covid- diagnosticians identify the rrt-pcr and serological tests that best balance availability, accuracy, reliability, and cost, reporting ilr's could provide added value for clinicians. ultimately, ed physicians' clinical impressions concerning the presence or absence of covid- are communicated to patients and families -usually without access to definitive testing. patient communication tools to convey the basics of covid- personal protection and infection prevention exist, , but shared decision-making instruments that communicate the uncertainties of clinical exam, imaging, and even rrt-pcr do not exist. figure provides one example of a cates plot that could be used to communicate the accuracy limitations of rrt-pcr based on current evidence. actual shared decision-making instruments will require scientific investigation using accepted methodology before widespread implementation. this scoping review has several limitations. the pace of publications around covid- and diagnostics in the first half of has been astonishing. at best, this review will serve as a snapshot in time, although hopefully illuminating issues that require higher methodological standards and peer-review attention moving forward. due to time constraints the search strategy was limited to english language and published research. more research undoubtedly exists in the gray literature. since earlier systematic reviews exploring aspects of covid- this article is protected by copyright. all rights reserved diagnostic testing did not identify or report additional measures of sensitivity, specificity, or likelihood ratios for hyposmia, hypogeusia, or rrt-pcr, we are confident that this search presents a complete scoping review of current knowledge. , others have also noted the absence of diagnostic accuracy reporting amidst the flurry of covid- publications. , additionally, this scoping review does not focus on special emergency medicine populations such as pediatrics, geriatrics, or obstetrics because other reviews already exist for these patients. , most importantly, we report no formal assessment of study quality using accepted instruments such as the quadas- , although informal assessment of published research to date suggests limited adherence to the full set of recommended methodological standards for studies of diagnostic test performance. clinicians should be aware of the current limited knowledge around history, physical exam, labs, and imaging for covid- . fever and acute onset disorders of taste and/or smell are the most common findings on history and physical exam associated with covid- . lymphopenia is associated with covid- diagnosis, while elevated ldh and pt are associated with severe disease. rrt-pcr has emerged as the primary diagnostic test for suspected covid- , but access has been limited, diagnostic accuracy is under-reported, and between-assay comparative accuracy is rarely evaluated. however, typical testing algorithms and diagnostic accuracy studies rely heavily on rrt-pcr results with frequent false negatives. chest ct is indicated for equivocal cases or when considering diagnoses like pulmonary embolism, but is not recommended as a general screening protocol. in cases with high clinical suspicions, repeat rrt-pcr testing with or without ct scanning may be beneficial to reduce community spread. antigen tests have only recently been approved, and diagnostic accuracy information is similarly limited. serology may identify past covid- exposure, but the role of antibody testing and implications for ed decision-making remain undefined. current clinical, imaging, and laboratory studies neglect diagnostic accuracy reporting standards and likely suffer from various biases. differential diagnosis for coronavirus disease (covid- ): beyond radiologic features. ajr american journal of roentgenology. :w . . fda: emergency use authorization (eua) information, and list of all current euas food and drug administration covid- testing: the threat of false-negative results the critical role of laboratory medicine during coronavirus disease (covid- ) and other viral outbreaks. clinical 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vs. rt-pcr: reflecting on experience from mers-cov. the journal of hospital infection chest ct in patients suspected of covid- infection: a reliable alternative for rt-pcr ct screening for early diagnosis of sars-cov- infection. the lancet infectious diseases performance of radiologists in differentiating covid- from viral pneumonia on chest ct ai augmentation of radiologist performance in distinguishing covid- from pneumonia of cautions about radiologic diagnosis of covid- infection driven by artificial intelligence. the lancet digital health sensitivity of chest ct for covid- : comparison to rt-pcr diagnosis of the coronavirus disease (covid- ): rrt-pcr or ct? a british society of thoracic imaging statement: considerations in designing local imaging diagnostic algorithms for the covid- pandemic managing high clinical suspicion covid- inpatients with negative rt-pcr: a pragmatic and limited role for thoracic ct test performance evaluation of sars-cov- serological assays covid- antibody seroprevalence in the promise and perils of antibody testing for covid- immunity passports" in the context of covid- . world health organization fda: policy for coronavirus disease- tests during the public health emergency effect of delay in diagnosis on transmission of covid- -ncov: the identify-isolate-inform ( i) tool applied to a novel emerging coronavirus. the western journal of emergency medicine radiology department preparedness for covid- : facing an unexpected outbreak of the disease clinical and imaging features of covid- the role of chest imaging in patient management during the covid- pandemic: a multinational consensus statement from the fleischner society evidence-based emergency medicine/editorial. the problem with sensitivity and specificity cdc. fact sheet for healthcare providers cdc - -ncov real-time rt-pcr diagnostic centers for disease control partial verification bias and incorporation bias affected accuracy estimates of diagnostic studies for biomarkers that were part of an existing composite gold standard multiple parameters required for diagnosis of covid- in clinical practice when should a new test become the current reference standard? evidence-based emergency care: diagnostic testing and clinical decision rules profile of rt-pcr for sars-cov- : a preliminary study from covid- patients temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study variation of a test's sensitivity and specificity with disease prevalence chest ct findings in cases from the cruise ship "diamond princess adherence to standards for reporting diagnostic accuracy in emergency medicine research overcoming the tower of babel in medical science by finding the "equator": research reporting guidelines doing research in emergency and acute care: making order out of chaos accepted article this article is protected by copyright. all rights reserved prospective multicenter evaluation of the pulmonary embolism rule-out criteria prediction models for diagnosis and prognosis of covid- infection: systematic review and critical appraisal clinical infectious diseases : an official publication of the infectious diseases society of america a tool to early predict severe corona virus disease (covid- ) : a multicenter study using the risk nomogram in wuhan and guangdong, china. clinical infectious diseases : an official publication of the infectious diseases society of america comparing rapid scoring systems in mortality prediction of critical ill patients with novel coronavirus disease. academic emergency medicine interval likelihood ratios: another advantage for the evidence-based diagnostician stopping the spread of masks and coronavirus disease state of the science: tools and measurement for shared decision making covid- diagnosis and management: a comprehensive review incorporating test characteristics into sars-cov- testing policy-sense and sensitivity. jama health forum web site all rights reserved . bachelet vc. do we know the diagnostic properties of the tests used in covid- ? a rapid review of recently published literature a systematic scoping review of covid- during pregnancy and childbirth covid- in older adults: key points for emergency department providers. geriatric emergency department collaborative quadas- : a revised tool for the quality assessment of diagnostic accuracy studies accepted article covid- covid- diagnostic testing covid- serotherapy covid- " or epidem*[tiab] or epidemic* or epidemy or new[tiab] or "novel"[tiab] or "outbreak" or pandem* or "sars-cov- " or "shanghai" or "wuhan") and ("coronavirus infections sensitivity and specificity"[mesh] or "point-of-care testing or "next generation sequencing"[tiab] or "point-of-care test"[tiab] or "point of care tests -ncov' or ' ncov' or 'cov ' or 'covid- ' or 'sars coronavirus ' or 'sars cov ' or 'sars-cov- ' or 'severe acute respiratory accepted article this article is protected by copyright. all rights reserved syndrome coronavirus ' or 'coronavirus ' or 'covid ' or 'covid- ' or ' ncov' or ' ncov' or 'corona virus disease ' or 'cov ' or 'covid- ' or 'covid ' or 'ncov ' or 'ncov' or 'new corona virus' or 'new coronaviruses' or 'novel corona virus' or 'novel coronaviruses' or 'sars coronavirus ' or 'sars ' or 'sars-cov- ' or 'severe acute respiratory syndrome coronavirus '):ti,ab,kw or (( or or ' -ncov' or 'beijing' or 'china' or 'covid- ' or epidem* or epidemic* or epidemy or new or 'novel' or 'outbreak' or pandem* or 'sars-cov- ' or 'shanghai' or 'wuhan'):ti,ab,kw and polymerase chain reaction'/exp or 'reverse transcription polymerase chain reaction'/exp or 'high throughput sequencing'/exp or 'sensitivity and specificity'/exp or 'point of care testing'/exp or 'antigen'/exp or 'serology'/exp or 'immunoglobulin g'/exp or 'immunoglobulin m'/exp or 'clustered regularly interspaced short palindromic repeat'/exp or 'crispr cas system'/exp or 'differential diagnosis'/exp or pcr:ti,ab,kw,de or 'digital droplet':ti,ab,kw,de or 'next generation sequencing':ti,ab,kw,de or 'point-of-care test':ti,ab,kw,de or 'point of care tests':ti,ab,kw,de or antigen:ti,ab,kw,de or analyte:ti,ab,kw,de or serology key: cord- -mp h dyl authors: abraham, louis; becigneul, gary; coleman, benjamin; scholkopf, bernhard; shrivastava, anshumali; smola, alexander title: bloom origami assays: practical group testing date: - - journal: nan doi: nan sha: doc_id: cord_uid: mp h dyl we study the problem usually referred to as group testing in the context of covid- . given n samples collected from patients, how should we select and test mixtures of samples to maximize information and minimize the number of tests? group testing is a well-studied problem with several appealing solutions, but recent biological studies impose practical constraints for covid- that are incompatible with traditional methods. furthermore, existing methods use unnecessarily restrictive solutions, which were devised for settings with more memory and compute constraints than the problem at hand. this results in poor utility. in the new setting, we obtain strong solutions for small values of n using evolutionary strategies. we then develop a new method combining bloom filters with belief propagation to scale to larger values of n (more than ) with good empirical results. we also present a more accurate decoding algorithm that is tailored for specific covid- settings. this work demonstrates the practical gap between dedicated algorithms and well-known generic solutions. our efforts results in a new and practical multiplex method yielding strong empirical performance without mixing more than a chosen number of patients into the same probe. finally, we briefly discuss adaptive methods, casting them into the framework of adaptive sub-modularity. lacking effective treatments or vaccinations, the most effective way to save lives in an ongoing epidemic is to mitigate and control its spread. this can be done by testing and isolating positive cases early enough to prevent subsequent infections. if done regularly and for a sufficiently large fraction of susceptible individuals, mass testing has the potential to prevent many of the infections a positive case would normally cause. however, a number of factors, such as limits on material and human resources, necessitate economical and efficient use of test resources. group testing aims to improve test quality by testing groups of samples simultaneously. we wish to leverage this framework to design practical and efficient covid- tests with limited testing resources. group testing can be adaptive or non-adaptive. in the former, tests can be decided one at a time, taking into account previous test results. in the latter, one can run tests in parallel, but also has to select all tests before seeing any lab results. a popular example of a semi-adaptive group test is to first split n samples into g groups of (roughly) equal size, pool the samples within the groups and perform g tests on the pooled samples. all samples in negatively tested pools are marked as negative, and all samples in positively tested pools are subsequently tested individually. figure : we formulate the group testing problem as a constrained information maximization problem. samples are grouped into testing pools so that the information gain is maximized while obeying practical constraints (i.e. no more than samples in one group). here, positive samples are shown in black and positive tests are shown in blue. the tests are decoded with error correcting probabilistic methods. practical constraints for covid- . although group testing is a well-studied problem, the recent covid- pandemic introduces specific constraints. in contrast to seroprevalence antibody tests, pcr tests aim to detect active cases, and only successfully do so during part of the disease course [ ] ). this results in a small prevalence (prior probability of population infection; we will assume a default value of − ), assuming we screen the general population rather than only symptomatic individuals. group testing has recently been validated for covid- pcr tests [ , ] . it is facilitated by the fact that pcr is an amplification technique that can detect small virus concentrations. nevertheless, there are limitations on the number of samples l that can be placed in a group ([ ] considers up to ), and constraints on the number of times a particular sample can be used ( [ ] uses serial incubation of the same respiratory sample in up to k = tubes). besides, there are practical issues: adaptive testing is time consuming and hard to manage. complex multiplex designs are prone to human error. existing research on non-adaptive group testing is generally concerned with identifying at most k positive samples amongst n total samples, which is referred to as non-adaptive hypergeometric group testing [ ] . this assumption yields asymptotic bounds on the number of tests needed to recover the ground truth [ , , , ] . however, these are of limited practical relevance when constructive results on small numbers of samples are required. the specific constraints for covid- force us to revisit the general framework of group testing. novel formulation. we formulate the problem based on the principle of information gain: given n people and m testing kits, the characteristics of the test and prior probabilities for each person to be sick, we seek to optimize the way the tests are used by combining several samples. for simplicity, samples are assumed to be independent analogous to [ ] . however, we focus on implementable tests, unlike [ ] which focuses on asymptotic results that are valid for large n. figure summarizes our approach. optimal characterization: by leveraging the framework of adaptive sub-modularity initially developed for sensor covering by [ ] , we prove near-optimality of a simple greedy-strategy for adaptive testing. despite the simplicity, it turns out that this greedy strategy has exponential running time and becomes infeasible for n ≥ . fortunately, the near optimally of the greedy-adaptive method points toward a simple and scalable non-adaptive solution leveraging randomization akin to the bloom filter structure [ ] . bloom origami assays: [ , ] recently showed that pooling using random hash functions, similar to a bloom filter structure, can lead to an efficient and straightforward group testing protocol. we will show that such a protocol, based on random hash functions, is unnecessarily restrictive. bloom filters were designed for streaming data, where there is no choice but to use universal hash functions for pooling. for covid- , the computational situation is much simpler. leveraging our information gain framework, we propose superior but straightforward hashing strategies. a bigger problem with bloom filters is the (necessarily) simple decoder. the decoder trades accuracy for efficiency, as it was designed for internet-scale problems where linear time decoding is prohibitive. for covid- , we instead propose a message-passing decoder, similar to counter braids [ ] , which is more accurate. our proposal of connecting probabilistic graphical model (pgm) inference with bloom filters could be broadly applicable to situations beyond covid- group testing. since the graphical model is a bipartite graph for which no narrow junction tree can be found, message passing does not necessarily converge to the global optimum. therefore, we propose a new method for graphical model inference leveraging probabilistic concentration and meet-in-the-middle (mitm) techniques, which may be of independent interest. our mitm method is particularly useful for the low prevalence scenario. this paper illustrates the power of algorithmic re-design to target practical constraints. we obtain significant gains even on the relatively well-studied topic of group testing. notations are progressively introduced throughout but are gathered in the appendix, which also contains the proofs. denote the number of patient samples by n. as previously mentioned, we consider the group testing task in the particular context of the covid- pandemic. this choice of problem setting naturally introduces new mathematical constraints of a practical nature: impracticality of adaptivity. adaptive methods require several hours in between each lab result of the adaptive sequence. this inspires us to only consider either non-adaptive methods or semi-adaptive methods with no more than two phases of testing. low concentration and test accuracy. excessive mixing of patient swabs may result in prohibitively low viral concentration with negative consequences for testing. a recent study reports that one can safely mix a patient swab up to times [ ] ; another relays that mixing up to patient samples into the same probe yields a false negative rate below % [ ] . there is clearly ambiguity in the limitations of the experimental protocol. for instance, [ ] validate double-digit numbers of patients per sample for pcr tests. while dilution effects are relevant for such large pools, they can be partly addressed by incubating respiratory swabs multiple times [ ] . also note that we are only concerned with the accuracy of the tests per se rather than the biological sampling protocol (i.e. whether swabs are taken when viral load is detectable in patients). in what follows we consider group sizes of n = as a sensible upper limit. notations and reminders denote the number of tests to run by m. tests are assumed to be imperfect, with a true positive rate (or sensitivity) tpr and true negative rate (or specificity) tnr. as simple default values, we will use tpr = % [ ] and tnr = % [ ] . patient sample i is infected with probability p i ∈ [ , ] and we assume statistical independence of infection of patient samples. denoting by a ' ' a positive result (infection), the unknown ground truth is a vector of size n made up of ' 's and ' 's. this vector describes who is infected and who is not. we call this the secret, denoted as s ∈ { , } n . a design of a test d ∈ { , } n to run in the lab is a subset of patient samples to mix together into the same sample, where d i = if patient sample i is mixed into design d and d i = otherwise. note that the outcome of a perfect design d for a given secret s can simply be obtained as d,s > where d, s := n i= d i s i . that is, a test result is positive if there is at least one patient i for which d i = (patient i is included in the sample) and s i = (patient i is infected). figure illustrates the problem setting. recall that the secret s is unknown. however, since we assume that patient sample i is infected with probability p i and that patient samples are independent, we have a prior probability distribution over the possible values of s. we hence represent the random value of s as a random variable (r.v.), denoted by s, with probability distribution p s (s) := pr[s = s] over { , } n . let us now recall the definition of the entropy of our random variable, the entropy represents the amount of uncertainty that we have on its outcome, measured in bits. it is maximized when s follows a uniform distribution, and minimized when s constantly outputs the same value. as we perform tests, we gain additional knowledge about s. for instance, if we group all samples into the same pool and have a negative result, then our posterior probability that all patients are healthy goes up. that is, p s (( , . . . , )) increases according to bayes' rule of probability theory. more generally, we may perform a sequence of tests of varying composition, updating our posterior after each test. our goal will be to select designs of tests so as to minimize entropy, resulting in the least amount of uncertainty about the test outcome for all individuals. given n people, test characteristics tpr & tnr and a set of prior probabilities of sample infection (p i ) ≤i≤n , the best multiset d of m pool designs is the one maximizing the information gain. the tests are order insensitive, which gives a search space of cardinality n +m m . evaluating the information gain of every multiset separately takes o ( n+m ) operations. hence, brute-forcing this search space is prohibitive even for small values of n and m. we resort to randomized algorithms to find a good enough solution. our approach is to use evolutionary strategies (es). we apply a variant of the ( + λ) es with optimal restarts [ ] to optimize any objective function over individuals (multisets of tests). detailed description. we maintain a population of individual between steps. at every step of the es, we mutate it in λ ∈ n + offsprings. in the standard ( + λ) es, each offspring is mutated from the population, whereas our offsprings are iteratively mutated, each one being the mutation of the previous. these offsprings are added to the population, and the best element of the population is selected as the next generation of the population. we initialize our population with the "zero" design that doesn't test anyone. our mutation step is straightforward: flipping one bit d i of one pool design d, both chosen uniformly at random. we also restrict our search space if needed: the number of 's in a column must be less than the number of times a given swab can be mixed with others, the number of 's in a line is constrained not to put too many swabs into the same pool. our iterative mutation scheme allows us to step out of local optima. after choosing a basis b proportional to n × m (which is approximately the logarithm of our search space), we apply restarts according to the luby sequence: , ...). this sequence of restarts is optimal for las vegas algorithms [ ] , and our es can be viewed as such under two conditions: (i) that the population never be stuck in a local optimum, which can be achieved in our algorithm using λ = n × m (note that much smaller constant values are used in practice); (ii) the second condition is purely conceptual and consists in defining a success as having a score larger than some threshold. the fact that our algorithm does not use this threshold as an input yields the following result, proved in appendix c. : theorem . under condition (i), the evolutionary strategy using the luby sequence for restarts yields a las vegas algorithm that restarts optimally [ ] to achieve any target score threshold. note that since tests are imperfect, for a given pool design d ∈ { , } n and a given secret s ∈ { , } n , the boolean outcome t (s, d) of the test in the lab is not deterministic. if tests were perfect, we would have t (s, d) = d,s > . to allow for imperfect tests, we model t (s, d) as a r.v. whose distribution is described by pr[t (s, d) = | d, s > ] = tpr and pr[t (s, d) = | d, s = ] = tnr. since the secret s is also unknown (and described by the r.v. s), the outcome t (s, d) has now two sources of randomness: imperfection of tests and unknown secret. in practice, one will not run one test but multiple tests. we now suppose that m tests of pool designs are run and let their designs be represented as a multiset d ∈ ({ , } n ) m . this leads us to the following question: given an initial prior probability distribution p s over the secret, how should we select pool designs to test in the lab? we want to select it such that once we have its outcome, we have as much information as possible about s, i.e. the entropy (uncertainty) of s has been minimized. since we cannot know in advance the outcome of the tests, we have to minimize this quantity in expectation over the randomness coming from both the imperfect test and unknown secret. this requires the notion of conditional entropy. conditional entropy. given pool designs d, we consider two random variables s (secret) and t := t (s, d) (test results). the conditional entropy of s given t is given by: in where it represents the amount of information (measured in bits) needed to describe the outcome of s, given that the result of t is known. the mutual information between s and t can equivalently be defined as i this criterion selects the pool designs d whose outcome will maximize our information about s. expected confidence. we report another evaluation metric of interest called the expected confidence. it is the mean average precision of the maximum likelihood outcome. the maximum likelihood outcome it defined by: m l is of particular practical interest: given test results t, a physician wants to make a prediction. in this case, it makes sense to use the maximum likelihood predictor. the interpretation of confidence is straightforward: it is the probability that the prediction is true (across all possible secrets). updating the priors. both scoring functions described above compute the expectation relative to the test results of a score on the posterior distribution p s|t =t (s). after observing the test results, we are able to replace the prior distribution p s by the posterior. by the rules of bayesian computation, this update operation is commutative, i.e., the order in which designs d and d are tested does not matter, and compositional in the sense that we can test {d , d } simultaneously with the same results. thus, we can decompose those steps and make different choices as we run tests (see the adaptive method below). although searching the space of all possible adaptive strategies would yield a prohibitive complexity of Ω( m ), it turns out that a simple adaptive strategy can yield provably near-optimal results. we describe an adaptive scheme in algorithm which greedily optimizes the criterion defined in eq. ( ). update p s accordingly (see eq. ( )) to the realization of d * in the lab ; decrease the number of remaining tests k by ; end leveraging the framework of adaptive sub-modularity [ ] , and assuming that the criterion defined by eq. ( ) is adaptive sub-modular , algorithm has the guarantee below. theorem . denote by 'algo' an adaptive strategy. let i(algo) be the expected mutual information obtained at the end of all m tests by running algo, the expectation being taken over all m outcomes of lab results. denote by 'optimal' the best (unknown) adaptive strategy. if we run algorithm for m tests and optimal for m tests, we have: where α is defined as follows: assume that our priors p i are wrong, in the sense that there exist constants c, d with cp i ≤ p i ≤ dp i for i ∈ { , ..., n}, with c ≤ and d ≥ , where p i denotes the true prior: we set α := d/c. remarks. accordingly, algorithm is (i) robust to wrong priors and (ii) near-optimal in the sense that the ratio of its performance with that of the optimal strategy goes to exponentially in the ratio of the numbers of tests run in each algorithm. for α = and m = m , this yields − e − . . our previous methods are effective, but they are prohibitively expensive for n > patients. to address this, we present a randomized approach to selecting d by grouping patients into pools using bloom filters [ ] . randomized test pooling may be attractive to practitioners because it is straightforward to understand and implement in the laboratory. the simplest method partitions n patients into random groups of equal size. patients are either re-tested or reported positive if their group tests positive (single pooling). in [ ] , the authors propose an extension to this idea that inserts patients into two sets of pools, named double pooling, which offers impressive advantages at the same cost. we present a generalization of this idea that uses an array of bloom filters to improve the error characteristics of the test. while bloom filters have been considered for the low-prevalence covid- testing problem [ , ] , current methods are based on a simple randomized encoding and decoding process that was designed for internet-scale applications where even linear time was prohibitive and where the keys are not known beforehand. this sacrifices accuracy. we now design an improved algorithm. empirical validation in appendix f. encoding. bloom filters use universal random hash functions for load balancing because the streaming algorithm setting does not allow us to control the number of items in each group. here, we can improve the filter with perfect load balancing. we divide the m tests into g groups of b pools. in each group, we assign the n patient samples to the b pools so that each pool contains n/b patients. . this procedure constrains the multiset d of possible test designs. with uniform prior probabilities, we implement a perfectly load balanced hash by assigning each patient a number based on a permutation π j of the integers { , ...n} thus patient i is assigned to pool h j (i) := π j (i) mod b in group j. for non-uniform priors, we can resort to a variable load hash to balance total weights into pools. due to the concavity of the entropy, the information gain is maximized if all pools have the same probability of testing positive. this is maximized for / , the mode of the binary entropy. load balancing implies information gain: load balancing, as exhibited by our encoding, maximizes the information gain for a practical subset of constrained bloom filter group test problems. theorem motivates bloom filters in the context of our information theoretic framework. with a constraint on the number of samples in each pool, our load balancing hash allocation is the optimal pooling strategy provided that pr[t b = ] is sufficiently small (∼ %). we defer a detailed discussion to the appendix. decoding for perfect tests. assuming perfect tests, one can easily decode the pooled test results t ∈ { , } b×g because all patients in negative pools are healthy. we can then identify positive (and ambiguous) samples by eliminating healthy samples from positive pools, as described in the appendix. in the case where g = and g = , we have the widely-used single pooling method and the recently-proposed double pooling method [ ] . assuming there are no false negative pool results, one can use the decoder to identify all positive samples and derive optimal dimensions b × g that minimize the number of tests, as shown in the below theorem: the analysis borrows tools from regular bloom filters and the results shown in [ ] . note that the problem with no test error and / prevalence is a #p-complete restriction of #sat, called monotone cnf [ ] . realistic tests with nontrivial fnr and fpr are technically more interesting. a natural idea is an algorithm dating back to [ ] when decoding diseases from the qmr database. decoding via message passing. indeed, false negative rates are often as high as %. the decoder fails for imperfect tests because even negative pools might contain positive samples. a small number of healthy pools might even test positive for some protocols (e.g. due to spurious contamination). when viewed as a probabilistic graphical model we can interpret t gb as a corrupted version of the true state y gb . it is our goal to infer the secret s that produced t gb . belief propagation is a common technique to estimate the posterior distribution p s|t =t for a graphical model. since our graphical model cannot be rewritten as a junction tree with narrow tree width there are no efficient exact algorithms. instead, we resort to loopy belief propagation [ ] . while inexact (loopy-bp isn't guaranteed to converge to the minimum) the resulting solution can classify samples as positive or negative with reasonable performance. while the degree of each pool figure : intuition behind probabilistic decoding. in each group, we suspect that patients in positive pools are positive. if a patient falls within multiple positive pools, the likelihood that their test status is positive increases. even if a false positive or negative occurs, we may still report the correct diagnosis thanks to information from other groups. this process is known as "error correction" and can be implemented with message passing or our mitm algorithm. figure : intuition behind the mitm approach. if the prevalence is low, then we do not need to consider inputs with many positives. this restricts the set of possible secrets and the set of ways we can encode those secrets. the figure shows the inputs for at most positives. given a (potentially corrupted) output, there are only a small set of true encodings that could have produced that output -it is highly unlikely that every test had a false result. the two conditions "meet in the middle" to produce a small set of states. our mitm algorithm efficiently approximates the posterior probabilities by summing over this restricted state space. node is so high that the clique potential would naively involve an intractable number of states, the clique potentials have a simple form that permits an efficient implementation (detail in the appendix). decoding for imperfect tests: meet-in-the-middle (mitm). the structure of the problem also enables an efficient approximation to the exact solution in the (realistic) setting where the tests are fairly accurate and the disease prevalence is low. low prevalence implies that there are relatively few "likely secrets" s ∈ { , } n , because most s i are with high probability. thus, we only need to consider secrets with a small number of positive patients. since the secrets concentrate in a small subset of { , } n , we expect to see relatively few bloom encodings y ∈ { , } t for low-prevalence problems. furthermore, the output space is likely to be corrupted in relatively few ways. the true state y gb is likely to be the same as the observed output t gb , so we only need to consider states that are similar to the observed output. by restricting our attention to "likely secrets" and "likely outputs", we can reduce the o( n ) complexity of the naive brute-force algorithm. this process constitutes a "meet in the middle" approach where we only need to consider illustrative values for mitm decoding. using stirling's formula n! ∼ √ πn(n/e) n , one can easily show that for a fraction x ∈ [ , ], we have f (xn) = o(( p x ) n ) when n → +∞. if k := xn is such that p x < , i.e. x > log( )/ log( /p), then f (k) will be exponentially small w.r.t. n. with our default p = . % we only need to consider secrets with a fraction smaller than x * = log ( )/ log ( / − ) ≈ . % of infected people to yield negligible error. for n = , choosing x = % reduces the search space of secrets from ≈ to * . − i= i < · with an error ε < ( p . ) < · − . we ran simulations to compare test designs for a large variety of group testing parameters (n, tpr/tnr, b × g, prevalence) in the appendix. in this section we present results for a practical scenario where tnr = . , tpr = . , and . % prevalence. in figure , we compare the entropy-minimizing solution found by genetic algorithms with several bloom filter designs. the bloom filter performance closely resembles the optimal solution, albeit with higher variance. this validates our claim that the load balancing permutation hash implies a good information gain. we also apply our graphical model framework to × arrays of bloom filters, single pooling and double pooling designs. we use the mitm technique to compute posteriors for all designs and we compare performance. while mitm provides the best results, computational constraints may demand belief propagation for situations where there are many positive group tests. in the high-prevalence scenario, belief propagation will still provide sufficient error correction for good diagnostic results (figure ) . the vanilla bloom decoding (single and double pooling) is unnecessarily inaccurate, clearly implying the need for specific tailored algorithms. we have presented a framework for group testing taking into account specifics of the current covid- pandemic. it applies methods of probability and information theory to construct and decode multiplex codes spanning the relevant range of group sizes, establishing an interesting connection to bloom filters and graphical models inference along the way. our empirical results, more of which are included in the appendix, show that our methods lead to better codes than randomized pooling and popular approaches such as single pooling and double pooling. furthermore, we provide an approximate inference algorithm through theorem that outperforms the message passing approach for realistic parameter values by pruning the exponential search space. we also prove compute-time bounds on its error, highly useful in practice because they are strict. we believe that the test multiplexing problem is an ideal opportunity for our community to make a contribution towards addressing the current global crisis. by firmly rooting this problem in learning and inference methods, we provide fertile ground for further development. as more information about test characteristics becomes available, we could take into account dependencies of tpr, tnr on pool size. the framework could be adapted to different objective functions, or linked to decision theory using suitable risk functionals, e.g., taking into account the downstream risk of misdiagnosing an individual with particular characteristics (comorbidities, probability of spreading the disease, etc.). it can be combined with the output of other methods providing individualized estimated of infection probabilities, to optimize pool allocation for non-uniform priors/prevalence. statistical dependencies (e.g., for family members) could be taken into account. finally, similar methods also permit addressing the problem of prevalence estimation. further details as well as some concrete design recommendations derived from our methods are available in the appendix. the motivation for this work was to help address the worldwide shortage of testing capacity for cov-sars- . testing plays a major role in breaking infection chains, monitoring the pandemic, and informing public policy. countries successful at containing covid- tend to be those that test a lot. on an individual level, availability of tests allows early and targeted care for high-risk patients. while treatment options are limited, it is believed that antiviral drugs are most effective if administered early on, since medical complications in later stages of the disease are substantially driven by inflammatory processes, rather than by the virus itself [ ] . finally, large-scale testing as enabled by pooling and multiplexing strategies may be a crucial component for opening up our societies and economies. people want to visit their family members in nursing homes, send their children to school, and the economy needs to function in order to secure supply chains and allow people to earn their livelihoods. however, the present work also poses some ethical challenges, of which we would like to list the below. the first family concerns the accuracy of the tests. indeed, when the number of tests and patients are equal, it is natural to compare the tpr/tnr of the individual test to the tpr/tnr of the individual results in our grouped test framework (obtained by marginalizing the posterior distribution). in some situations with unbalanced priors, the marginal tpr/tnr of some people in the group could be lower than the test tpr/tnr, even if the test will be more successful overall. however, reporting the marginal individual results gives doctors a tool to decide whether further testing should be needed; hence we cannot rule out that individuals might be worse off by being tested in a group. we furthermore show in the appendix that some designs are more fair than others, in that the individual performances are more equally distributed. the second family of concerns, directly resulting from the first, is the responsibility of the doctor when assigning the people to batches and giving them prior probabilities (using another model). the assignment of people in batches should be dealt with in a future extension of our framework, while the sensitivity of our protocols to priors should be studied in more depth. the adaptive framework may be more robust with respect to the choice of priors than the non-adaptive one. finally, the possibility of truly large scale testing may allow countries with sufficient financial resources to perform daily testing of large populations, with significant advantages for economic activity. this, in turn, could exacerbate economic imbalances. we use upper case letters exclusively for random variables (r.v.), except for mutual information i and entropy h. different objective functions. we have used the number of tests and samples as given, and then optimized a conditional entropy. however, from a practical point of view, other quantities are relevant and may need to be included in the objective, e.g. the expectation (over a population) of the waiting time before an individual is "cleared" as negative (and can then go to work, visit a nursing home, or perform other actions which may require a confirmation of non-infectiousness). semi-adaptive tests. instead of performing m consecutive tests, one could do them in k batches of respective sizes m , ..., m k satisfying m + ... + m k = m. adaptivity over the sequence of length k could be handled greedily as in algorithm , except that instead of selecting a single pool design d * , we would select m i designs at the i th step. we named this semi-adaptive algorithm the k-greedy strategy. further practical considerations. a good practical strategy could be to perform one round of pooled tests to disjoint groups every morning as individuals arrive at work, being evaluated during work hours. those who are in a positive group (adaptively) get assigned to a second pool design tested later, which can consist of a non-adaptive combination of multiple designs, tested over night. they receive the result in the morning before they go to work, and if individually positive, they enter quarantine. if the test is so sensitive that it detects infections even before individuals become contagious (which may be the case for pcr tests), such a strategy could avoid most infections at work. "bloom" denotes the use of the bloom encoding described in section while "entropy" denotes the use of the conditional entropy / mutual information encoder described in section . in both comparisons, we observe that the entropy encoder yields more similar pr curves across patients, compared to the bloom encoder. dependencies between tpr, tnr and pool size. the reliability of tests may vary with pool size. in our notation, the outcome of the tests is a random variable that need not only depend on whether one person is sick ( d,s > ) but it may also depend on the number of tested people |d| and the number of sick people d, s (cf. footnote ); it could even assign different values of tpr and tnr to different people. the tpr may in practice be an increasing function of the proportion of sick people d, s /|d|. estimating prior infection probabilities. currently, we start with a factorized prior of infection that not only assumes independence between the tested patients but is also oblivious to the individual characteristics. we could, however, build a simple ml system that estimates the prior probabilities based on a set of features such as: job, number of people living in the same household, number of children, location of home, movement or contact data, etc. those prior probabilities can then be readily used by our approach to optimize the pool designs, and the ml system can gradually be improved as we gather more test results. prevalence estimation. similar methods can be applied to the question of estimating prevalence. note that this is an easier problem in the sense that we need not necessarily estimate which individuals are positive, but only how many. c. theorem statement: under the condition that the population never be stuck in a local optimum, the evolutionary strategy using the luby sequence (b, b, b, b, b, b, b, b, b, b, b, b, b, b, b , ...) for restarts yields a las vegas algorithm that restarts optimally [ ] to achieve any target score threshold. proof. let us remind the main result we use on optimal restarts [ ] : the simple luby sequence of times of restart given by (b, b, b, b, b, b, b, b, b, b, b, b, b, b, b , ...) is optimal (up to a log factor) for las vegas algorithms (i.e. randomized algorithms that always provide the correct answer when they stop, but may have non-deterministic running time). our theorem is a direct consequence of conceptually casting our problem as a las vegas algorithm: indeed, we seek to optimize a fitness function f . for a given threshold a > , we can replace the maximization of f by the condition f > a. applying the result of [ ] for an exhaustive family of thresholds yields the desired result. we wish to invoke theorem of [ ] . in order to do so, we need to prove that the conditional entropy which we introduced in eq. ( ) is adaptive monotone. concerning adaptive sub-modularity, we make it an assumption upon which our results is conditioned, and validate it numerically with high precision for small values of n (see appendix f). direct respective correspondence between our notations and that of [ ] is given by: • pool designs d : items e; • test results t : realizations Φ; • set d of selected designs : set e(π, Φ) of selected items by policy π; this allows one to define, following definition of [ ] , the conditional expected marginal benefit of a pool design d given results t as: it represents the marginal gain of information obtained, in expectation, by observing the outcome of d at a given stage (this stage being defined by p s , i.e. after having observed test results t). adaptive monotonicity holds if ∆(d) ≥ for any d. adaptive sub-modularity holds if for any two sets of results t and t such that t is a sub-realization of t , for any pool design d: the below lemma concludes the proof. lemma. with respect to ∆ defined in eq. ( ), adaptive monotonicity holds. proof. adaptive monotonicity is a consequence of the "information-never-hurts" bound h(x | y ) ≤ h(x) [ ] . we are interested in the information i(s, t ) for a single bloom filter row with b cells. because each test in the row contains a disjoint set of patients, i(s, t ) is the sum of the information for each test (i.e. the t b random variables are independent and there are no cross terms). using the basic definition of h(t b ), we have that we use the fact that since the relationship between the ideal test results y b and the patient statuses s i is deterministic, conditioning on s i is the same as conditioning on y b . in particular, one can write pr(y b = ) = ( − p i ). observe that tpr = pr(t b = |y b = ) and tnr = pr(t b = |y b = ) and let ρ b = pr(y b = ). this gives us a simple expression for pr[t b = t] and thus we approach the second term h(t b |s patients ∈b ) the same way. = − t∈{ , } y∈{ , } put β = (tnr log (tnr)+( −tnr) log ( −tnr)) and α = (tpr log (tpr)+( −tpr) log ( −tpr)). then, the information i(s, t ) is equal to information is concave in ρ: to show that there is a single, constant, and optimal probability for each group test to be positive, we prove that i(s, t ) is concave in ρ. it is sufficient to show that each term i(s, t b ) in the sum is concave in ρ b . taking derivatives, we have the second derivative is we wish to show that d dρ b i(s, t b ) ≤ , which we will do by proving that the two fractions are both positive. the squared terms in the numerators are positive, as is the expression ( tpr − )ρ b + − tnr because tnr > . . this leaves the ( − tnr)ρ b + tnr term in the denominator. this term is linear in ρ b ∈ [ , ], with a minimum of -tnr. thus, i(s, t ) is concave. optimal value of ρ b : since the information is concave, there is an optimal value of ρ b that maximizes the information gain from each grouped test. since h(t b ) depends only on tpr, tnr and ρ b , it is easy to see that this value is constant and the same for all groups b. this proves the theorem. however, it is of practical importance to find or approximate the optimal value of ρ b . if one wanted to load balance a variety of (possibly different) priors into groups that have the optimal probability of testing positive, one needs to know the desired value of ρ b . we obtain the following equation by setting the derivative to zero: where c = ( − tnr) + ( tpr − ) + log( )(β − α). one can obtain the optimal ρ b by numerically solving this equation. when tpr = tnr, we have c = and the optimal value of ρ b = . . we prove the theorem using an analysis that is similar to the one for standard bloom filters. the bloom filter decoder identifies a sample as positive if all of the pools containing the sample are positive. it is easy to see that the decoder cannot produce false negatives under perfect tests, because each positive sample will always generate a positive pool result. we now analyze the systemic false positives introduced by the pooling operation. each pool contains either n b or n b − patients, where the latter situation occurs when b does not perfectly divide n and there are a few "leftover" elements. thus, any given sample will share a bin with up to n b − other elements, each of which has independent probability ρ of testing positive. to correctly identify a sample as negative, we require that all of these n b − samples also test negative. hence the probability that our sample will not collide with a positive sample is at least the - arises from the fact that the sample cannot collide with itself. this analysis holds for a single bloom filter row, but we have g independent opportunities to land in a negative pool. the rows are independent because independent random hash functions are used to form the groupings. the probability that we collide with a positive in all g groups is at most this expression gives the probability that we fail to identify the sample correctly. we want to bound the failure probability p f and choose parameters that minimize the bound. note that we replaced n b − with n b -the inequality still holds because ( − ρ) < . the optimal dimensions for the bloom filter come from minimizing the upper bound. we use the relation m = b × g to put p f in terms of m and g. we find that the optimal g = m n ρ log . notations. we use tildax to denote the estimation of a quantity x. error bounds and confidence levels. given a test result t ∈ { , } m , and a patient i ∈ { , ..., n}, we seek to estimate p [s i |t], i.e. the probability of patient sample s i being positive. we can rewrite: where we defined λ := p [s i , t] and µ := p [s i , t]. hence, we seek to estimate λ, resp. µ. we use the term "code space" to refer to the space { , } m of encodings of secrets s ∈ { , } n . we write λ and µ in terms of the joint distribution of secrets s, encodings c, and results t. summing across the code space yields: suppose that we have (under-)estimatesã andb such that ≤ max c (a(c) −ã(c)) ≤ ε and ≤ c (b(c) −b(c)) ≤ ε. later, we will describe how to obtain these estimates. for now, observe that we can (under-)estimate λ = c a(c)b(c) withλ := cã (c)b(c), with the following error bound : and similarly ≤ µ −μ ≤ ε, which would imply ≤ (λ + µ) − ( which concludes the proof that we can estimate p [s i |t] with error less than ε/p [t], wherep then, similarly, letã this concludes our presentation of the estimatorsã(c) andb(c). note that we presented a confidence interval together with a bound on its size, i.e. we showed that the true value p [s i |t] is within an interval that depends on the observed quantityp [s i |t]. however, we can also provide an interval for the observed quantity as a function of the true value: whose size can be bounded by: where we assumed ε < λ/ to justify that λε (λ+µ) − ε λ+µ < ε λ+µ . one might also be interested in the error rather than a confidence interval. we will now present an algorithm that efficiently computes these estimators. in our algorithm, a( ) is the number of secrets with at most k nonzeros, c( ) is number of codes produced by this restricted set of k-sparse secrets, and b( ) is a set of probable ideal codes for the potentially-corrupted output t that we observe. preprocessing: (independent of results t) compute k such that f (k) < ε and initialize c = ∅; enumerate all the codes c := enc(s) for s with less than k positives a ; use these codes to approximatep [s i , c] andp [s i , c] using the formula forb(c) in eq. ( ). store the results in c; query: (dependent upon results t) compute p := i t i , n := m − p and a(c) (see eq. ( )) for f p ≤ p , f n ≤ n ; complexity analysis. since the outcome of a test t is conditionally independent to s w.r.t. c, we can pre-compute all encodings c := enc(s) for s belonging to the reduced search space of size a(ε) := k− i= n i . saving all these resulting encodings with a hashmap or a set structure gives a space of complexity proportional to c(ε) ≤ a(ε), since the output function image of an input set is always smaller than (or equal to) the size of the input set. finally, at query time, we seek to estimate p [s i |t]. note that we have pruned two search spaces: the space of encodings of a(ε) many secrets, reduced from m to c(ε), and the space of codes c such that for our given t, prob[f p ][f n ] > ε, reduced from m to b(ε). given a test result t, we can compute n, p in o(m) operations, which then allows us to compute b(ε) for this t. also note that we approximate p [s i , t] via cã (c)b(c). sinceã(c) = for c such that t doesn't belong to the reduced test results space of size b(ε), we can choose to perform this sum on either this set, or the reduced code space of size c(ε): whichever is the smallest. this is where the denomination "meet-in-the-middle" comes from. the c++ code can be used in the browser through an interactive webassembly demo: https://bloom-origami.github.io/ the following features are implemented: • bloom assay generation • greedy adaptive strategy simulation • design optimization using genetic algorithms • posterior decoding using mitm our designs assume that the prevalence ρ is known, at least approximately. however, we can also use our bloom filter design to estimate the prevalence in the overall infected population. when we randomly and independently sample an individual from the population, they have probability ρ of being infected. the prevalence estimation problem is to determine ρ using as few tests as possible. here, we assume perfect tests to simplify the analysis. of course, one could individually test a large number of people from the population and report the fraction of positive test results. the challenge is that if we screen individuals, we end up with a random variable for which the mean to variance ratio is unfavorable. consider a random variable x ∈ { , } with e[x] = ρ and variance var[x] = ρ − ρ = ρ( − ρ). the error of the empirical average of m individual tests is the relative error is −ρ ρ . clearly this is minimized for ρ = . unfortunately, this value is entirely useless since it corresponds to the situation where every test returns positive. in practice, we encounter the unfortunate situation of ρ << where the relative error diverges. under a naive random sampling approach to prevalence estimation, a very large number of tests are required. to amend this situation, it is beneficial to increase the probability of a positive test by testing multiple candidates at once. our pooled tests are no longer positive with probability ρ but with probability q = − ( − ρ) k , where k is the number of samples combined in a single pool. knowing q, we can solve for ρ via we will use the central limit theorem and the delta method to show that we need fewer bloom filter pooled tests than random individual tests to estimate the prevalence. the central limit theorem states that suppose we combine k samples into each bin. now x is the test status of the bin and it is positive with probability q = − ( − ρ) k . hence µ = q and σ = q( − q). use the delta method with space/time trade-offs in hash coding with allowable errors a note on double pooling tests non-adaptive group testing: explicit bounds and novel algorithms graphconstrained group testing elements of information theory adaptive submodularity: theory and applications in active learning and stochastic optimization near-optimal sensor placements in gaussian processes temporal dynamics in viral shedding and transmissibility of covid- non-adaptive hypergeometric group testing efficiently decodable non-adaptive group testing variational probabilistic inference and the qmr-dt network non-adaptive group testing in the presence of errors probabilistic graphical models: principles and techniques pooling of samples for testing for sars-cov- in asymptomatic people. the lancet infectious diseases counter braids: a novel counter architecture for per-flow measurement optimal speedup of las vegas algorithms nonadaptive group testing with random set of defectives bloom-filter inspired testing of pooled samples (and splitting of swabs!) probability and computing: randomization and probabilistic techniques in algorithms and data analysis reconstructed diagnostic sensitivity and specificity of the rt-pcr test for covid- . medrxiv fact -frankfurt adjusted covid- testing -a novel method enables high-throughput sars-cov- screening without loss of sensitivity. medrxiv the trinity of covid- : immunity, inflammation and intervention model counting of monotone cnf formulas with spectra paper-origami-based multiplexed malaria diagnostics from whole blood evaluation of covid- rt-qpcr test in multi-sample pools << aux ( { } ) << ' ' << aux ( { t e s t } ) << ' ' << aux ( { t e s t } ) << ' ' << aux gary bécigneul is funded by the max planck eth center for learning systems. benjamin coleman and anshumali shrivastava are supported by nsf- , nsf-bigdata , afosr-yipfa - - - , amazon research award, and onr brc grant for randomized numerical linear algebra. key: cord- -zb h q k authors: nan title: what to expect from covid- serology in a period of deconfinement? date: - - journal: bull acad natl med doi: . /j.banm. . . sha: doc_id: cord_uid: zb h q k nan what to expect from covid- serology in a period of deconfinement? ଝ despite the significant impact of containment on the course q of the covid- epidemic, the circulation of the virus persists on the french territory, even among the least affected regions. as of may , the date set for the end of the containment, a model from the pasteur institute estimated that the infection would have affected . % of the population, with significant regional variations, from less than % in brittany, new aquitaine and pays de loire to - % in the grand est and Île-de-france [ ] . the level of immunity of the french population to sars-cov- thus seems very low, far from the theoretical threshold of % which would allow us to expect a collective level of protection. this situation makes it necessary to implement iterative population-based sero-epidemiological surveys, representative of each region, each age group and each socio-professional category to assess the spread of the epidemic in the population. in addition, there is a strong demand for serological tests from the professionally exposed workers and, more widely, from many worried people anxious to know their immune status. numerous serological tests have been developed for the detection of igg and igm antibodies against sars-cov- in a sample of venous or capillary blood. these are the elisa tests that can be used in large series on automatic machines and the unit tests (rapid diagnostic tests, tdr, doi of original article:https://doi.org/ . /j.banm. . . . ଝ press release from the french national academy of medicine and q the national academy of pharmacy, may . and rapid diagnostic orientation tests, trod), which can be performed individually on a drop of capillary blood obtained by fingertip pricking [ ] . their evaluation by the national centres of reference (cnr) for respiratory infection viruses has made it possible to select tests that meet the performance requirements of the french high authority for health (sensitivity ≥ % and specificity ≥ %), but these tests have not yet been validated by the health authorities and do not give the right to reimbursement. it should be noted, however, that even if a test with a specificity of % is used, the positive predictive value of seropositivity will only be % in all regions of the country spared by the epidemic, where seroprevalence is estimated an average of % [ ] . furthermore, while positive serology indicates immunity to the virus, it does not allow to predict with certainty that the person will be protected in the event of a reinfection. in the current context, given the sharp increase in individual requests for serological tests without medical prescription, access to tests must remain controlled in order to avoid any behavioural drift that could be induced by misinterpretation of the results. the national academies of medicine and pharmacy recommend: • that only those tests that will be recommended by the cnrs and validated by the ministry of health and solidarity be used, whether they are unit tests or elisa tests; • that the sero-epidemiological population surveys be coordinated by the regional health authority (ars) and that each person recruited be informed personally and confidentially of his or her serological status; • that the covid- serological tests should be carried out neither at a simple individual request, nor at the behest of employers; • that the serological tests be carried out only on medical prescription, the general practitioner having to judge their necessity after consultation or teleconsultation; • that prescribing physicians have access to interpretation algorithms, helping them to comment on their patients' results, to request additional virological tests if necessary, and draw the possible consequences; • that a positive test result does not lead to the establishment of a ''certificate of seropositivity'' or of an ''immunological passport''; • that medical confidentiality be scrupulously preserved. q the authors declare that they have no competing interest. estimating the burden of sars-cov- in france tests covid- : applications collectives et individuelles place des tests sérologiques rapides (tdr, trod, autotests) dans la stratégie de prise en charge de la maladie covid- key: cord- -qa uph authors: nan title: poster discussion session pds date: - - journal: allergy doi: . /all. sha: doc_id: cord_uid: qa uph nan objectives: since bradykinin is a short-lived, low-abundance mediator in the systemic circulation, the discovery of additional biochemical biomarkers correlating hae disease activity with contact system dysregulation may be useful for further elucidation of hae pathophysiology and pharmacodynamic therapeutic modulation of the contact system. results: activated pkal cleaves single chain high molecular weight kininogen to generate bradykinin and cleaved chain hmwk. cleaved -chain hmwk was measured in human plasma using both a semi-quantitative western blot assay with fluorescent detection (licor) and a novel elisa with a capture antibody that specifically binds -chain hmwk. the western blot assay was previously used to monitor pharmacodynamic activity in hae patients treated with lanadelumab, a fully human antibody inhibitor of pkal that is in clinical development for hae attack prophylaxis. lanadelumab inhibited -chain hmwk generation following contact system activation in vitro, confirming that -chain hmwk is a product of pkal activity. plasma -chain hmwk levels from hae patients during or between attacks were compared to that from healthy volunteers using both the western blot assay and elisa. roc curve analyses with both methods suggest that -chain hmwk is a trait-specific biomarker capable of differentiating hae patients from healthy volunteers. the elisa was able to differentiate samples from hae patients collected during an attack from those collected between attacks with moderate sensitivity and specificity (c-statis-tic= . ). a comparison of -chain hmwk levels in citrated plasma versus plasma that contains protease inhibitors (scat plasma) provides estimates of endogenous versus ex vivo activation. the measurement of -chain hmwk using the specific assays described may find use in further dissecting the role of the contact system in disease pathology, to identify additional indications for modulators of this pathway, and to investigate therapeutics targeting the contact system. | g protein coupled receptor kinase (grk ) regulates endothelial permeability induced by bradykinin | pharmacokinetics (pk) and pharmacodynamics (pd) of c esterase inhibitor of chronic urticaria challenges most commonly identified were the following: time of onset of disease; frequency/duration of and provoking factors for wheals; diurnal variation; occurrence in relation to weekends, holidays, and foreign travel; shape, size, and distribution of wheals; associated angioedema; associated subjective symptoms of lesions; family and personal history regarding urticaria, atopy; previous or current allergies, infections, internal diseases, or other possible causes; psychosomatic and psychiatric diseases; surgical implantations and events during surgery; gastric/ intestinal problems; induction by physical agents or exercise; use of drugs; food allergies; relationship to the menstrual cycle; smoking habits; type of work, hobbies; stress; quality of life and emotional impact; previous therapy and response to therapy, and previous diagnostic procedures/results. we included all of these aspects in our guide and as a result we developed a chronic urticaria check list. conclusions: our guide of clinical history for chronic urticaria (gur) contributes to have an easy tool in order to achieve a better diagnosis and evaluation of chronic urticaria. | clinical and diagnostic features in acquired cold urticaria patients in a coruña sanitary area, spain physicians and dermatologists/allergists; c/sa patients were more likely to visit dermatologists/allergists ( % vs. %) and less likely to visit general physicians ( % vs. %) than european patients. emergency room visits due to cu were more common in c/sa ( %, mean [sd] number= . [ . ] ) than europe ( %, mean [sd] number= . [ . ] ). conversely, hospital admissions due to cu were more likely to occur in europe ( %) than c/sa ( %), but the average (sd) number of admissions among those hospitalised was greater in c/sa ( . [ . ] vs. . [ . ]). variations were seen in subregion comparisons. mean (sd) overall wpai scores were . ( . ), . ( . ), . ( . ), and . ( . ) for absenteeism, presenteeism, work productivity loss, and activity impairment, respectively; patients in c/sa reported a higher rate of impairment (range, %- %) on all domains compared with patients in europe. conclusions: cu is associated with substantial hru and work and activity impairment in both europe and c/sa. general physicians should be considered key members of the treatment team in the care of patients with cu in these regions. objectives: cu patients (n= ) received monthly subcutaneous injections of omalizumab for up to six months. urticaria-related symptoms were assessed by both the urticaria control test (uct) and the chronic urticaria quality of life score (cu-q ol). peripheral blood was drawn prior to each injection for determining the concentration-dependent reactivity of patients' basophils to specific anti-fceri and unspecific fmlp stimulation by basophil activation test. furthermore, the impact of anti-ige treatment on ige-bearing cell populations was characterized by flow cytometry analyzing the surface expression of both fceri (e.g. on monocytes, dendritic cells, basophils) and the low-affinity receptor for ige, fcerii (e.g. on b cells, eosinophils). results: anti-ige treatment of cu patients significantly improved clinical symptoms of cu already after the first injection as evaluated by cu-q ol and uct, the latter of which correlated with an increase of basophil numbers and a decrease of basophil surface bound ige. of note, cell-bound ige on fcerii-expressing cells was not altered. furthermore, while clinical amelioration also was accompanied by reduced fceri expression on basophils, the basophil responsiveness to anti-fceri stimulation increased in % ( / ) of treated patients. in contrast, ige-independent activation of basophils by fmlp was unchanged. conclusions: clinical improvement of cu patients treated with omalizumab is associated with characteristic immune alterations in basophils, like rapid, cell-specific reduction of surface bound ige and fceri-expression as well as normalization of basophil responsiveness to fceri-stimulation. while our findings might help to better understand the mode of action of anti-ige therapy in cu, they also can shed new light on the pathomechanisms underlying cu. | omalizumab in patients with severe active chronic spontaneous urticaria (csu) heavily treated with corticosteroids and cyclosporine introduction: increased levels of blood d-dimers (d-d), the byproducts of fibrin degradation, is linked to the severity of chronic spontaneous urticaria (csu) and to poor response to antihistamines h (ah ). omalizumab (oma) is a human monoclonal anti-immunoglobulin-e antibody registered as an add-on treatment of csu in adults and adolescent (≥ years old) and with insufficient response to ah . the sunrise study assessed the efficacy of omalizumab on csu symptoms and the correlation between d-d levels and response over time to treatment with oma to explore its potential predictive value. objectives: sunrise was a french prospective non comparative phase study. included patients had to have been diagnosed with csu for at least months, be resistant to ah treatment, and have a uct score (assessed by patient over the last weeks, values from (maximal disease)to (full control)) < , indicative of a poorly controlled disease. the widely used uas score (assessed by patients over week which captures intensity of pruritus and number of hives, values ranging from (no disease) to (severe disease)) was further used to evaluate the proportion of patients achieving a well controlled disease(uas≤ ). all patients received mg oma by sub-cutaneous injections at day , weeks (w) and . blood levels of d-d were assessed (turbidimetric immunoassay) at d , w and w . response to treatment was evaluated at w by means of the uas . results: median level of d-d assessed at d in patients was increased at baseline ( ng/ml, extremes - ) and normalized as early as w reaching ng/ml ( - ) at w . correlation between d-d concentration and uas score at w was weakly positive (spearman coefficient . ). among the patients with a very high baseline de d-d level (> ng/ml) were responder (uas ≤ ) at w . conclusions: baseline d-d levels were increased in more than half of patients of this study in line with relevant literature. a fast normalization was observed with oma as early as w of treatment. d-d levels at w were weakly correlated with uas . subgroup analyses may help to better understand the link between d-d and clinical response, as these preliminary results do not yet allow the predictive use as a biomarker. the sunrise study explored for the first time in a prospective way the impact of oma on dd and found weak correlations were measured between dd level and response to oma. further studies will be needed to evaluate its predictive value for response. (crp, esr, il- , il- , il- , ccl /mcp- ), and the disease severity in patients with chronic spontaneous urticaria introduction: pru p is the primary sensitizer of some fruits and responsible for severe reactions in the mediterranean area. sublingual immunotherapy (slit) using peach extract enriched in pru p (prup -enriched-slit) brings a new perspective to treat patients with reactions to peach considering that currently the treatment of the allergy to peach is based on avoidable ingestion of fruit. we performed a pilot study to examine the immune modulation by slit in patients with peach allergy over a -year treatment period. objectives: we aimed to evaluate the effect of the slit during one year in patients with peach allergy. we analysed the capacity pru p enriched-slit to modulate immune response, from a th to th response with increases of treg cells. we studied three groups of subjects: peach allergic patients who received prup -enriched-slit for year, peach allergic patients non treated, and healthy controls who tolerated peach. monocyte-derived dendritic cells (dcs) maturation, peripheral blood mononuclear cell phenotype and lymphocyte proliferation after prup stimulation were assessed by flow cytometry from samples obtained before, and , and months during slit. results: we found statistically significant differences in dcs activation and maturation between allergic patients and controls at the basal state. when we analyzed the effect of prup -enriched-slit over time, we found a significant reduction of activation and maturation markers (ccr , cd , cd , cd and cd ) at the first month of treatment that was maintained after year. concerning lymphocytes, we observed a significant decrease of effector cells immune cells. recent studies showed that fructo-oligosaccharides (fos) increase the efficacy of oral immunotherapy (oit) in a mouse model for cow's milk allergy, however, the mechanism is unknown. objectives: investigating the effect of oit+fos on the effector response and the process of tolerance induction. methods: female c h/heouj mice ( - weeks old, n= /group) were sensitized to the cow's milk protein whey ( mg in pbs, intragastrically (i.g.)) with cholera toxin ( lg) once a week for weeks (d -d ). the mice received a diet with % fos or a control diet from d -d . oit ( mg in pbs or pbs) was provided days a week for weeks (d -d ). intradermal (i.d.) and i.g. challenges were performed to measure the acute allergic response. serum, bone marrow, caecum content, small intestines and mesenteric lymph nodes (mln) were collected at d , d and d . spleen-derived t cell fractions (whole spleen, cd +cd -and cd +cd +, using macs) were transferred to na€ ıve recipient mice at d . the recipients were sensitized and challenged as described for the donor mice. conclusions: this study shows that oit+fos results in an early induction of functional tregs and a reduction of mast cell degranulation upon challenge. the latter may be caused by inhibition of mast cell activation by galectin- and/or butyric acid. moreover, the effect of fos on bone marrow suggests possible epigenetic changes reducing development of mast cells. further research is needed to investigate if this approach may be of potential value to treat food allergies. | safety and feasibility of slow low-dose oral immunotherapy sugiura s; kitamura k; tajima n; takasato y; kato t; tajima i; ono m; tagami k; sakai k; nakagawa t; ito k aichi children's health and medical center, obu, japan introduction: slow low-dose oral immunotherapy (sloit) is an ongoing clinical trial conducted in our institute (umin registry number ). this is a type of oral immunotherapy with a low dose antigen increased very slowly. objectives: to evaluate the safety and feasibility of the protocol. results: sloit enrolled the patients who were diagnosed as severe egg, milk or wheat allergies, with a threshold dose of g (or ml) or less in the oral food challenge (ofc, -minutes boiled egg white, whole milk, udon noodle). subjects were divided into two groups, intervention (sloit) group or elimination (control) group, based on their preference. sloit group began to ingest / to / amount of the final dose of the ofc based on the severity of provoked symptoms. intake was continued everyday with an increasing dose less than . times/ month, expecting a times increase from the starting dose after months. feasibility was evaluated based on the proportion of patients who complied the protocol. safety was evaluated based on the frequency of immediate allergic reactions observed in the programmed intakes. fifty-nine patients were enrolled from april to december , and of them (egg: , milk: , wheat: ) preferred the sloit group. among them, patients ( . %) dropped out from the study protocol because of provoked allergic symptoms (n= ) or the other personal reasons (n= ). among a total of ingestions by patients who continued the protocol over months, mild symptoms were observed times ( . %), to which rescue medicine such as oral antihistamines was used in cases ( . %). no one needed an emergency visit or an adrenalin auto-injector. low threshold dose at the initial ofc ( . g or less, n= ) was associated with higher proportion of provoked allergic symptoms in the protocol (low threshold: . %, non-low threshold: . %, p=. ). the level of specific ige titer was not associated with the safety. conclusions: sloit protocol has sufficient safety and feasibility, but low threshold patients should be monitored closely. the efficacy of this protocol is being evaluated by an ofc after - months of the treatment, and the overall data will be presented after march . objectives: the aim of this phase i, randomized, non-controlled, multicenter, opened, with parallel groups clinical trial, is to evaluate the safety and tolerability of subcutaneous immunotherapy (scit), in a polymerized mixture ( / ) depot presentation. patients with rhino-conjunctivitis polysensitized to olea europaea/ phleum pratense received a schedule consisting of two weeks of initiation with three weekly injections; or a program comprising two administrations in the same day separated by minutes. both treatments continued with a maintenance period of three months with a monthly administration. the primary outcomes are the number, percentage, and severity of adverse reactions. secondary endpoint included subrogate efficacy parameters evaluation: changes in immunoglobulin titers (specific ige, igg and igg ) and changes in cutaneous reactivity at different concentrations. systemic reactions were registered, representing . % of the included patients: one grade , described as general discomfort plus dizziness and one grade i, such as rhinoconjunctivitis. there were no local reactions. all were classified as of mild intensity and took place with the cluster schedule. symptomatic treatment was not required. conclusions: both schedules with polymerized mixture of phleum pratense/olea europaea, ( / ), presented a good safety and tolerability. a statistically significant decrease in cutaneous reactivity to olive and grass allergens was observed after immunotherapy. a | design of the pivotal phase iii study to assess the efficacy and safety of subcutaneous hdm allergoid immunotherapy in patients with hdm induced allergic rhinitis/ rhinoconjunctivitis introduction: in order to comply with ema guidelines on development of allergen immunotherapy products, a clinical development program was started to obtain full marketing authorization for a allergoid subcutaneous immunotherapy (scit) product for the treatment of house dust mite (hdm) allergy. previously, the safety and tolerability of increasing doses of this allergoid scit product was evaluated in patients with hdm-induced allergic rhinitis/rhinoconjunctivitis (arc) [eudract - - ] . no safety or tolerability issues were identified for doses up to aueq. subsequently, a dose-finding study to identify the optimal, i.e. effective and safe dose in hdm arc with or without concomitant asthma was performed [eudract - - ; pfaar, allergy ] . this study demonstrated a dose response relationship with doses of aueq ( . ml of aueq/ml) up to aueq ( . ml of aueq/ml) showing significant improvements compared to placebo. the current pivotal phase iii study [eudract - - ] aims to confirm safety and efficacy of this hdm allergoid scit product at a dose level of aueq/ml ( . ml) compared to placebo after one year of treatment in patients with hdm-induced arc. objectives: the current study is a multi-center ( clinical study centers in european countries) randomized, double-blind, placebocontrolled, parallel-group study in adult patients, with moderate to severe hdm induced arc with or without mild to moderate persistent asthma. the primary outcome of the study is the difference in mean combined symptom and medication score (nasal symptoms only) (csms (n)) between aueq/ml allergoid scit and placebo treatment, assessed during the last weeks of the approximately year treatment period. results: patients from centers, (mean age . years) have been included and analyzed. the . % are men, . % presented associated asthma. a large majority of patients have received subcutaneous sit ( . %), and . % of them containing a single allergenic source. . % in polymerized formulation and . % in depot. accelerated schedule has been the most prescribed ( . %), followed by clustered one ( . %). from the patients who have completed the study, . % of them improved from persistent to intermittent rhinoconjunctivitis (p<. ) and . % from moderate/severe to mild intensity (aria) (p<. ). moreover, % of asthmatic patients at baseline, did not have any bronchial symptoms after -year treatment. the improvement in quality of life was possible to be analyzed in patients. mean values in rqlq questionnaire (total score) decreased from . to . points ( . % of score reduction) in final visit, reflecting a statistically significant improvement (p<. ). mean value of treatment satisfaction was . (sd= . ) and . (sd= . ) for physician and patients respectively. for safety assessment, out of analyzed patients, only systemic reactions were reported in patients ( . %). seven of them were classified as grade i, and one as grade ii according to eaaci grading system. strasbourg is a m chamber, located into the university hospital of strasbourg at less than to minutes to the intensive care unit. one of the characteristics of this unit is that the maximum parameters are controlled: temperature, relative humidity, ventilation rate, particles number and particles size, concentration of airborne of der p and airborne voc. mite allergens extract were nebulized through a nebulizer. airborne der p concentrations were sampled using glass fiber filters and measured with an elisa assay. particles number and particles size were monitored continuously during nebulization, using particles counters distributed inside the exposure room. the cleaning process was also controlled and validated. objectives: to validate the technical parameters of the environmental exposure chamber (eec) of strasbourg with mite allergens. results: the reproducibility was excellent for the indoor temperature, relative humidity and airflow ( cv interassay < %). three concentrations of der p were measured: , , ng/m (n= ). for all concentrations, the cv intra-assay of airborne der p was ae . %, the interassay was less than %. for the particle size . - and - lm, the cv interassay was and %, respectively (n= ). the cv of the mmad was . % (n= ). no measurable airborne der p was detected in the toilets and the medical supervision room (n= ) neither in the exposure room minutes after the end of the allergen exposure (n= ). no airborne voc was measured in the chamber and the other rooms of the clinical unit (n= ). there was no significant change in particles size and number when to persons entered the room (n= ). introduction: pathogenesis of systemic sclerosis (ssc) includes vasculopathy with endothelial dysfunction which is considered to be one of the earliest changes in the pathogenesis of ssc. several biological molecules, including e-selectin (e-sel), inter-cellular adhesion molecule (icam- ), endothelin (et- ), von willebrand factor (vwf) and interleukin (il- ) have been associated with endothelial activation. objectives: we aimed to determine if these vascular biomarkers are associated with distinct capillaroscopic ssc patterns and/or more severe disease in ssc patients. results: correlations between serum levels of all vascular biomarkers were good to moderate and statistically significant, with r indices varying between . and . , the only exception being et- which did not correlate with e-sel. good correlations (r . to . ) were also found between all biomarkers and crp. patients with severe vasculopathy, as reflected by the nfc "late" pattern, had higher levels of il- (median . vs . pg/ml, p=. ), et- (median . vs . pg/ml, p=. ), vwf (median vs iu/ml, p=. ) and e-sel (median . vs . ng/ml, p>. ), compared to patients with nfc "early" or "active" patterns. there was a significant, negative correlation between lung transfer for carbon monoxide (dlco) and e-sel, icam- (both p<. ) and vwf (p=. ). et- was higher in patients with more severe disease (dcssc, patients positive for anti-topoisomerase antibodies and patients with a history of digital ulcers-all p<. ). conclusions: serum endothelial activation biomarkers are elevated in patients with more severe ssc-associated vasculopathy and correlate with serum crp. together with nfc data they may be used for assessing vasculopathy severity in ssc. objectives: here we present the imagination findings of eye involvement in a family whose members have mws. method: clinical data was collected during the course of ongoing patient care. results: we evaluated the clinical features of patients who were referred to our center. the median age of the patients was years (range: - years). the ratio of females /males was . ( / ). all patients had arthritis with exacerbation on exposure to cold and ocular involvement, mostly in the form of conjunctivitis and far less other forms. the median age of onset of ocular involvement was years ( - y). chronic eye damage were detected in three patients. corneal involvement and clouding was detected in four patient. two conclusions: in this study, it has been shown that eye findings related to mws can vary from conjunctivitis to severe uveitis. we want to emphasize that ocular involvement in mws should be carefully assessed, since it can lead to visual impairment. | antiretroviral activity of the conjugates '-azido- 'deoxythymidine and derivatives of , -diacylglycerides case report: aids epidemics remain the critical problem due to both their emergent and long development. treatment of aids with azt reduces p antigenemia, increases cd + lymphocyte counts, reduces the frequency and severity of opportunistic infections and prolongs life. however, zidovudine and other dideoxynucleotides do not decrease the ability to isolate hiv from pbmc, and in addition, these drugs are very toxic. this phenomenon is caused by insufficient inhibition of hiv due to low levels of nucleoside kinases in ccr -positive cells, including in macrophages, which are a major reservoir of hiv. potential advantages of these liponucleotide prodrugs include: greater in vivo efficacy and lower toxicity due to a greater delivery to monocytes/macrophages, ability to bypass the initial anabolic phosphorylation due to the presence of the phosphorous center in the structure, and the prospect of improved pharmacokinetics and prolonged intracellular persistence. the aim of this work is the study of cytotoxicity and anti-hiv activity of glycerolipids derivatives of azt. evaluation of the cytotoxicity of azt and test compounds was per- | bone mineralisation defect in patients with hax- deficiency and osteopenia (z score <À ) in patients. bone mineralisation defect was found in all female patients while only one male had osteopenia (table ) . conclusions: in this study, a significant decrease ( . %) of bone mineralization was observed in patients with hax- deficiency. female patients were found more prone to bone mineralisation defect. to conclude on this subject, more studies are needed with large number of patients having not only hax- deficiency but also ela- mutations. gene mutation age ( introduction: bronchopulmonary diseases are kept as one of the actual problems of the pediatricians. nevertheless fulfilment of several scientific works on study of these diseases, presently we meet the complication of the respiratory diseases, recurrency, changing to the chronical type. objectives: the main purpose of our work to study the cytokine status and substance p, mutual connection they in frequently ill chil- results: in fic with respiratory diseases in the acute period of the disease increase of levels proinflammatory cytokines il- beta, il- , il- , tnf-alpha and substance p,decrease of levels il- and ifngamma was marked. clinical remission in these children is not accompanied by normalization of cytokine status and substance p. the high level of proinflammatory cytokines and substance p testifies to proceeding of inflammatory process that is possible connected with persistence of the infections agent. acute decrease in level of cytokines il- and ifn-gamma in these children,most likely, is caused by the presence of a immunodeficiency of cellular type. conclusions: in this connection it is necessary to carry out an adequate therapy of fic with arvi. introduction: atopic diseases are known to be characterized by a t helper (th) -skewed immunity. th -skewed immunity at birth, th -associated cc chemokine ligand (ccl)- , appears to be associated with high total ige levels but not of allergic outcomes later in life. the prevalence of asthma increases with a rapid upward trend after age ; however, there are few studies addressing the changes of ccl chemokine levels during infancy related to the development of atopic diseases in early childhood. objectives: we investigated children followed up regularly at the clinic for years in a birth cohort study. the levels of th related chemokine ccl were quantified in cord blood and age . by multiplex luminex kits. specific immunoglobulin e antibodies against food (egg white, milk, and wheat) and inhalant allergens (d. pteronyssinus, d. farina, and c. herbarum) were measured at months as well as . , , and years of age. results: a total of pairs of ccl chemokine levels from birth to age . were recruited in this study. k-means clustering was performed using r software and package mfuzz and this resulted in groups of ccl chemokine levels that declined from around to pg/ml (cluster a, n= ), from around to pg/ml (cluster b, n= ) , and raised from around to pg/ml (cluster c, n= ) . in children with raised ccl chemokine levels appeared to be associated with a higher prevalence of house dust mite sensitization at age . . furthermore, raised ccl levels during infancy were significantly associated with higher risk of asthma at age (p=. ). conclusions: raised ccl chemokine levels during infancy appear not only to be associated with an increase in the prevalence of house dust mite sensitization but also the risk of asthma in early childhood. | serum periostin is "not" a biomarker for pediatric asthma suzuki n ; hirayama j ; nagao m ; kameda k ; kuwabara y ; kainuma k ; ono j ; ohta s ; izuhara k ; fujisawa t mie national hospital, tsu, japan; shino-test corporation, kanagawa, japan; saga medical school, saga, japan introduction: periostin is a matricellular protein induced by type helper t-cell cytokines, expressed by airway structural cells and is thought to contribute to airway remodeling and progressive lung function decline in severe asthma in adults. we sought a possible clinical utility of serum periostin in children with asthma. objectives: we recruited volunteer children and adolescents (age range, to years) who were otherwise healthy except for allergic diseases including bronchial asthma. allergic diseases were classified with isaac questionnaire and serum levels of periostin were measured with elisa. abstracts | results: a total of volunteers were enrolled. among them had no allergic diseases (na), had only allergic rhinitis (ar) and the rest of had bronchial asthma (ba) and/or atopic dermatitis (ad) . serum levels of periostin in na younger than were significantly higher than the older counterpart and the levels in children < years old were similar across each age. data distribution of serum periostin in ar were very similar with that in na and we defined na and ar groups as reference population. reference values, geometric mean (+ geometric sd range), for serum periostin were ( ) and ( ) ng/ml in children/adolescents < and ≥ , respectively. there were no gender differences in serum periostin in the reference population. we then compared the serum levels of periostin in ad and/or ba with the reference group and found that serum periostin in ad and ad+ba, not ba, in < years old were significantly higher than the reference group. in addition, severity of asthma had no association with serum periostin levels in age group of < . on the other hand, the levels in ba aged ≥ were slightly higher than non-ba (statistically significant). conclusions: serum periostin is physiologically high in children and adolescents, possibly in growing age, and the levels are elevated in those with ad, not ba. serum periostin is "not" a useful biomarker for pediatric asthma. | clinical, biochemical and radiological factors for response to aspirin desensitization in patients with aspirin exacerbated respiratory disease-pilot study introduction: aspirin desensitization is regarded as an effective and well-tolerated therapy for patients with aspirin exacerbated respiratory disease (aerd). despite many studies investigating the pathophysiology of aerd, the underlying mechanism responsible for the beneficial effects of aspirin therapy has not yet been clarified. the aim of the study was to evaluate the influence of aspirin desensitization on clinical, biochemical and radiological changes in aerd individuals. objectives: this is a prospective study of twenty-one aerd patients subjected to one-year aspirin desensitization. all participants were hospitalized three times over the period of one year. at baseline and during each follow-up visit ( nd and th month) blood, urine, induced sputum (is) and nasal lavage (nl) were collected from all participants. the acquired material was processed in order to evaluate ) is and nl cell count ) concentrations of is and nl eicosanoids ) leukotriene e (lte ) in urine and ) periostin in blood. additionally, participants underwent a ct scan of the paranasal sinuses at baseline and after months of aspirin therapy. the lund-mackay score values were compared. for statistical analysis, summary statistics and repeated measures anova with post-hoc test were applied. results: twenty participants completed a one-year aspirin therapy. there was a statistically significant decrease in the number (p=. ) and percentage (p=. ) of eosinophils in is between baseline and after aspirin desensitisation. significant increase of urine lte in the course of aspirin therapy was observed (p=. ). the levels of prostaglandins and leukotrienes in is and nl as well as blood periostin level and the differential cell count in nl did not change during aspirin desensitization. in ct scan images the regression of the lesions in paranasal sinuses was observed in %, the worsening in % and in % of patients no changes were noted. in is count of eosinophils in aspirin-sensitive individuals, which may potentially be used in disease monitoring and tailoring asthma therapy. aspirin desensitization did not lead to significant changes in local eicosanoid levels in is and nl. blood periostin level is not a good marker for patient's response to aspirin desensitization. introduction: one of the main severe asthma phenotype is the "severe eosinophilic" or "eosinophilic refractory" asthma, for which novel biologic agents are emerging as therapeutical options. in this context, blood eosinophils count are one of the most reliable biomarker. objectives: the aim of our study is to evaluate the performance of a point-of-care peripheral blood counter in a clinical setting of severe asthmatics. seventy-six patients with severe asthma were evaluated, for blood cells count, by both a point-of-care and a standard analyser. results: the inter-and intra-assay variation was acceptable for leukocytes, neutrophils, lymphocytes and eosinophils. this was not the case of monocytes and basophils. a significant correlation between blood eosinophils assessed by the two devices was found (r = . , p<. ); similar correlations were found also for white blood cells, neutrophils and lymphocytes. the point-of-care device showed ability to predict blood eosinophils cutoffs used to select patients for biologic treatments for severe eosinophilic asthma, and the elen index, a composite score useful to predict sputum eosinophilia. introduction: over years ago there was revealed periostin should play an important role in pathogenesis of allergic inflammation including asthma and processes of tissue remodeling and fibrosis. its expression has been observed in the thickened basement membrane as well as in serum of asthmatic patients. thus, measuring of periostin serum levels may shed some light on these elusive asthma features. periostin has already demonstrated a convenient value in clinical studies as a companion diagnostics for lebrikizumab, tralokinumab or omalizumab treatment. however, to date, the changes of periostin serum levels following asthma therapy except for inhaled corticosteroids remain unclear. objectives: to emphasize this issue we have collected clinical and laboratory data including serum periostin of asthma patients ( males/ females) in a cross-sectional study. all patients were treated either by conventional therapy comprising inhaled corticosteroids (n= ) or by inhaled corticosteroids with additional biological therapy (omalizumab) (n= ). asthma phenotype, control, complications, comorbidities and other available biomarkers have been assessed and statistically analysed. results: we have observed a weak but statistically significant correlation between serum periostin and total ige levels (p=. ) and absolute eosinophil count (p=. ). association between periostin and total ige had nonlinear character (p=. ), and was expressed particularly in non-severe asthma patients without omalizumab treatment (p=. ). despite mutual correlation between serum periostin a total ige levels, both biomarkers showed different reaction on asthma treatment. multivariate analysis demonstrated, that only periostin levels, in contrast to all other assessed biomarkers, were significantly decreased in severe asthma patients treated by omalizumab (p=. ). this relationship was independent of asthma control (assessed by asthma control test -act), exacerbation rate, hrct or spirometry measurement results or comorbidities, except chronic rhinosinusitis with nasal polyps (crswnp) (p<. ). conclusions: we demonstrate, serum periostin levels are dependent on therapy, thus it may contribute not only to asthma phenotype stratification, prediction of treatment responsiveness, complications such as remodeling but probably more precise monitoring of therapy effect too. | usefulness of serum pteridines as a biomarker for childhood asthma kasuga s ; hamazaki t ; fujitani h ; fujikawa s ; niihira s ; shintaku h department of pediatrics, osaka city university graduate school of medicine, osaka, japan; the national institute of special education, tokyo, japan introduction: reliable and stable biomarker of airway inflammation is essential to determine intensity of asthma treatment. exhaled nitric oxide (feno) has been introduced to assess useful marker of airway inflammation but it fluctuates depending on steroid inhalation. nitric oxide is produced by nitric oxide synthase which requires tetrahydrobiopterin (one of pteridines) as a cofactor. objectives: to assess pteridines as a biomarker of childhood asthma control. results: asthmatic children were recruited for periodical asthma checkup program in japan to assess asthma control status by using objective questionnaire, respiratory function tests, airway resistance, feno, and serum pteridine levels. serum pteridine levels were measured by high performance liquid chromatography. total japanese children ( - years) were participated in this program. children who have no asthma attack over three years were divided as remission group to evaluate the long-term asthma control. the other children were divided as asthma group. furthermore, we divided asthma group for three groups by childhood asthma control test (c-act) scores to evaluate the short-term asthma control. and we had age matched children as control group. pteridine levels tended to decrease in patients who showed higher feno in asthma group. asthmatic children showed lower pteridine levels than other groups. there are significant differences between control group and remission groups and asthma groups (p<. , tukey's honestly significant difference test). but there are no significant differences between the three groups in asthma group (well-controlled group, partly-controlled groups and uncontrolled groups) which were divided by c-act scores. the low concentration of serum pteridines in children with stable asthma may indicate poor long-term control of asthma. but that not indicate poor short-term control of asthma. since pteridine biosynthesis pathways were suppressed by th mediated immune response, these results suggest that th mediated immune response was dominating the th response in asthmatic children. therefore, serum pteridines could be a novel biomarker of stable asthmatic children. introduction: asthma is a syndrome with chronic airway inflammation. the goal in the treatment of asthma is to control the inflammation. however, there has been a scarcity of useful noninvasive tests for monitoring the airway inflammation in clinical setting. metabolites of the eicosanoids pathways in induced sputum of the patients with asthma could be valuable biomarkers that can reflect the airway inflammation. objectives: to investigate eicosanoid metabolites and to find out their phenotypic differences, induced sputum supernatants from patients with refractory asthma, patients with controlled asthma, and normal control subjects were analyzed by using liquid chromatography tandem mass spectrometry. in addition, we evaluated the relationship between asthma exacerbation and eicosanoid metabolites. results: among metabolites which were measured, metabolites were detected in the induced sputum. we found that normal control subjects had higher concentrations of prostaglandin (pg) d (normal subjects vs controlled asthma vs refractory asthma, median conclusions: eicosanoid profiles in induced sputum supernatant were different between patients with refractory asthma, those with controlled asthma, and normal control subjects. our findings suggest that they could be biomarkers to differentiate refractory asthma from controllable asthma or non-asthma. this work was supported by the research program funded by the korea centers for disease control and prevention ( -er - ) . | serum periostin in asthma is related to disease severity, eosinophilia and il- introduction: introduction: asthma is a chronic inflammatory disease where more than powerful inflammatory mediators are associated with airway hyperresponsiveness, mucus hypersecretion, activation of fibroblasts and hyperplasia and hypertrophy of smooth muscles of the airways and if they do not use preventive antiasthma treatment can cause irreversible airway remodeling. objectives: the aim of this study was to determine the effect of adding montelukast to combined therapy icss/labas in patients with uncontrolled asthma by analyzing of serum level of il- , il- , eosinophils and symptom score. methods: in study we included patients, they were treated with icss/labas ( / mcg-twice daily) plus montelukast ( mgdaily). in each of them were measured serum levels of il- and il- by the elisa method, value of eosinophils were obtained with visual examination of peripheral blood smear, and assessing symptom scores with -point likert scale of breathlessness at the beginning and after months of therapy. objectives: this study has been focussed on a detailed comparison of two samplers-cyclone and chemvol-and on the parameters that could influence their efficiency. results: airborne concentrations of two key olive and grass allergens, ole e and phl p , respectively, were monitored over two years with different weather patterns, and , in c ordoba, located in south-western spain. allergenic particles were quantified by elisa assay and results were compared with pollen concentrations monitored using a hirst-type volumetric spore trap over the same study periods. the influence of weather-related parameters on local airborne pollen and allergen concentrations was also analysed. inter-year differences were observed with regard to pollen season timing and intensity. for both olive and grass, the pollen season was longer and the pollen index (pi) higher in ; that year the peak value was higher and it was recorded earlier. although a positive correlation was detected between results obtained using the two samplers during the pollen season, results for the cumulative annual allergen index varied considerably. the two samplers revealed a positive correlation between pollen concentrations and both minimum temperature during the warmer year ( ) and maximum temperature during the cooler year ( ); a negative significant correlation was observed in both cases with rainfall and relative humidity. conclusions: in summary, although differences were observed between the two samplers studied, both samplers may be suitable for allergen detection. objectives: the scientific council of rnsa was asked to update the allergy potency (ap) of plant species that can be established in urban areas. to update the allergy potency of plant species, the rnsa used scientific work on the subject, and also the opinions of allergists and botanists. the pollen grains of anemophilous species are transported by wind; they produce very large quantities of pollen grains so that the fertilization of female flowers has a greater chance of being effective. the majority of allergenic species are anemophilous. results: the pollen allergy potency of a plant species is the ability of its pollen to cause an allergy to a significant part of the population. the allergenic potential can be: low or negligible: no problem to plant them in urban garden moderate: only a few species can be planted in the same garden high: this species cannot be planted in urban places. the table presented on the poster will permit to know the level of allergy potency of more than species. conclusions: species or genus with a strong ap should be labeled as "not to be planted in habitation or residence area ", those with moderate ap should be labeled as "not to be planted in big quantities in habitation or residence area". other species with low or negligible ap may not be affected by public information. gadermaier g ; metz-favre c ; stemeseder t ; de blay f ; pauli g universit e de salzbourg, salzbourg, austria; chru strasbourg-allergologie, strasbourg, france introduction: the purpose is to study the profile of cutaneous and molecular sensitization of patients sensitized to plantain pollen living in the north-east of france. objectives: the sera of patients with seasonal pollinosis and cutaneous polysensitization including a positive test to plantain, are investigated through immunoblot (ib), elisa and immunocap. the plantain immunoblot is inhibited with plantain, grass, ash and birch pollen extracts as well as with pla l . the specific iges against pla l , phl p - and profilin are measured. results: pla l , the major plantain allergen is detected by ib in cases out of , either in glycosylated or non-glycosylated form. an allergen of kda is detected in out of cases, always and exclusively inhibited by the grass extract. the intensity of the spot is proportional to the anti-phl p / phl p ige levels, and corresponds to an allergen which is cross-reacting with grass. other cross-reacting allergens with grasses are detected at kda ( / ), and at - kda ( / ). at the molecular weights of to kda, we detected in addition to pla l , cross-reacting allergens with grass, ash and birch pollen which predominantly corresponded to profilin which was confirmed by specific ige measurements in cases. conclusions: among the patients included in this study, only % had genuine sensitization to plantago, which never corresponded to a monosensitization in our cohort. most often cutaneous sensitizations to plantain pollen were based on ige cross-reactivity with grass pollen allergens mainly through a kda allergen and/or profilin. the strong environmental grass pollen pressure, compared to the low plantain pollen exposure, seems to be at the origin of this profile of molecular sensitization. these results reinforce the superiority of molecular diagnosis in patients with pollinosis, who are polysensitized. | sensitisation to peach tree pollen in a highly exposed population results: the % of subjects were sensitized to pp, which was the most prevalent after olive tree, grass and cypress pollens, respectively. sensitization to peach fruit was %. pru p spt was tested in / pp positive cases, being % positive ( / ). specific ige to pru p was detected in / pp sensitized individuals. immunoblot showed specific ige to different components in the pp extract, being the most frequent band recognised a - kda protein. conclusions: pp is a prevalent inhalant allergen in highly exposure areas. in our population pru p was not identified as the major allergen. other pp molecular components need to be identified and their clinical relevance should be further investigated. introduction: allergic respiratory diseases increase after an exposure to airborne pollen, as asthma and allergic rhinitis, are deeply increasing and nowadays, they represent one of the major public health problems. olive pollen is one of the main causes of allergic disease in the mediterranean area, especially in northwest and west of the turkey. olive pollen has been characterized proteins with allergic activity and ole e is the major allergen of olea pollen. objectives: the aim of this study was to estimate the correlation between daily airborne olive pollen and ole e in the atmosphere. aeroallergen load of ole e detected by cascade impactor (chemvol) using prewashed polyurethane foam and pollen counts recorded by hirst trap. chemvol sampler collects particles at l/minutes and it contains impaction stages pm> micron and >pm> . lm. this sampler is being tested in the frame of the project hialine. results: generally, similar behaviour of pollen count and total allergenic load of ole e was observed during the main pollen season. nevertheless, in some occasions, before and later of main period, airborne ole e activity was recorded and some differences between pollen grain/m and allergen concentration/m were detected. pollen from different days released -fold different amounts of ole e per pollen. average allergen release from pollen was much higher in ( . pg ole e /pollen, r =. ) than in ( . pg ole e /pollen, r =. ). indeed, yearly olive pollen counts in were . times higher than in , but ole e concentrations were . times higher. these results have shown that ole e is mostly associated with olive pollen grains but aeroallergen load was not always directly proportional to airborne pollen counts. this suggests that ole e quantification is a better marker for olive allergen exposure. in conclusion, aeroallergen monitoring may contribute to a better understanding of the ole e exposure from airborne pollen. objectives: to describe the clinical profile of the patients sensitized to alt at and to assess the sensitivity of the prick test with the alternaria extract in comparison to the patients sensitized to both allergens alt a and alt a . out of the patients, ( . %) were sensitized to alternaria with specific ige of ≥ . isu to alt at or alt a . twenty patients ( females and males, age - years old) who were sensitized to alt a were selected. we analyzed the clinical profile, total ige values, other co sensitizations as well as the clinical relevance of alternaria sensitization in these patients. : of the patients sensitized to alternaria, ( . %) were sensitized to alt a , of which ( . %) were monosensitized to alt at . the mean age was lower in monosensitized (ẋ . vs . ). among the patients monosensitized to alt a , ( %) had prick test negative with the alternaria extract. eight out of patients were polysensitized to more than three different aeroallergens and were asthmatics ( persistent). the median total ige was higher in monosensitized ( ku/l vs ku/l). of these patients, alternaria sensitization has clinical relevance in ( %), of which have positive prick test to alternaria. all the patients ( / ) sensitized to both allergens have positive prick test to alternaria. ten of them were polysensitized, were asthmatic ( persistent) and sensitized patients showed clinical relevance. introduction: the role of vitamin d as a potential immune-modulator has been recently elucidated. dendritic cell, a key regulator driving towards th immune response in allergic diseases is known to be affected by vitamin d. however, the role of vitamin d in the pathogenesis of allergic rhinitis is unclear and its anti-allergic effect has not been established yet, especially in the mouse model. objectives: the aims of this study are to evaluate ) the anti-allergic effect of topically applied vitamin d in the allergic rhinitis mouse model, and ) the effect of vitamin d on dendritic cell activation. results: balb/c mice were intraperitoneally sensitized with ovalbumin (ova) and alum, and they were intranasally challenged with ova. intranasal , -dihydroxyvitamin d was given to treatment group and solvent was given intranasally to sham treatment group. allergic symptom scores, eosinophil infiltration, cytokine mrna levels (il- , il- , il- , il- , ifn-c) in the nasal mucosa, serum total and ova-specific ige, igg , and igg a were analyzed and compared with negative and positive controls. cervical lymph nodes were harvested for flow cytometry analysis. in the treatment group, allergic symptom scores, eosinophil infiltration, and the mrna levels of il- and il- were significantly reduced compared to positive control. il- mrna level, serum total ige, and ova-specific ige and igg levels showed a tendency to decrease in the treatment group, but did not reach to a significant level. il- did not show a significant difference between groups. cd c + , mhcii hi , cd + activated dendritic cells were significantly reduced in the treatment group. cd + , cd + , foxp + treg cells tended to increase in the treatment group, however it was not significant. the intranasal instillation of , -dihydroxyvitamin d has an anti-allergic effect in the allergic rhinitis mouse model. we believe that the anti-allergic effect of vitamin d is mediated by the inhibition of dendritic cell activation, and therefore decreased objectives: we wanted to assess whether treatment with cyclosporine and tacrolimus allows children with vkc to improve the level of vitamin d due to the higher summer sun exposure for good control of the ocular symptoms. objectives: our objective was to assess the expression of smad and smad proteins in patients with asthma in correlation with clinical parameters and the expression's changes in response to allergen and methacholine challenge test. the study included patients with asthma and healthy volunteers. spirometry, skin prick tests (spt), allergen and methacholine provocation tests were performed in compliance with standards. personalized clinic surveys including act tm were collected. venous blood was collected before and after provocation. the expression levels of il- and il- and smads were evaluated by qrt-pcr using isoform-specific primers. results: we showed correlation between the mrna expression of smad and the asthma control according to act tm (p<. ). the expression of smad is higher in the group of uncontrolled ( -Δct = . , p<. ) and in the group of partially controlled patients ( -Δct = . , p<. ) in comparison to the group of patients with controlled asthma ( -Δct = . ). we proved that expression of mrna of smad correlates significantly with expression of il- and il- in patients with asthma (il- r= . ; il- r= . ) and in the control group (il- r= . ; il- r= . ) (p<. ). expression of smad elevates more after methacholine provocation test (median -Δct = . ) rather than after allergen provocation test (median -Δct = . ; p=. ). we showed also that skin prick test results correlate positively with smad level after the provocation (p<. ). conclusions: the loss of asthma control is connected with expression of smad , which is part of tgf-ßrii related pathway. il- and il- correlates with smad expression, which can indicate the participation of these cytokines in the regulation of this pathway. the expression of smad elevates after methacholine and allergen provocation as well as it correlates positively with skin prick test results, which can be useful clinically. to sum up, tgf-ß-tgfßrii-smad proteins are an important mediators of inflammation in asthma. | deletion of nfatc in t lymphocytes affects th and th cell differentiation as well as il- -mediated mast cell activation in allergic asthma objectives: analysing the role of nfatc in the allergic trait of human asthma. additionally, we investigated the influence of nfatc on t cell differentiation and immunoglobulin class switch and explored its impact on mast cell differentiation in experimental asthma. with the children s hospital in erlangen, we studied nfatc mrna expression in freshly isolated pbmcs from pre-school children with and without asthma. in asthmatic children, we found increased nfatc mrna expression, especially in those with a positive skin test. these results were confirmed in the asthma bio-repository for integrative genomic exploration (asthma bridge) study, where the isoform a and d of nfatc were found significantly increased in asthmatic adults with a positive skin test. moreover, il- was also found increased in the supernatants of pbmcs of asthmatic children with a positive skin test. furthermore, mice with a deficiency of nfatc in cd + t cells display significantly lower levels of il- . additionally, these mice show reduced numbers of lung th and th cells. moreover, basic leucine zipper atf like (batf), which is known as an important transcription factor for t cell differentiation as well as immunoglobulin class switch, was found decreased in these mice. consequently, ova-specific ige and total igg levels were found significantly decreased after allergen exposure and in the absence of nfatc . furthermore, nfatc deletion also resulted in decreased mast cell numbers. we then analyzed the effect of il- on mast cell differentiation and histamine release. we observed that bone marrow differentiated mast cells incubated with ova and il- had an induced histamine release. conclusions: thus, nfatc deficiency in t cells results in defective ige production affecting ige-orchestrated mast cell activation mediated through il- . therefore, nfatc emerges as a novel target for anti-allergy intervention. | efficiency of the use of nitric oxide donors for the treatment of bronchial asthma bazarova s; djambekova g center of therapy, tashkent, uzbekistan introduction: to study the influence of nitric oxide donor-l-arginine-on indicators of endothelial system in patients with bronchial asthma. objectives: patients aged - years ( ae . years) with moderate persistent bronchial asthma were examined. ratio of men to women was / . two age-and sex-matched groups were randomly selected. main group ( patients) received nitric oxide donor -l-arginine in addition to standard background therapy (gina, ) . the medication ( ml of . % solution, tivortin, "yuria-farm", ukraine) was administered intravenously once daily for days. the control group ( patients) only received the background therapy. the efficiency was assessed with the use of conventional methods of study (clinical laboratory methods, instrumental methods: spirography, peak flow monitoring, bronchomotor tests). concentration of nitric oxide stable metabolites in exhaled breath condensate (ebc) and in blood was studied. their ratio was also assessed. results: baseline data in patients of both groups demonstrated the increase of level of nitric oxide stable metabolites in blood ( . ae . mmol/l) and in ebc ( . ae . mmol/l). after the treatment the positive clinical efficiency of inclusion of l-arginine was much higher than that in the control group (p<. ). in the main group, reduction of requirement for beta -agonists, decrease of frequency of night-time symptoms, decrease of frequency of lowest pef rate in the morning and improvement of respiratory function were observed on average on the rd/ th day compared to the control group were such improvements were evident on the th/ th day. in the main group the concentration of nitric oxide stable metabolites significantly increased in blood ( . ae . mmol /l, p<. ) and in ebc ( . ae . mmol/l, p<. ). in the control group the concentration of nitric oxide stable metabolites changed in blood ( . ae . mmol/l) and in ebc ( . ae . mmol/l), but not significantly. introduction: abpa is currently believed to be an exaggerated form of aspergillus sensitization, and is probably the first step in its development. objectives: the aim of this study was to investigate the clinical and immunologic characteristics of fungal-sensitive asthma (fa), nonfungal-sensitive asthma(nfa) and abpa. conclusions: there were different clinical and immunological features among nfa, fa and abpa. the abpa had worse function as well as higher percentage of bronchiectasis, and higher dose of oral corticosteroid. besides, the sensitivity to aspergillus was more severe in abpa. the level of sige-a.f was associated with the damage of lung function. | self-reported allergic rhinitis and/or allergic conjunctivitis associate with il rs genotypes in finnish adult asthma patients introduction: the increased prevalence of asthma and allergic diseases is a major public health problem worldwide. atopy, family history, inhaled irritants, and upper airway inflammation are known risk factors of asthma. a population-based sample of finnish adult asthma patients (n= ) and matched controls (n= ) filled a questionnaire. asthma was diagnosed based on a typical history of asthma symptoms and lung function tests. skin prick tests (spt) with aeroallergens and blood tests including analysis of interleukin (il ) rs (g/a) genotypes were performed for a subsample (n= ). objectives: our aim was to observe in adult asthmatics with and without allergic co-morbidities e.g. subject-reported allergic rhinitis and/or allergic conjunctivitis (ar/ac) association with il rs genotypes and other factors. results: the proportion of asthmatics reporting ar was . % and ac was . %. after adjustments, the presence of il rs aallele (or= . ci= . - . , p=. ) or multi-sensitization (adjusted or= . , ci= . - . , p=. ) associated with ar/ac-asthma. nasal polyps and aspirin-exacerbated respiratory disease associated also with ar/ac-asthma. conclusions: adult ar/ac-asthma could putatively be a phenotype, characterized by the presence of atopic and/or eosinophilic factors and a high prevalence of the il rs a-allele. studies on the mechanisms behind this and in other populations are needed. | immunoregulatory role of nfatinteracting protein (nip) in adaptive and innate immune responses in allergic asthma introduction: nfat-interacting protein (nip) is a th associated transcription factor. after t cell receptor stimulation, the arginine methylation domain of nip supports the interaction with nfat, thereby enhancing the production of the th cytokine il- . moreover, nip deficient mice have been shown to be deficient in il- and ifn-gamma production indicating that nip controls both th and th cytokine production and might therefore play a protective role in allergic asthma . objectives: we wanted to analyze the importance of nip in allergic asthma in pre-school children as well as adults. furthermore, we investigated the role of nip in a murine model of allergic asthma to find out more about its contribution to adaptive as well as innate immune responses in the disease. results: in the european study predicta, in collaboration with the children s hospital in erlangen, we analyzed nip mrna expression by using quantitative real time pcr in rna extracted from pbmcs isolated from pre-school children with and without asthma. in the pbmcs of the asthmatic children, nip mrna expression was found significantly increased compared to healthy control children. furthermore, nip mrna expression was also found induced in cd + t cells in adult asthmatics from the asthma bio-repository for integrative genomic exploration (asthma bridge) study. we further analyzed the importance of nip in a murine model of allergic asthma. after allergen sensitization and challenge nip (-/-) mice showed decreased airway hyperresponsiveness, inflammation and mucus production, three of the main patho-physiological features of asthma. additionally, we discovered that nip (-/-) mice released decreased th type cytokines and also expressed less st , which is the receptor for il- , after allergen challenge. furthermore, a defect in innate lymphoid cell type (ilc ) differentiation was observed in the absence of nip in allergic asthma and in bone marrow differentiated ilc s indicating a crucial role for nip in mediating asthma via ilc s. conclusions: in summary, we found that the lack of nip influences not only immune responses of the adaptive immune system but also influences components of innate immunity resulting in a abstracts | protective phenotype to allergic diseases such as asthma. objectives: in the study were included ap and healthy controls (hc). fraction of exhaled no (feno), standard lung function parameters, complete blood count and absolute count of cells, serum ige, crp, il- , il- a and periostin were measured. results: four clusters were identified by cluster analysis: cluster (c )(n= )-late-onset, non-atopic, eosinophilic asthma with impaired lung function, cluster (c )(n= )-late-onset, atopic asthma, cluster (c )(n= )-late-onset, aspirin sensitivity, eosinophilic asthma and cluster (c )(n= )-early-onset, atopic asthma. we have found higher levels of il- in all clusters ap as compared to hc (c : p=. , c : p=. , c : p=. and c : p=. ). tendency for higher levels of serum il- in c compared with c or c (p=. or p=. , respectively) was observed. periostin levels were significantly higher in c (p<. ), c (p<. ) and c (p<. ) as compared to hc. there were no differences in periostin levels between all clusters (anova, p=. ). il- a levels were significantly higher only in c as compared to hc or to c and c (p<. , for each comparison). we have found correlation between il- and crp (r=. ; p=. ) in c , il- a and periostin in c (r=. ; p=. ) and in c (r=. ; p=. ). interestingly, we have observed negative correlation between the duration of asthma and il- a (r=À. ; p=. ), but positive between the duration of asthma and crp (r=. , p=. ) in c . our results have shown higher levels of il- in all clusters as compared to hc that are associated with marker for systemic inflammation. periostin levels were significantly elevated in c , c and c as compared to hc with no differences between the clusters. a positive correlation between periostin and il- a in c and c was observed, that rising the question about their interrelationship in the pathogenesis of late-onset asthma. serum il- a was significantly higher in c in comparison with hc or c and c suggesting that th mediated immunity may be involved in early-onset, atopic asthma. these data support the concept of heterogeneity of the bronchial asthma. | eosinophil activation with autophagy and extracellular dna traps is involved in severe asthma results: il- +lps treatment significantly increased autophagy and eet levels from pbes of the study subjects (p<. for all), which were in a positive correlation (r=. , p<. ). compared to nsa patients, both untreated and il- +lps-treated pbes from sa patients had significantly higher autophagy levels (p=. and . , respectively), while only il- +lps-treated pbes from sa patients had higher eet level (p=. ). eet level from untreated pbes was correlated with serum eosinophil cationic protein level (r= . , p= . ) and fev % predicted value (r=À. , p=. ). co-culture of aec with pbes slightly increased il- production, which was significantly enhanced by il- +lps treatment (p<. ). the il- production in co-culture system was reduced by pretreatments with dexamethasone ( mm, p=. ), antibodies against major basic protein ( ng/ml), il- receptor ( mm) and il- receptor ( mm, p=. for all), but increased by cotreatment with micrococcal nuclease ( iu/ml, p=. ). conclusions: pbes from sa patients are highly susceptible to be activated to produce high levels of autophagy and eet, which could enhance and maintain airway inflammation. we suggest that steroid and anti-il- /il- receptor antibodies may be beneficial to control airway inflammation in severe eosinophilic asthma via inhibition of eet production, while dna digesting reagents may increase airway inflammation. introduction: it has been demonstrated that exposure to stress induce hyporeactivity of the hpa system by modifying the secretion of cortisol and also that psychosocial stressors such as poor social status are associated with an increased risk of childhood asthma, decreased serum cortisol and high ige response. thus, from this concept it could be postulated that a blunted hpa axis response may increase the risk for allergic inflammatory reaction. objectives: aim of this study was to evaluate the association of serum cortisol in pediatric allergic bronchial asthma and its influence on the ige immune response in a poor children community with psychosocial chronic stress. results: this was a pilot analytical case control study( ipa positive subjects and healthy control paired by age and gender, both from poor areas of barranquilla objectives: in order to characterize bp an immunoproteomics analysis was conducted, i.e. electrophoretic separation of cypress pollen extracted proteins, ige western blotting using cypress pollen allergic patient's sera and mass spectrometry (lc/ms/ms) for identification of ige-binding proteins. results: ms analysis using chymotrypsin identified in bp a peptide also found in the family of protein snakin/gibberellin-regulated protein (grp). the snakin- , an anti-microbial peptide of potato, produced as a amino-acid recombinant protein (homologous to the c-terminal part of grp), is recognized by ige from cypress pollen allergic patients with ige to bp . this ige reactivity is abolished after reduction of disulfide bridges and is inhibited by a cypress pollen extract. ige reactivity to bp is however barely inhibited by the recombinant potato snakin- . conclusions: bp exhibits a molecular mass closer to grp than to snakin and the absence or very low inhibition of the ige reactivity to bp with snakin may be explained by peptidic ige epitopes on the n-terminal part of bp . the potato snakin- share % sequence identity with peamaclein, the peach allergen pru p , also shown in citrus. these results might explain the peach/cypress and citrus/cypress syndromes described and point out bp as the cross reactive allergen. the proteins of snakin/grp family present in many fruits and vegetables might include allergens involved in pollen/food associated syndromes. introduction: exposure to high levels of grass pollen may lead to a high degree of allergic inflammation, sensitization to minor allergens, such as profilin, and development of severe profilin mediated food reactions, similar to those described due to sublingual immunotherapy (slit). objectives: our objective here was to identify genetic biomarkers in order to generate a model that can improve the classification and treatment of patients with a higher probability of developing severe adverse reactions. results: healthy subjects (group , control) and patients with mild (group ) or severe (group ) profilin mediated food reactions were studied. rna extraction was performed on ficoll-isolated pbmcs using the rneasy ® mini kit (qiagen) and its integrity was analyzed with experion rna stdsens analysis kit (bio-rad). the gene expression profile of all the samples was analyzed using the gene-chip ® wt plus reagent kit (affymetrix) and two specific software: affymetrix ® expression console ™ and affymetrix ® transcriptome analysis console (tac). finally, the microarray data was validated by quantitative real-time pcr (qpcr). the hierarchical clustering of the samples shows the separation of the patients into three clusters coincident with the three established clinical groups (control, mild and severe). genetic profile of patients with mild reactions is similar to healthy patients while severe subjects were significantly different from the other two groups. genes regulated in the severe group were related to histone modification pathways, human complement system, cell adhesion and tgf-b and its receptor. these changes may be associated with the different degree of inflammation between patients in each experimental group. in the course of our study we found out that severe patients had different rna expression patterns compared to mild and non-allergic patients. this lead to the identification of genetic biomarkers useful for the generation of a model able to predict severe reactions and/or adverse reaction during immunotherapy, thus improving the diagnosis and treatment of this type of allergic results: his-tagged recombinant allergens, namely parvalbumin, aldolase, enolase and tropomyosin from c. idella and l. crocea, as well as cod parvalbumin, were synthesized in e. coli and purified using immobilized metal-chelate chromatography. children with history of immediate-type fish allergy were included in this study and their serological ige reactivity to the fish allergen components were measured by elisa. children were positive to at least one allergen component, with nine of them being positive to parvalbumin. despite the high similarity between l. crocea, c. idella and cod parvalbumins ( . - . %), three children only reacted to l. crocea and c. idella parvalbumin but not to cod parvalbumin, while the other six children were positive to all three parvalbumins. competitive inhibition elisa revealed that c. idella parvalbumin inhibited > % of the binding of specific ige to both l. crocea and cod parvalbumin, while reciprocally only inhibition of % and % could be achieved respectively. two children were reactive to aldolase and enolase but not parvalbumin. one of them had positive sige to both enolase and aldolase from l. crocea, while the other reacted to aldolase from both species. these two children exhibited relatively mild subjective allergy symptoms (itchy skin and throat). notably, three children were non-reactive to all components tested, and two of them were outgrowing fish allergy clinically. introduction: anti-a-gal antibodies are naturally produced in response to the gastrointestinal flora. in red meat allergy, patients develop ige antibodies towards the a-gal epitope, which itself are structurally closely related to the blood group b antigen. objectives: this study aimed to explore the relationship between a-galand b-antigen-specific antibodies in red meat allergic patients compared to healthy individuals with blood group b or a/o. sera from red meat allergic patients and healthy blood donors of whom belonged to blood group b and to blood group a or o were included. ige reactivity against a-gal and the b-antigen were determined using immunocap. allergen-specific igg, igg , igg , igg , igg and ige were assessed by indirect elisa assay. statistical analysis was performed using spearman rank correlation and unpaired t-tests. results: all red meat allergic patients, of the healthy a/o and of the healthy b donors were ige positive to a-gal. however, the ige levels to a-gal were significantly higher in the allergic group compared to the healthy a/o and b individuals. the majority of the meat allergic patients, but none of the healthy individuals had ige antibodies against the b-antigen. a moderate correlation between a-gal and b-antigen specific ige was noted (r =. ). the red meat allergic patients had significantly higher igg levels against a-gal with igg and igg antibodies as the predominant difference compared to the healthy individuals. the healthy a/o ige positive individuals had significantly higher igg , igg and igg compared to the ige negative individuals. the igg response to the b-antigen followed the same pattern as to a-gal. there was a low correlation between the igg levels against a-gal and the b-antigen in both meat allergic patients and healthy a/o individuals (r =. and . ). introduction: fx , a food mixture of milk, egg white, fish, peanut, wheat and soybean, is largely used for food allergy detection. besides the fact that it is questionable if this is the better approach to identify a food allergy, the information that the test provides may represent a pitfall because a positive or negative result does not mean food allergy presence or absence, respectively. objectives: the goal of our study was to access the reason for fx request in a pediatric hospital and to analyze its suitability. methods: the fx requests, performed in a pediatric population of d. estefânia hospital over a five months' period, were analyzed, concerning demographic data, reason for request and attitude taken due to the result. this test was requested due to respiratory symptoms in patients, gastrointestinal symptoms in patients, cutaneous symptoms in patients and nonspecific complaints in patients. all of these symptoms were not directly related with food intake. a positive result was obtained in patients; of those, only were referenced to our immunoallergology department. in all of them a detailed clinical history was obtained and diagnostic tests (skin prick tests and specific ige) were performed in the ones considered suitable. food allergy was diagnosed in only one patient. conclusions: in the vast majority of patients, fx was asked for nonspecific complaints and often without a clinical history suggestive of food allergy. moreover, a positive fx test does not mean clinical reactivity or food allergy. on the other hand, the clinical history allows us to identify a suspect trigger in most of the children with food allergy. in such cases, it is preferable to request the specific ige towards the allergen, which gives a more precise and accurate result, instead of the fx . as our results showed, in the majority of the cases, the fx request was often made without complying with a reasonable criterion, implying unnecessary costs. the high number of requests verified may be explained because it is an easily accessible analysis but this attitude should be discouraged. tuppo l ; alessandri c ; pasquariello s ; petriccione m ; giangrieco i ; tamburrini m ; rafaiani c ; ciancamerla m ; mari a ; ciardiello ma istituto di bioscienze e biorisorse -ibbr-cnr, naples, italy; caam -centri associati di allergologia molecolare, rome, italy; cra, research unit on fruit trees, caserta, italy introduction: pomegranate, punica granatum l., is one of the oldest cultivated fruit trees. the fruit contains the arils, which are seeds covered by a red pulp, that is a juice sac. the arils are surrounded by the white and fleshy mesocarp. pomegranate can trigger allergic reactions, but the allergenic pattern of this fruit is still poorly characterized and only one allergen, the ltp pun g , was reported. objectives: the aim of this study was the investigation of the allergen pattern in pomegranate tissues and cultivars. reported symptoms were food impaction ( %), dysphagia ( %), heartburn ( %) and vomiting ( %). the first symptoms were more frequent in adolescents and adults ( %). children's main complaint was vomiting ( %) and cases presented failure to thrive. most patients had associated allergic diseases ( %), % had previous food allergy and % were sensitized to aeroallergens. endoscopic evaluation revealed esophageal stricture in patients. at least half of diagnostic esophageal biopsies had > eosinophils per highpower field and % showed microabscesses. food sensitization was found in % of the patients, mainly to cow's milk ( %), nuts and peanut ( %), cereals ( %) and egg ( %). considering therapeutic approach, % were treated with swallowed fluticasone and dietary elimination was recommended in %. oral corticosteroids were prescribed in patients. at present time patients had done endoscopic reevaluation, ( %) showed histologic resolution. five patients had clinical and histologic relapse during follow-up. conclusions: eoe has a balanced distribution but a distinctly clinical presentation accordingly to age group: children may present unspecific symptoms like vomiting, whereas adolescents and adults complain of food impaction and dysphagia. other atopic diseases and food sensitization is very common. introduction: air pollution, particularly ambient air particulate matter (pm), is considered as one of the most important environmental risks for human health. pm could potentially disrupt immune regulatory mechanisms and predispose exposed individuals to asthma. in contrast, children exposed to traditional farm environment seem to have a natural resistance to asthma. this phenomenon links with exposure to stable dust and subsequent immune regulatory mechanisms initiated in the airways. the underlying exposure agents and definitive pathways determining the risk of asthma are still to be identified. objectives: our aim was to investigate the effect of urban air pm (high risk environment) and farm dust (protective environment) on immune responses in finnish children. briefly, peripheral blood mononuclear cells (pbmcs) of -year-old children (n= ) were stimulated with farm dust extract ( lg/ml, stable in northern savonia, finland) and pm samples ( lg/ml, pm . - , pm - . or pm < . , nanjing, china) for hours. expression of immunogenic cd and tolerogenic ilt in circulating myeloid dendritic cells (mdcs) and plasmacytoid dcs (pdcs) and monocytes were analyzed by flow cytometry. pm samples were analyzed for polycyclic aromatic hydrocarbons (pahs), inorganic ions and elements. farm dust sample will be analyzed for microbial content. results: pm stimulation decreased the percentage of cd + monocytes and dcs among children's pbmcs, whereas farm dust stimulation increased the percentage of cells positive for this marker. the percentage of tolerogenic ilt + was decreased in all cell types after stimulation with pm. farm dust also decreased the percentage of ilt + monocytes, but not dcs. specific metals and pahs in pm associated with the studied immunological parameters. conclusions: samples from high risk and protective environments have differing capacities to influence immunogenic and tolerogenic properties in children's immune cells. the importance of these findings in relation to the risk of asthma in exposed populations will be studied further. introduction: alterations in cell surface glycosylation pattern is a common feature of tumor cells that might be related to immune evasion and malignancy. objectives: to study the capacity of the carbohydrate a (ca ) located in the surface of murine ehrlich tumor (et) cells and also in certain human adenocarcinomas to condition the phenotype and function of human dendritic cells (dcs) and the capacity to polarize t cell responses. results: nf-jb/ap- are not activated in thp cells by ca , however, this carbohydrate partially impairs the activation of these transcription factors induced by the tlr ligand pam csk. ca induces the expression of the tolerogenic marker pdl in human monocyte-derived dcs (hmodcs) as well as the production of il- and il- , analyzed by flow cytometry and elisa assays respectively. ca -activated hmodcs generate functional il- -producing cd + cd high cd -foxp + regulatory t (treg) cells that were able to inhibit the proliferation of cd + t cells from pbmcs in a dose-dependent manner. supporting the role of ca in the induction of treg cells, our in vivo data showed that the ca is present in the sera of tumor bearing mice and the percentage of foxp + treg cells is increased in the regional (inguinal) lymph nodes from tumor bearers. our results showed that ca -activated hmodcs induce the generation of foxp + treg cells both in vitro and in vivo, which might well condition the immune response against the tumor and promote the tumor escape. | assessment of changes in expression of immune system biomarkers to assist the differential diagnosis of acute bacterial infections introduction: biomarkers for acute infections include c-reactive protein, mmp- , sicam- , procalcitonin, and neutrophil band counts for bacterial infection. a rapid means of assessment of acute bacterial infections via biomarker assessment was sought. objectives: the expression of toll-like receptors (cd and cd ), complement receptors (cd and cd ), integrins (cd b and cd c), fc-receptors (cd and cd ) and l-selectin (cd l) on the surface of blood neutrophils and monocytes stimulated with inactivated e. coli, l. acidophilus, e. coli derived bacterial ghosts, e. coli lps and l. acidophilus cell walls was assayed using flow cytometry. both the percent of expression and mean fluorescence intensity (mfi) were analyzed for each molecule. results: all the bacterial components used exerted similar activation capabilities even in low concentrations. while the expression of cd b, cd c, cd , cd and cd was enhanced by both neutrophils and monocytes under activation, the expression of cd significantly increased only in neutrophils. the expression of tlr and tlr was slightly increased by neutrophils and monocytes. the expression of cd l by monocytes and neutrophils (the percent of activated cells as well as the mfi) was decreased during activation. there was a negative correlation between cd l expression and integrins (cd b and cd b). the activation index was calculated for each molecule as a ratio of expression of molecule by activated cells vs cells used as a negative control (resting). the highest values for the activation index was seen with cd b, cd c, cd , cd , cd l and cd mfi by neutrophils and monocytes, and the percent of cd expression by neutrophils. conclusions: e. coli and bacterial ghosts significantly increased the expression of cd b, cd c, cd , cd , cd l and cd by neutrophils and monocytes even in very low concentrations, suggesting use as potential biomarkers in the differential diagnosis of the etiology of acute infections. objectives: the aim of this study was to evaluate changes in peripheral blood monocyte expression of cd , cd , cd , cd , hla-dr, and cd in kidney allograft recipients. in total, patients who underwent renal transplantation from a deceased donor were enrolled in the study. the phenotype was evaluated by a multicolor flow cytometry in defined time points and in the case of complications requiring fine needle aspiration biopsy procedure. the results confirmed our pilot data, proportions of peripheral cd +cd + monocytes were downregulated during the first week after the kidney transplantation while the percentage of cd +cd + monocytes dramatically increased early after the kidney transplantation and remained high for at least four months in most patients. the expression of cd (marker of m macrophages) was limited only to a small population of monocytes (less than % in most patients) but the receiver operating characteristic (roc) curve analysis showed its potential importance by significant correlation with acute rejection with a sensitivity of % and specificity of . % (area under the roc curve . , p-value: . ). no correlation between two different m markers cd and cd has been found. the expression of cd (dc-sign) was low and did not show any changes in time or association with acute rejection. hla-dr (mhc ii) and cd (integrin associated protein) were constitutively expressed without any significant changes in patients with acute rejection of the allograft. we assume from our data that kidney allograft transplantation is associated with early reciprocal modulation of monocyte subpopulations (cd +cd + and cd +cd +). a decreased proportion of cd positive blood monocytes seems to be associated with an increased risk of acute rejection of kidney allograft. introduction: thioredoxin (trx), a -kda oxidoreductase enzyme, is well known to be a redox-active protein that regulates reactive oxidative metabolism. in addition to its anti-oxidative activ- | progranulin-dependent regulation of th airway inflammation by house dust mite allergen introduction: progranulin is a growth factor that consists of amino acids including / repeats of cysteine-rich motifs, and produced by variety kinds of cell. progranulin is involved in the regulation and maintenance of inflammatory response, and its role is wellstudied in neuronal and metabolic diseases such as neurodegeneration and type diabetes. however, the role of progranulin during the development of airway inflammation induced by inhaled allergen is still obscure. objectives: in this study, we evaluated the role of progranulin in the development of th airway inflammation induced by house dust mite allergen. results: to find the main source of progranulin, we stimulated each cell line with various doses of house dust mite allergens. the production of each cytokine, including progranulin, was estimated in culture supernatant by elisa. to investigate the role of progranulin in airway inflammation, we intranasally administrated house dust mite allergens to -week-old female progranulin knock-out mice (macrophage-specific) or littermate mice. lung inflammation and immunological parameters were evaluated at h after first sensitization with allergen or h after final allergen challenge. the production of progranulin was significantly elevated by house dust mite allergen stimulation in innate immune cells, especially in alveolar macrophages over other cells. in the house dust mite allergeninduced airway inflammation model, we found that the level of progranulin increased earlier than other pro-inflammatory cytokines. in addition, in macrophage-specific progranulin knock-out mice, airway inflammation was down-regulated in the earlier phase after exposure to house dust mite allergen. moreover, we stimulated mice with house dust mite allergen for a longer period to observe the changes in the adaptive immune response of th airway inflammation, which was found to be decreased in conditional knock-out mice. conclusions: these findings indicate that th airway inflammation induced by house dust mite allergen is dependent on progranulin. objectives: the aim of the present study was therefore to investigate the immunomodulatory effect of epinephrine on m a macrophages and its consequence on cross talk to mast cells in a human model of allergic inflammation. results: primary monocytes from healthy pbmcs were first differentiated into m a macrophages using m-csf in the presence of il- and il- cytokines. after overnight incubation with epinephrine, supernatants were collected and analyzed by elisa for il- , tnf, il- , ccl , il- and ifn-c, whereas cell surface markers including cd , cd and cd were evaluated using flow cytometry. subsequently, both m a and epinephrine-treated m a supernatants were transferred onto cord blood-derived mast cells (cbmcs) for further overnight incubation, after which ige-mediated degranulation was assessed by the ß-hexosaminidase release assay. after overnight epinephrine treatment, m a macrophages showed an increase in il- , ccl , tnf and il- production, but no ifn-c and il- expression was observed. epinephrine treatment also downregulated surface markers cd and cd and upregulated cd . when supernatants from epinephrine-treated m a macrophages were added to cbmc cultures, ige-mediated degranulation was impaired compared to cbmcs treated with supernatants of unstimulated m a macrophages. conclusions: taken together, epinephrine promoted a phenotypic shift of m a polarized human macrophages toward an m b-like regulatory phenotype that was able to reduce the ige-mediated degranulation of cbmcs. we conclude that prolonged acute stress exposure in allergic patients may attenuate symptoms of acute allergy by directing macrophages towards an immunosuppressive phenotype, which can further dampen mast cell degranulation. objectives: a murine local lymph node assay was used to investigate the effect of oa on the immune response to the known skin sensitizer hexyl cinnamic aldehyde (hca, % w/v). the ear lobes tape stripped prior to immunization. test solutions ( ll) were applied on the dorsal side of each ear on three consecutive days. female balb/c mice ( groups a mice), were exposed to the vehicle acetone:olive oil ( : ) alone, or in combination with hca, with or without oa in the concentrations , and %, or oa alone ( , and %). on day , the animals were weighed and exsanguinated by cardiac puncture. the auricular lymph nodes were harvested for single cell preparation, stimulation with cona and cytokine release of il- and il- . the earlobes were excised and fixed for immunohistochemistry. results: no group differences were found for bodyweights or bodyweight change, number of lymph node cells or il- secretion. il- showed a tendency of dose-related increase, but a significant difference were only found between hca and hca+ % oa (p=. ) in one out of the two experiments. in he stained sections, the epidermal thickness was significantly increased in groups given hca + and % oa (p≤ . ). sections immunostained with anti-ly g showed significant increase in neutrophil influx for the same groups as above (p≤ . ). oa alone showed no effects or effects significantly lower than hca + oa. objectives: we hypothesized that plasma s p levels in cf patients might be associated with cftr mutations and could influence disease presentation. results: plasma was collected with a defined standard operation procedure to impede unspecific s p release from blood cells from double lung transplanted adult cf patients as well as sex-and age-matched, non-allergic healthy controls all being fasted overnight. total plasma s p was measured by mass spectrometry and unbound plasma s p by elisa. levels were correlated with cftr mutation status, routine laboratory parameters and clinical symptoms. we observed higher total and unbound plasma s p levels in healthy controls compared to cf patients with the latter value reaching statistical significance (p=. ) after exclusion of two statistical outliers. unbound plasma s p levels were significantly higher in df homozygous cf patients compared to patients with df heterozygosity (p=. ). patients with other mutations were excluded. levels of unbound s p were positively correlated with hemoglobin and negatively correlated with triglyceride levels. additionally, we observed a positive correlation of total plasma s p levels in cf patients with hba c. gastrointestinal symptoms were more common in df heterozygous ( / ) compared to df homozygous cf patients ( / ). fecal calprotectin levels were found to be significantly higher in df homozygous compared to heterozygous cf patients (p=. ). differences in unbound s p levels were not correlated with immunosuppressive treatment after transplantation. conclusions: to the best of our knowledge this is the first clinical study directly correlating plasma s p levels with cf genotypes and clinical presentation in cf patients. we emphasize to evaluate s p as a potential novel disease biomarker as well as a therapeutic target for cf in future studies. supported by the austria science fund grant kli (to eu). ochoa-grull on j ; tejera-alhambra m ; guevara k ; guzm an-fulgencio m ; benavente cm ; mart ınez r ; p erez c ; peña a ; rodr ıguez de la peña a ; llano hern andez k ; rodr ıguez-fr ıas e ; s anchez-ram on s objectives: we show preliminary data of one study aimed to evaluate the use of this strategy in the prevention of rrti in infants and preschool children. results: patients: children ( male and female, age range - months) were included in a randomized double blind and placebo-controlled study (eudract - - ) . all of them showed negative in vivo and in vitro allergy tests. active treatment consisted in a suspension of a mixture of selected strains, grown and inactivated in optimal conditions, of s. aureus ( %), s. epidermidis ( %), s. pneumoniae ( %), k. pneumoniae ( %), m. catarrhalis ( %) and h. influenzae ( %) in physiologic saline solution with % glycerol at a concentration of formazin turbidity units (ftu)/ml (equivalent to bacteria/ml). placebo did not contain any bacteria. patient were treated for a period of months, receiving daily sublingual puffs of active or placebo and with a follow-up of other months (total period of evaluation was year). symptom (cough, dyspnea, wheeze, mucus, fever, discomfort) and medication (inhaled corticosteroids, beta adrenergics, montelukast, antibiotics) scores were evaluated since the first day of treatment to the end of the study ( year) . any adverse event was recorded to assess safety. for the comparison between both groups, t test was used. patients who received active treatment experienced an improvement of % over placebo in overall symptoms and % in medications scores (p<. ). in the combination of symptoms and medication scores the improvement was % (p<. ). no adverse events related to treatment were recorded. conclusions: immunostimulation with these selected strains of bacteria is safe and can be successfully used in infants and preschool children in order to prevent rrti. introduction: to reduce the duration and the risk of the allergen specific immunotherapy using commonly used allergen extracts, new highly immunogenic and non reactogenic vaccines are needed. objectives: the goal of the present study was to employ the ap spytag/catcher system to develop a virus-like particle (vlp) vaccine based on the major house dust mite (hdm) allergen der p and to evaluate its reactogenicity in vitro. spycatcher-ap vlps and recombinant der p , fused at the c-terminus to the amino acid spytag binding-partner, were expressed in e. coli. purified spytagged der p was mixed with spycatcher-vlps, which resulted in covalent conjugation of der p to the surface of spycatcher-vlps. excess unbound der p was removed by dialysis. dynamic lightscattering (dls) was used to analyse the size and aggregation state of vlp-der p . the ige reactivity of vlp-der p was assayed by direct elisa and by rat basophil degranulation assays. conclusions: our results demonstrate that coupling of spy-tagged der p to ap spycatcher-vlps dramatically reduces the reactogenicity of the allergen, suggesting that vaccination with ap vlp-der p may be a safe and effective treatment for hdm allergy. objectives: the qm s hybrid protein is a qm variant where cysteine amino acids have been replaced by serine. the expression of qm s hybrid protein was performed in e. coli bl (de ) after iptg induction. the purification of qm s protein was performed from inclusion bodies by a three-step chromatography process. the stability of qm s was analyzed by sds-page and total protein assay. qm s ige-binding capacity was compared with natural der p and der p by elisa-inhibition and allergenicity was studied by mediator release from rbl cells. immunogenicity was evaluated in mice by analysis of the specific igg response to der p and der p . results: qm s was expressed in complex media as inclusion bodies that were solubilized in urea. soluble protein was purified by anionic ion exchange, hydrophobic interaction, and size exclusion chromatography in the presence of a detergent. qm s purification process was shorter and more efficient than that of qm . the purity obtained was > %. elisa inhibition assay showed that qm s hybrid protein was almost unable to inhibit ige-binding to the hdm extract, less than % in all the range of concentrations tested ( . - ng/ml) and representing a -fold reduction as compared to qm . qm s showed a great reduction of the b-hexosaminidase release in rbl cells, compared to der p and der p . qm s was able to induce der p -and der p -specific lgg antibodies responses comparable with those induced by the mixture of wildtype allergens. mouse igg antibodies induced by the hybrid proteins qm s and qm showed similar ige-blocking antibodies properties to mixture of der p and der p . the stability of qm s was studied in solution at °c, °c, and - °c and lyophilized at °c, being the frozen and lyophilized forms the best conservation conditions. the qm s hybrid exhibited less ige-binding activity than qm and the natural der p and der p while retained the immunogenicity. these properties together with the improved manufacturability made qm s a good candidate for sit to hdm allergy. objectives: slit tablets of cockroach, slit tablets of parthenium, slit tablets containing both allergens together (mix) and slit bilayer tablets containing one layer with parthenium allergen and other layer with cockroach allergen, compress to single tablet were prepared. punches and dies of mm were used for compression. slit drops containing cockroach, slit drops of parthenium and slit drops containing both allergens together, were prepared and filled in ml amber colored dropper vials. results: tablet formulations were evaluated for thickness ( . - . mm), weight variation ( - mg), hardness ( . - . kg/cm ), disintegration time (not more than min.), and biologically active content ( %- % of the stated label claim). in-vitro dissolution test was performed as per usp using distilled water as the medium and the release was shown between to % in minutes. the liquid formulations were analyzed for ph ( . - . ), the biological content ( % - % of the label claim), specific gravity ( introduction: virtually all patients suffering from the common birch pollen allergy exhibit ige against the bet v relevant allergen. as such, an elisa method for the quantification of bet v was selected and validated as part of the bsp project, aiming to establish reference methods for the european pharmacopoeia. herein, we report the mapping of the epitopes recognized on recombinant bet v allergen by the two specific murine monoclonal antibodies (mabs) used for the accurate and precise quantification of bet v within birch pollen extracts. objectives: in order to investigate the ability of mabs b and h to recognize various bet v isoallergens, we first carried out immunochromatography combined with electrophoresis. epitope mapping was performed by hydrogen/deuterium exchange (hdx) coupled with mass spectrometry (ms) analysis, using a gmp-grade purified rbet v molecule. results: immunochromatography unveiled that both mab b and mab h capture most of bet v isoallergens present within birch pollen natural extracts. those two mabs cross-react with the aln g allergen from alder pollen but do not react with the cas s chestnut pollen allergen. hdx-ms experiments combined with site-directed mutagenesis evidenced that mabs b and h target two distinct epitopes. the hdx-defined b epitope is discontinuous and contains a dominating sequential element (i.e., loop ile -lys ). the hdx-defined h epitope is also discontinuous and mainly composed of regions ile -lys and arg -phe . conclusions: overall, this study provides a precise molecular characterization of epitopes within bet v recognized by mabs b and h , confirming that these two antibodies target distinct non-overlapping epitopes and recognize the vast majority of currently introduction: short or common ragweed (ambrosia artemisiifolia), belonging to the aster plant family, sheds enormous amounts of highly allergenic pollen late in the summer. due to its high allergenic potential ambrosia artemisiifolia is becoming a health threat in north america and europe. hal allergy is developing a subcutaneous immunotherapy for patients suffering from ragweed pollen allergy. a standardized ragweed pollen extract, chemically modified and adsorbed to aluminium hydroxide (al(oh) ), is being investigated for its potential use in immunotherapy. objectives: ragweed extract (re) was modified by glutaraldehyde followed by adsorption to al(oh ). in vitro, a mediator release assay (mra) using hurbl (humanized rat basophil leukemia) cells was performed. hurbl cells were pre-sensitized using individual sera of ragweed-allergic patients and challenged with serial dilutions of re and modified re starting at lg/ml followed by eight / dilutions ( - . ng/ml). antigen-specific release of ß-hexosaminidase was measured and calculated in relation to % release values. in vivo, the immunogenic potency of modified re was evaluated by measuring the induction of re-specific igg in mice. female balb/c mice (n= per group) were subcutaneously (s.c.) injected with . aueq/ml re or modified re adsorbed to al(oh) ( . mg/ml) per mouse on days , , and . control mice (n= ) were injected with matrix only. specific igg titres were determined in serum obtained at days - , and . results: the potency of modified re in mra was drastically reduced in all patients, with a mean reduction of fold or more. chemical modification resulted in a later onset of activation as well as a lowering of the maximum release of ß-hexosaminidase. in vivo, both re and modified re show comparable levels of re-specific igg antibodies in mice at day of the immunogenicity model. shown that chemical modification impairs the capacity of re to activate basophils while retaining its capability to be immunogenic. therefore, chemical modification of re may be a promising approach for the development of a safe and effective immunotherapy for ragweed allergy. objectives: the children who had taken subcutaneous conventional venom immunotherapy in our pediatric allergy outpatient clinic between and were evaluated with respect to the side effects. in addition, each child was called to ask if the patient was exposed to bee sting and the result of a sting during immunotherapy. introduction: the major unmet needs for allergen immunotherapy (ait) are improved efficacy with good tolerability, and high adherence. to achieve these, allergoids, peptides and recombinant proteins are potentially the answer but their low rate of systemic aes make selection of the optimal dose difficult. to select the dose for an ultra-short course subcutaneous birch ait, the company has adopted the use of a conjunctival provocation test (cpt), a wide range of doses and the multiple comparison procedure -modelling (mcp-mod) statistical analysis to test for a dose response and to determine the shape of the dose response curve. objectives: a range of dose regimens of su, , and su were compared with placebo with respect to reduction of total symptom score elicited by cpt after treatment. patients were administered weekly injections outside the pollen season. cpt was performed at screening, at baseline and weeks after completion of treatment. the study was undertaken in sites in germany and austria with patients. the primary efficacy analysis was performed on a modified full analysis set (fas). the mcp-mod methodology was used to test for a dose-response using the placebo and above doses to describe the shape of the dose response curve. three candidate models were pre-specified: a maximum possible effect for the agonist (emax) model, a logistic model, and a linear in log-dose model. a statistically significant dose-response (p<. ) was shown for the range of cumulative doses, which approached a plateau with the su dose. the median effective dose (ed- ) was su. only minor differences were observed between the six active treatment groups in prevalence of treatment-emergent adverse events (between . % and . % of patients with overlapping % two-sided confidence intervals), majority of which were local reactions, short-lived and mild. teaes classified as systemic reactions were seen in . % ( su group) and in up to . % ( su group) of patients in the active treatment groups, and in . % of patients in the placebo group. no treatment related saes were observed. adherence was > % in all treatment arms. the ed- was su, demonstrating that the currently marketed dose ( su) is effective. the highest su dose will be further investigated in a pivotal phase iii trial having achieved an increase in efficacy by % without differences in the onset of aes between the treatment arms. introduction: in order for allergen immunotherapy (ait) to induce long-term immunological and clinical effects prolonged administration is required. therefore adherence to treatment is crucial for its efficacy. there is currently limited data available on ait adherence beyond clinical trials i.e. in real-life clinical practice. objectives: this eaaci immunotherapy interest group endorsed survey aimed to prospectively evaluate adherence to sublingual and subcutaneous immunotherapy in adults with allergic respiratory diseases and hymenoptera venom allergy in real life practice across different european countries. in addition, the reasons for lack of adherence and discontinuation of treatment were explored. this was a prospective, multi-centre, observational survey which took place in eight countries: czech republic, georgia, germany, greece, italy, poland, portugal and spain. data collection involved an online survey that followed participants four-monthly for a period of months from the start date of ait. results: a total of participants were included in the analysis. introduction: allergic rhinitis is a multiple gene-regulated disease involved in many immune cells such as mast cells and eosinophils, and various inflammatory mediators, and mirna probably plays a critical regulatory role in its pathogenesis. therefore, studies on the functions of critical mirna and its regulatory mechanisms in activated mast cells will lay an important theoretical foundation for our understanding of ar pathogenesis and the development of therapeutic strategies. objectives: to investigate the effect of mir- a- p on mast cell activation in an ar mouse model. the number of sneezes and the frequency of nasal rubbing in ar+mir- a- p group were significantly reduced compared to those for ar+mir-nc group (p<. ). histological examination showed that inflammation in the nasal mucosa from ar+mir- a- p group was slighter than that in ar+mir-nc group. the number of mast cells in ar+mir- a- p group was increased compared to ar+mir-nc group (p<. ). the levels of histamine and il- in nasal lavage fluid supernatants, histamine in plasmas and il- in sera were significantly decreased in ar+mir- a- p group compared to ar+mir-nc group (p<. ). conclusions: upregulation of mir- a- p can reduce allergic inflammation in the nasal mucosa of ar and alleviate ar symptoms through inhibiting mast cell activation in vivo. mir- a- p probably becomes a new target for gene therapy of ar. | correlation between chronic cough and chronic rhinosinusitis in adults: nationwide, population-based, and cross-sectional study the second hospital of shandong university, ji nan, china; national university of singapore, singapore, singapore introduction: nasal polyp implies a refractory clinical course in case of chronic rhinosinusitis (crs). although hypoxia is believed to be associated with nasal polyposis, little is known about the mechanism underlying polypogenesis. objectives: the aim of this study was to assess mrna and protein introduction: nasal polyp is a multi-factorial disease commonly associated with inactive ciliary beating frequency (cbf), a condition partly attributed to the mis-localization of dnah , a component of the outer dynein arm in ciliary axoneme. so far however, there have yet to be a systematic histopathological investigation directly linking dnah localization pattern in nasal polyps. therefore, we sought to examine the localization of dnah in cilia structure of both nasal polyps and inferior turbinates from healthy individuals, and assess whether there are any localization changes that can account for the extensive inactive cbf observed in nasal polyps. objectives: the focus of this work is to compare the localization of dnah from the nasal polyps biopsies (n= ) and normal inferior turbinates (n= ) by immunofluorescence. the characterization of each sample was obtained from an average of fields at magnification. results: from the samples, we observed three distinct localization patterns of dnah in the nasal cilia. the three patterns were as follows: ) the localization of dnah in normal cilia is present throughout the entire axoneme (pattern a); ) the localization of dnah is within the axoneme except at their proximal regions (pattern b); ) the localization of dnah is restricted exclusively at the ciliary base and not present in the entire axoneme (pattern c). approximately % of the samples exhibited more than one distinct localization patterns for dnah within the observed fields. the percentage of pattern a, pattern b and pattern c were observed in . %, . %, and . % fields for samples from nasal polyps. correspondingly, . %, . %, and . % were observed for samples from healthy controls. the results indicated that the predominance of "pattern c" in nasal polyps countered by "pattern a" in inferior turbinates from healthy individuals. conclusions: our study indicated that there is a significant increase in the mis-localization of dnah among the cilia in nasal polyps as compared to controls. this mis-localization may account for the inactive cbf, a hallmark characteristic, observed in nasal polyps. zhao l ; zhi l ; jin p ; zi x ; tu y ; li a ; li t ; shi l ( . , . - . , p<. ) and +gc np patients ( . , . - . , p<. the results showed that the number of th + cells were correlated with eosinophil cells and macrophage (r=. , p<. , r=. , p <. ), but no correlation was found between th + cells and neutrophil cells. the significantly correlation were found between il- objectives: this study aimed to reveal if some features of the sinus wall and content (as homogeneity and density of the sinus content, or the continuity, thickness and density of the sinus wall), differ between the afrs and other forms of crs. we tried also to establish early diagnostic parameters for recognition of fungal rhinosinusitis on ct. results: the study included adult patients (mean age: . ae . years, m:f ratio= . : ) with clinically diagnosed crs. out of all maxillary sinuses (n= ) from study patients, ( . %) were opacified, and only these sinuses were included in further analyses. we found out that: ( ) positive fungal finding had % ( / ) crs patients and % ( / ) of these patients had severe forms of crs, ( ) patients with positive fungal finding had more often positive specific ige ab than those without fungi in sinuses ( . % vs. . %, p=. ), ( ) foci of non-homogeneity, mean and maximum densities and wall density were more common found in maxillary sinuses with present fungi than those without fungi (p=. , p=. , p=. ; respectively) and ( ) patients with crs lasting more than years had more often foci of non-homogeneity and presence of hyperattenuation centres, than patients with shorter length of crs. results: neutrophil-related gene mpo and eosinophil recruitment genes ccl and ccl showed higher expression level in acp than in controls, which were in line with the significantly elevated neutrophils and eosinophils infiltration in acp compared to control. increased cd + t cells, macrophages and cd + t cells infiltration in acp were also observed. the expression level of t-reg transcription factor foxp was significantly higher in patients with acp than in controls, but the expression of th /th /th transcription factor tbet, gata and rorc were significantly decreased in acp vs controls. we further investigated the relationships between these t-cellassociated genes in acp. the expression of foxp was positively correlated with t-bet, gata , il r and il a, while no significant correlation with rorc was evident. il was observed positively correlated with t-bet, gata , foxp , and il r. il had significant correlation with t-bet and il a. objectives: the aim of this study was to find the olfactory change pattern of crs after ess in short-term and the differences between crswnps and crssnps, secondary aim were to identify the relationship among olfactory dysfunction, ct scores and quality of life(qol). in this study, crs patients who underwent ess were evaluated preoperative by t&t recognition threshold tests, snot- score and lund-mackay ct score. patient outcomes were re-evaluated at clinical follow-up month, months and months postoperative. analysis of variance was performed and correlation was calculated, with results analysed separately for crswnp and crssnp subgroups. . subgroups of crs differed in the degree of olfactory dysfunction reported before and after the ess. a significant difference in the changes of olfactory dysfunction between the two groups was found at month postoperative. . the mean t&t and snot- scores showed significant improvement within months after ess in both crswnp and crssnp subgroups, however, no significantly recovery of olfactory dysfunction was observed at months compared to month postoperative. there is a plateau of olfactory recovery at months postoperative. . in crswnps, the mean t&t scores preoperative were correlated with lund-mackay ct score significantly(r=. , p<. ; r=. , p<. ). however, no relations were found in crssnps and the changes of olfactory dysfunction at the months postoperative with lund-mackay ct score. . olfactory scores, before and after the ess, and their changes did not correlate with sont- scores. conclusions: olfactory dysfunction was more severe in crswnps. olfaction and qol of crs patients were significantly improved after ess in both groups, but there was a plateau of olfactory recovery at months postoperative. ct scan may predict olfactory disorder, but the olfactory scores were not related with the qol. objectives: in this study, we investigated the effect of hgf, tgf-b , and pge as effective components for allergic rhinitis treatment using in vitro and in vivo mouse model studies. results: pge decreased infiltration of eosinophil in nasal mucosa. tgf-b decreased the infiltration of eosinophil in nasal tissue and increased the number of treg in spleen. however, there was no antiallergic effect of hgf in this experiment condition. in case of the combination treatment group (tgf-b +pge +hgf), eosinophil infiltrations and the expression of eotaxin- were reduced in the nasal tissue, and treg was increased in the spleen. in all treatment group, serum ige and systemic cytokine levels were not decreased due to intranasal administration rather than systemic administration. in vitro study showed that phosphorylation of map kinases such as erk, jnk, and p and translocation of p were inhibited after treatment of hgf, tgf-b and pge , suggesting their anti-allergic mechanism. conclusions: we found that tgf-b , and pge decreased allergic inflammation and these effects might be derived from changes in the frequency of treg and the activation of map kinase and p in the t cell receptor signaling pathway. furthermore, we hypothesized that tgf-b , and pge would be effective components for allergic rhinitis therapy. introduction: interleukin (il)- is implicated in suppression of allergic inflammation. the role of il- in the early-phase reaction in type hypersensitivity has been unclear, however. we investigated the contribution of il- in a mouse model of the ige-mediated early-phase reaction in allergic conjunctivitis. objectives: ige-mediated allergic conjunctivitis was induced in c bl/ -kit(+/+) wild-type mice, kit(+/+) il- -deficient mice, and kit(w-sh/w-sh) mast cell-deficient mice by means of passive conjunctival anaphylaxis. the mice were thus subjected to subconjunctival injection with anti-dinitrophenol ige (dnp-ige) followed after h by intravenous injection with dnp antigen. kit(w-sh/w-sh) mice that had received a subconjunctival graft of cultured bone marrowderived mast cells from kit(+/+) wild-type mice or kit(+/+) il- deficient mice were similarly treated. vascular permeability of the conjunctiva was examined min after antigen injection by colorimetric evaluation of the extravasation of evans blue dye. results: passive transfer of dnp-ige followed by intravenous antigen injection increased vascular permeability in the conjunctiva of kit(+/+) wild-type mice but not in that of kit(w-sh/w-sh) mice, suggesting that this effect was dependent on mast cells. vascular permeability was increased to a significantly greater extent in kit(+/+) il- -deficient mice than in kit(+/+) wild-type mice. reconstitution of kit(w-sh/w-sh) mice with kit(+/+) wild-type or kit(+/+) il- deficient mast cells restored the dnp-ige-and dnp-induced increase in vascular permeability to similar extents. our results suggest that il- produced by cells other that mast cells suppresses the mast cell-mediated early-phase reaction in ocular allergy. objectives: our aim was to evaluate the effectiveness and the safety of ccl treatment for keratoconus in children with vkc. forty-two boys (mean age . ae . years) and girls (mean age . ae years) with vkc were included in the study. tarsal, limbal and mixed vkc were detected in . %, . % and . % of the subjects, respectively. evaporative dry eye was detected in children out of ( . %), schirmer test results were < mm/ minutes in . % and < mm (severe dry eye) in out of children ( . %) and % of the subjects (n= ) had confirmed keratoconus/forme fruste keratoconus with corneal topography (sirius, cso, italy). allergic symptoms were controlled with topical steroids, cyclosporine, dual action antihistaminic/mast cell stabilizers and lubricant agents before the procedure. ccl surgery was performed under topical anesthesia. the children were followed-up at least year and preoperative and postoperative corneal topographic parameters were compared using paired sample t test. results: the visual acuity was between . and . (moderate visual loss) in . % of the subjects and less than . (severe visual loss) in . % of the children. ccl procedure was performed to eyes of children. at the end of one year, the disease was stable in all children with no differences in k and k corneal parameters before and after cxl (p>. ). there was a statistically significant improvement in maximum keratometry value after the procedure (before . ae d, after . ae . d, p=. ). in one subject, a corneal infiltrate was detected days after ccl, which was treated successfully with topical moxifloxacin. otherwise, no complications were observed in the postoperative period. conclusions: as keratoconus is common in vkc, these children should be referred to ophthalmologists for an eye examination and corneal topography. ccl seems to be a safe and effective option to halt the progression of keratoconus, which might be very aggressive in children with vkc. results: surprisingly, we found among them cases of celiac disease, cases of thyroid dysfunction (thyroiditis), cases of crohn's disease and case of ulcerative colitis, case of anterior uveitis and case of pemphigus respectively. we realized that an average percentage of % of the total of vkc cases are affected by an "autoimmune" systemic disease. limbal form of vkc was prevalent and more than % of children showed it. we can suppose that a racial and genetic predisposition to systemic diseases can coexist with vkc or that there is a group of vkc affected subjects in which the immune disorder is predominant on the allergic disease. introduction: nasal polyposis (np) is a heterogeneous inflammatory disease of nasal mucosa affecting - % of the population with a high rate of recidivism. polyps arise from nasal sinuses to nasal cavity and are often associated with a strong local eosinophilia. the pathophysiology of np remains controversial, as it seems to be a phenotypic manifestation of multiple possible immunologic processes, such as respiratory allergy, despite a lack of correlated systemic response. here we propose a multiparametric assessment of np patients, in order to shed light on the underlying mechanisms of the disease in allergic and non-allergic patients and aiming to find new predictive biomarkers. objectives: our main aim was to unravel the link between systemic and local allergic inflammation and polyp development, as well as the nasal epithelium condition in polyps and surrounding healthy tissue. methods: four groups of patients were included in the study: healthy donors with or without allergy and np patients with or without allergy. in this regard, several different approaches were followed: a metabolomics serum study, a polyp and nonpolypous nasal epithelium histology and transcriptomic study. results: as for the histological study, luna staining revealed differences in eosinophilia between allergic and non-allergic patients, especially when patients were polysensitized, including perennial allergens; and between nonpolypus tissue and polyps being higher in polyps. pas staining showed differences in epithelium integrity and submucous and goblet cell (pas positive) distribution. immunohistochemistry for cd + and cd c+ reveal a significant inflammatory infiltration in polyps. this inflammatory response was also asses by abstracts | gene expression quantitation. no differences were seen in the metabolic profile in patient sera between groups. for the first time, nasal epithelium from polyps and neighboring tissue were studied. histology techniques and image analysis revealed differences in eosinophil concentration in both mucosa and submucosa areas, as well as different features in epithelium and submucous tissue structure. some of these findings were confirmed by gene expression quantitation. conclusions: our data show an increased eosinophilia and inflammatory infiltration in polyp tissue suggesting a role for allergic inflammation in the progression of np. additionally, we provide clues for the role of inflammation in the damage on nasal mucosa and the following progression of the disease. | is specific immunotherapy effective in subjects suffering from vkc? a tertiary referral center ten years experience. objectives: our work shows the results of sit additional to usual treatments, in children suffering from vkc and followed in our tertiary referral center (lavagna hospital, genova, italy). we retrospectively analyzed the clinical data of subjects ( males and females); their mean age at the beginning of treatment was ae . years. the patients were treated both with scit (sub-cutaneous immune-therapy- . %) and slit (sub-lingual immune-therapy - . %) depending on patient's wishes. they had to be mono-sensitized to one of the usually more frequent allergens (dust-mites, grass pollen, and pellitory) which was detected by means of recombinant rast, prick test and conjunctival provocation test (cpt); these tests were performed after a complete ophthalmological and allergological history and examination. children selected for sit needed to be positive to all performed allergy tests. systemic involvement included cases of asthma, cases of atopic dermatitis and case of rhinitis; the remaining cases were asymptomatic. local involvement included only vkc cases, the % of which were of the limbal type and only subjects were suffering from the tarsal papillary type. mean follow-up was . years. all the patients included into the study completed their treatment and followed the therapeutic protocol. after one year of sit, no variation in clinical course and treatment was recorded. after the third year of sit, an average improvement in symptoms and signs score ( %) and an average decreased need for allergy systemic medications ( %.) (i.e. antihistamines and corticosteroids) was registered. also topical therapy (including steroid and cyclosporine eye-drops) was discontinued in % of children, in this group, short courses of steroid drops were necessary in less than % of children (as rescue treatment in the acute phases of the disease). these positive results after sit treatment were stable for the following years. few (only local sub-cutaneous) side effects were recorded and the treatment was generally well-tolerated. conclusions: our experience shows positive results with sit in vkc which can have sensitive-to sit-treatment subtypes. results: deaths occurred in children ( boys, %). median age at death was years (iqr - ). pamr of any cause was . ( %ci, . - . ) per children per year, with a decreasing rate over time (annual change: - . %; %ci, - . to . ). triggers were iatrogenic causes (n= , %), insect venom (n= , %) and food (n= , %). unspecified causes were frequently reported (n= , %). there was no difference in overall pamr between boys and girls (p=. ). there was no age group related differences in fatalities: preschool children (< years) (n= , %), school children ( - years) (n= , %), adolescent and toddlers (> years) (n= , %). the number of fatal cases was similar comparing the southern (n= , %) and the northern regions of france (n= , %) (p=. ). the first episode of anaphylaxis for each patient was captured to calculate incidence. we estimated incidence rate ratios using poisson regression models. results: between and there were anaphylaxis episodes in patients younger than years in hong kong. the incidence of admission for anaphylaxis increased markedly from . to . per person-years during the study period (p<. ). the incidence of food-related anaphylaxis increased significantly from . to . (p<. ). increases in anaphylaxis and food-related anaphylaxis were seen in all age groups, with the largest increase in those aged to years. at the beginning of the study period ( ), medication was a more common trigger for anaphylaxis than food ( . vs . per person-years). by , food had become the predominant trigger ( . vs . per personyears for medication). the incidence of medication-related anaphylaxis decreased significantly (p<. ). the incidence rate of anaphylaxis was significantly higher in boys than girls in the - and - year age groups, while there was no significant gender difference in the - year age group. the most common food triggers of anaphylaxis were peanuts, seafood, eggs, milk products, tree nuts & seeds (in descending order). conclusions: even though the incidence of anaphylaxis among children in hong kong is lower compared with other western countries, it has recently increased significantly, with food-related anaphylaxis predominant. | prevalence of anaphylaxis and prescription rates of epinephrine self-injector in korea based on national health insurance data results: the prevalence of anaphylaxis over the years were . %. the annual prevalence of anaphylaxis increased over the years. anaphylaxis was more prevalent in male than female ( % vs. %) and in population aged - years old. for the regional prevalence of anaphylaxis in korea, gangwon province showed the highest prevalence of anaphylaxis ( . per individuals) and relatively low prescription rates ( . %) of epinephrine self-injector for the patients with anaphylaxis. on the contrary, seoul showed relatively low prevalence of anaphylaxis ( . per individuals) and the highest prescription rates ( . %) of epinephrine self-injector for patients with anaphylaxis conclusions: the prevalence of anaphylaxis has increased annually in korea. the prevalence of anaphylaxis and prescription rates of epinephrine self-injector showed regional difference in korea. objectives: the aim of the study was to analyze the prevalence of allergic symptoms and anaphylaxis in mastocytosis patients analyzed in the registry of the ecnm. results: methods: a total of patient with mastocytosis were enrolled. in these patients, the prevalence of allergy, anaphylaxis, triggers of allergic reaction, and disease subtypes were analyzed. results: symptoms of allergy were observed in % of all patients. the most affected group were patients with bone marrow mastocytosis (bmm: . %) and indolent systemic mastocytosis (ism: . %). insect venom allergy (iva) was reported in . % of all subjects. in ism/bmm patients iva affected . % of the cases, while in other patient groups, only . % of the cases were affected (p<. ). most patients ( %) had wasp allergy, % had bee allergy, % polistes allergy, and . % allergy to more than one venom. in . % the culprit insect was not identified. food allergy was reported in . %, drug intolerance/allergy in . %, inhalant allergy in . %, and physical triggers in . % of patients. in mastocytosis patients iva is the most prevalent cause of anaphylactic reactions exceeding the prevalence of iva in the general population by far. iva affects mainly bmm and ism patients ( . % of cases). but ( . %) subjects didn't know whether adrenaline was administered. only within patients who had adrenaline autoinjectors used their autoinjectors during an anaphylaxis attack. most common symptoms were skin (n= , . %) and respiratory symptoms (n= , . %). syncope, hypotension or hypoxemia were present in cases( . %), at least three organ dysfunctions in ( . %) cases; patients ( . %) had to be hospitalized (f: , m: ).nearly a third ( . %) of the patients had stage - anaphylaxis and patients( . %) had stage - reactions. in cases ( . %), basal tryptase levels were examined and the average value was correlated with the severity. concomitant drugs being used by the patients were antihypertensives ( . %),oral antidiabetics ( . %); angiotensin converting enzyme inhibitors or angiotensin receptor blockers( . %), beta blockers( . %), diuretics( . %) and nsaid's ( . %). conclusions: male sex was noted as a risk factor for severe reactions and recurrent anaphylaxis. anaphylaxis requiring hospitalization was more frequent in the patients using oral antidiabetics or diuretics. baseline tryptase levels were higher in patients with neurological and gastrointestinal symptoms. cardiovascular symptoms were found to be higher if a cofactor was present. skin symptoms were seen more frequently and higher rate of hospitalization occurred in anaphylaxis in the presence of infections or nsaid use. this study is important to elucidate the factors affecting anaphylaxis severity. | serum levels of a, ß-pgf in combination with apolipoprotein a or cysleukotrienes are reliable biomarkers of anaphylaxis objectives: we analyzed mast cell mediators in sera derived from patients with acute anaphylactic symptoms (n= ) versus patients with acute cardiovascular or febrile reactions (n= ) and patients with a history of anaphylaxis but without displaying any symptoms when sera were taken (n= ). in addition, we identified proteins with substantial changes during anaphylaxis. matched serum samples were used to compare basal mediator levels with corresponding levels during acute anaphylaxis in the same patient (n= ). roc curve analysis was performed to determine the sensitivity/specificity of each mediator. results: serum levels of histamine and tryptase were not increased upon anaphylaxis and showed no relation to anaphylaxis severity. however, serum a, ß-pgf , a metabolite of pgd , was significantly increased in acute anaphylactic patients (~ -fold) and abstracts | correlated well with anaphylaxis severity. a, ß-pgf distinguished anaphylaxis from cardiovascular or febrile reactions and showed the highest diagnostic power observed by roc curve analysis. cys-leukotrienes (cys-lts=ltc , ltd , lte ) were increased upon anaphylaxis while apolipoprotein (apo) a was significantly decreased. the highest diagnostic power was observed with the combination of a, ß-pgf and apoa . conclusions: in conclusion, histamine might only be used to detect anaphylaxis when assessed shortly after onset of an anaphylactic response because of its short half-life, whereas tryptase is a useful biomarker if the baseline level of the same patient is known. a, ß-pgf seems to be the most reliable marker as demonstrated by the distinct increase upon anaphylaxis and could be supported by apoa or cys-lts. further investigations are needed to prove the suitability of these markers. objectives: objective of this study was to estimate the long-term bv of tryptase using certain chronic disease models and to compare it with those in food and drug allergy. results: serial determinations of tryptase concentrations (n≥ data points per patient) obtained from patients diagnosed with mastocytosis (n= ) or chronic urticaria (n= ) during a period of sometimes several years were measured by the immunocap assay and evaluated using sigmaplot software. polynomial curve fitting was performed and data points outside the % confidence interval of the curve were appointed as outliers and excluded. because the data points were not normally distributed due to long-term fluctuations in homeostatic set-point, a non-linear fitting was applied and used to compute the standard error of the estimate. these standard errors of the fit divided by the estimates themselves were used to calculate the total coefficient of variation within a subject (cv t ). the analytical cv (cv a ) was calculated based on quality control samples ( levels, n= data points) in a conventional way, while the within-subject bv (cv i ) was defined as cv l =(cv t À cv a ) ½ . eleven patients with a chronic disease were selected, of which patient was treated as a potential outlier and patients had to be excluded because of cv t ). total cost of the stock epi program over a one-year period varied by ontarian stakeholders: $ for the mall, $ for fast-food restaurants, and $ for sitdown restaurants. conclusions: this is the first study to evaluate the implementation of a stock epi program. the stock epi program was well received abstracts | and sustainable. implementing a stock epi program provides enhanced access to emergency medication, however it does not replace the responsibility of individuals with food allergy to self-manage. objectives: to identify the optimal needle length for epinephrine prefilled syringe. results: three hundred seventy-two children aged month to years were enrolled. skin to muscle depth (stmd) and skin to bone depth (stbd), which can represent the minimum and maximum needle length respectively, were measured using an ultrasonography at the mid-anterolateral thigh. number of children who had stbd less than needle length (too long needle) and stmd greater than needle length (too short needle) were calculated. one hundred thirty-seven children weight < kg, children weight > - kg, and children weight > kg were enrolled: ( . %) children were male. one inch needle was too long in ( . %) children weight < kg, ( . %) children weight > - kg. it was too short in ( . %) children weight > kg. age≥ months, weight≥ kg, height≥ cm, bmi≥ kg/m and thigh circumfer-ence≥ cm, provided the sensitivity of - % in predicting the appropriateness for using inch needle for children weight < kg. in children weight > kg, thigh circumference≥ . cm provided the sensitivity of % and specificity of % for predicting the inappropriateness for using inch needle. objectives: we present a patient with a probable mdh syndrome to unusual drugs, including ah and cct. results: we report a case of a -years-old female, with history of moderate-persistent asthma and chronic urticaria, who experienced angioedema and exacerbation of urticaria hours after the administration of multiple ah (desloratadine, loratadine, cetirizine), systemic cct (hydrocortisone, methylprednisolone, deflazacort) and nonsteroidal anti-inflammatories (nsaids) (paracetamol, ibuprofen, flurbiprofen). patch tests (pt) with excipients (bial arestegui ® ) and drug provocation test (dpt) with placebo were negative. skin prick tests (spt) and intradermal tests (id) with hydroxyzine, hydrocortisone, methylprednisolone and prednisolone were positive to hydroxyzine ( mg/ml) and pt with corticosteroids (bial arestegui ® ) and hydroxyzine were negative. dpts with desloratadine and an alternative ah, dimetindene, were positive with facial angioedema and generalized urticaria within hours. lymphocytic transformation test (ltt) was positive to desloratadine, ebastine and clemastine. dpt with dexamethasone was negative, however, when administered as treatment, a reproducible reaction occurred. since dpt with montelukast was also positive, omalizumab mg was initiated to control angioedema and chronic urticaria. after year of treatment, dpt with nimesulide was negative. omalizumab dose was reduced to half after the patient found out she was pregnant. there were no further episodes after anti-ige therapy introduction and pregnancy went uneventfully. conclusions: mdh syndrome is rare, more so when the drugs reported are ah and cct. hr to ah was confirmed, but diagnostic workup remains incomplete, postponed due to the patient's pregnancy. this case is as challenging in terms of diagnosis as it is in terms of therapeutic, so much so that omalizumab was initiated as an off label therapy, maintained during pregnancy based on the premise that risk was lower than benefit. objectives: in this study, we aimed to present our patients who were admitted with oral iron hypersensitivity. conclusions: according to our clinical experience, we think that oral iron salts with different conjugates are safe and acceptable option in patients with suspected oral iron hypersensitivity. introduction: antineoplastic agents are consider nowadays an essential treatment for many kinds of cancer. the increased use of these drugs in recent years is in parallel with a high rise of hypersensitivity reactions to them. these reactions range from mild to severe and as other allergic reactions, are not predictable. a nursing protocol in the desensitization schedules with these drugs is essential in allergy daily hospitals. objectives: the aim of this study are to describe a nursing protocol during desensitization schedules with antineoplastic agents carried out in our allergy unit in order to detect symptoms suggestive an allergic reaction during drug administration and to assess a correct intervention in case of reaction. conclusions: an appropriate nursing protocol in desensitization schedules with antineoplastic agents is essential in order to achieve the correct administration of the treatment in safety conditions. | long term clinical effects of aspirin desensitization in patients with nerd: comparison of maintenance doses of mg vs mg aspirin Çelik ge ; karakaya g ; erkekol f € o ; dursun ba ; gelincik a ; celebioglu e ; y€ ucel t ; yorulmaz i ; dursun e ; tezcaner Ç ; s€ ozener zÇ ; b€ uy€ uk€ ozt€ urk s ; kalyoncu f ; aydin Ö introduction: aspirin desensitization (ad) treatment has been shown to be effective in relieving the respiratory symptoms as well in reducing recurrency of nasal polyps in patients with nsaids exacerbated respiratory diseases (nerd). however, a conflict occurs about effective maintenance doses of aspirin on clinical parameters. objectives: in this study, our aim was to compare the effects of two different maintenance doses of aspirin on clinical outcomes for years of ad. this was a multicenter study which involved tertiary centers. patients who completed at least one year of ad treatment were included to analysis. study outcomes were number of nasal surgery, sinus infections, asthma morbidity (number of severe asthma attacks, hospitalization) as well as medication uses for both clinical conditions. the study included subjects, of whom were under mg aspirin daily as maintenance treatment whereas remaining on mg aspirin for a mean of . ae months of ad duration. regardless of maintenance doses, number of nasal polyp surgery gradually decreased at ( . ae . /year) and years ( . ae . /year) compared to that of before ad ( . ae . /year) (p<. ) in all subjects and were comparable in and mg. considering asthma outcomes, decrease in asthma attacks were observed only in mg aspirin group (p<. ) at and years whereas hospitalization due to asthma and systemic corticosteroid use decreased in both groups at and years. conclusions: ad has a reducing effect on nasal polyp recurrence for at least years in patients with nerd. this effect was similar for both and mg maintenance doses of aspirin. considering both treatment arms provided decreased hospitalization due to asthma and systemic corticosteroid use, we think that at years evaluation both and mg/day aspirin has comparable effects on asthma as well. however, reducing effect of ad on asthma attacks was only existed in patients taking mg. aspirin. objectives: pregnant women with syphilis and history of immediate hypersensitivity reaction (hsr) to penicillin were enrolled. according to the risk stratification, which was based on the initial hsr, serum specific ige and skin tests, patients were re-exposed to penicillin either through desensitization or provocation. patients with a clinical history suggestive of penicillin-anaphylaxis and/or positive serum specific ige to penicillin and/or positive immediate skin test were considered at high risk and were desensitized. the remaining patients underwent penicillin provocation test. results: we evaluated pregnant women with latent syphilis and history of penicillin allergy. clinical history was suggestive of immediate hsr in out of these ( %) patients, who were desensitized. all of them had negative serum specific ige to penicillin. intradermal tests were positive in / ( %). three out of those four were desensitized with an oral protocol and reacted during the procedure. one patient had a severe breakthrough reaction with uterine contraction and did not finish the procedure. the only patient with positive intradermal test that didn't react during the rdd underwent an intravenous protocol. the remaining / ( %) patients had negative skin tests and an uneventfully rdd. there was a statistically significant association between positive intradermal tests and breakthrough reactions during the rdd (p=. ). the other / ( %) patients with inconclusive history and negative skin test were submitted to penicillin provocation, which were negative in all of them. conclusions: risk stratification based on the initial clinical reaction and skin testing to guide penicillin re-introduction was safe and effective, as well as rdd. skin testing identified allergic patients to penicillin with increased risk of reactions during rdd. | utility of basophil activation test for monitoring the acquisition of clinical tolerance after subcutaneous desensitization to brentuximab-vedotin in two patients many hypersensitivity reactions (hsrs) produced by biologic agents have been seen and their true incidence is unknown. desensitization is a method to counter hsrs from monoclonal antibodies in patients with no other adequate alternative options. objectives: we describe a successful rapid desensitization to bv in two patients with scleronodular type hl, refractory to several lines of chemotherapy and asct. this clinical tolerance to bv is easily observed through the basophil activation test (bat) as a decrease in activated basophils after desensitization was done as a treatment of hsrs. because there was no therapeutic alternative in the two patients, we planned to pursue bv administration using a rapid desensitization -step protocol. a total dose of mg of bv was given through increasing rate and concentration. the patients completed their infusion without difficulty. after desensitization to bv, bat was done in both patients. the percentage of activated stimulated basophils with bv descended in both patients. both values are similar to their corresponding negative controls. conclusions: the bat continues to be a useful in vitro tool for the study of drug allergic disease. also, the bat in flow cytometry is able to monitor an acquired tolerance induced by a desensitization treatment in hsrs to bv. however, studies involving a larger number of patients will be required to assess the safety and efficacy of this approach to bat as a method to validate rapid desensitization in patients with hsr to bv. objectives: we retrospectively reviewed desensitizations in patients with a history of ihsrs to chemotherapy agents performed in our center from january to december . the protocol consists of increases in infusion rate every to minutes, in a to steps depending on the drug. in all cases the protocol was performed without premedication (only using regular medication according to instructions for every drug). results: a total of patients with a history of (ihsrs) received desensitization protocol without premedication to chemotherapy agents. the most common involved drug was carboplatin in ( . %) patients (of these % presented positive skin test (st)), followed by paclitaxel in ( . %) patients (of these . % presented a positive st) and oxaliplatin in ( . %) patients (of these . % o the st were positive). other chemotherapy agents involved were cetuximab, rituximab, irinotecan, epirrubicin, etoposide, cisplatin and cyclophosphamide. all patients were able to successfully complete the desensitization protocol without premedication and none of them need to withdraw the drug. conclusions: this protocol for rapid desensitization to chemotherapy without premedication is safe and effective. in addition, minimizes secondary effects of the premedication in these patients that are polymedicated. | rapid desensitization for the management of hypersensitivity reaction to biologicals-infliximab and adalimumab in inflammatory bowel disease patients objectives: to identify barriers to best practice with regards to drug allergy history taking and documentation, and to elaborate the potential strategies to overcome them. results: a total prescribers responded to the survey: doctors in training . % consultants . % non-medical prescribers . % most respondents . % ( %ci . - . %) were not aware of the availability of penicillin allergy testing in our trust. among those that were aware of it, . % ( %ci . - %) had not referred any penicillin-allergic patient to immunology during the past year. barriers to accurate allergy history collection: . % ( %ci - . %) concurred that often it is not possible to draw a firm conclusion based on history alone. . % ( %ci . - . %) agreed with the statement saying that, regardless of the details of the allergy history, it is always better to "play it safe" and not to use alternative beta-lactams in patients labelled as being penicillin-allergic (figure will be attached in the poster). among the interventions proposed; practical educational sessions, an interactive questionnaire to guide allergy history taking and classification and a modified antibiotic policy to guide prescribing based on the allergy classification, were all rated as useful (average score > on a scale from -not useful at all-to -very useful). | the regulatory role of germinal center maturation during the early b cell response to inhalant allergens investigated in the piama cohort using the medall allergen microarray introduction: in contrast to common belief, igg to airborne allergens is higher in allergic subjects, even before immunotherapy. one of the confusing aspects of the allergic immune response is that not only the igg response, but also the ige response can follow more than a single trajectory (with or without gc maturation). for ige we assume that the direct isotype-switching pathway (igm to ige) is the most relevant for the initial, mature-gc independent phase of sensitization to low-dose airborne allergens (such a pollen, mite). in later phases and for higher exposure situations as well as for other immunization routes, indirect switching is assumed to be the more relevant pathway. methods: ige, igg and igg antibodies were measured using the medall allergen microarray in children from the piama cohort at age and . these results were analyzed in relation to the ige levels at age and . objectives: to find support for the hypothesis that the ige/igg ratio reflects not only exposure, but also details on immunological processes during sensitization, such as germinal center maturation. results: sigg and sigg levels to the major inhalant allergens were low at age and remained in general low at age . however, children who at that time were positive for ige an allergen had a significant increased sigg to the allergen in question. sigg also appeared, but this response was low. the sigg level at age in sigenegative children was not consistently predictive for sige at age . conclusions: the initial igg response to inhalant allergens is synchronized with the ige response. this result fits with the hypothesis abstracts | that in the initial phase of sensitization to inhalant allergens the allergen initiates a weak and incomplete germinal center response that allows parallel ige-and igg production. one of the consequences of the multiplicity of b cell developmental pathways is that the igg/ige ratio is potentially diagnostic: if a subject has sigg levels in the microgram range, and thus a high sigg/sige ratio, this indicates involvement of mature gcs and the indirect class-switching pathway for some or all of the sige in this subject. | synthetic allergoid consisted of plga nanoparticles covered with synthetic peptides from bet v objectives: the aim of this study was to test a hypothesis that the ahr signaling is critical in controlling sl homeostasis through the regulation of key sphingolipid enzymes involved in the s p synthesis. results: we found that an ahr ligand and a tryptophan photoproduct, -formylindolo ( , -b) carbazole (ficz; nm), induced a increase in s p level in a ros and ca + -dependent manner, leading to the degranulation as well as il- secretion in mast cells, when compared to those seen in vehicle-treated cells. this was concomitant with an increased level of sphk phosphorylation and with a reduction in the enzymatic activity of s p lyase, which could be reversed by the addition of an anti-oxidant, nac. moreover, s pl was found to be directly oxidized by ros in vitro and in vivo. conclusions: our findings suggested that ahr-mediated ros and ca + signals are critical for controlling sl homeostasis through regulating sphk and s pl metabolic pathways, providing a new regulatory pathway in mast cells. methods: peptide cytokine mimetics were selected by phage display technology. flow cytometry, elisa, elispot, t cell proliferation, reporter gene, mediator release, intravital microscopy and peritonitis assays were conducted to evaluate the capacity of the mimetic peptides to modulate the immune response. results: the synthetic tgf-b -like peptide was able to down-regulate the production of tnf-a, il- , ifn-c and il- , up-regulate il- , decrease basophil degranulation and induce t reg cell differentiation. furthermore, this peptide was able to decrease leukocyte rolling and neutrophil migration during an inflammatory condition in vivo. the synthetic il- -like peptide was able to decrease basophil degranulation and to inhibit the proliferation of allergen-specific t cell lines established from the peripheral blood of birch pollen-allergic patients. conclusions: the peptide cytokine mimetics tested herein, were able to modulate the immune response in the tested conditions. they, thus, represent promising novel candidates for therapeutic approaches. nonetheless, most studies focus on changes occurring early in life and there are rare data on differences in responses between allergic and non allergic subjects. objectives: we aimed to evaluate i) the maturation trajectory of the tlr antiviral pathway ii) if this trajectory varies between atopics and non atopics. peripheral blood mononuclear cells (pbmcs) were isolated from otherwise healthy atopic and non atopic subjects. atopy was assessed by medical history and skin prick testing to common aeroallergens and egg white. selected cytokines involved in the antiviral response were measured by luminex multiplexing technology in hour culture supernatants of poly:ic-stimulated pbmcs. data were analyzed by estimating the non-parametric correlation between age and cytokine expression in atopics and non atopics and comparison of regression curves for each cytokine between the groups was performed. results: the analysis comprised data from atopic and non atopic patients (mean age . years, age range - and mean . years, range - . , respectively). significant age-related increases in the production of ifn-a , ifn-c, il- b, il- a, tnf-a, and mip- b were found only in non atopics and of il- and il- in both groups. significant differences in the trajectories (slopes) of cytokine responses over time between atopics and non atopics were observed for ifn-a , ifn-c, il- , il- b, tnf-a and mip- b, with suboptimal production in atopics. conclusions: age-related increases in cytokines implicated in innate antiviral responses were observed mostly for non atopics. atopy was associated with suboptimal trl- induced cytokine responses. differences in the developmental pattern of those cytokines between atopics and non atopics may account for the reported increased susceptibility of atopics to infections. | a systems-immunology approach identifies a set of micrornas in shaping the th phenotype in allergic airway inflammation introduction: mouse allergy is a common disease in inner city households, affecting up to % of children who are exposed as determined by house dust analysis. it is associated with allergic rhinitis, atopic dermatitis and asthma and it has been reported that exposure and sensitization to mouse allergens is a strong predictor for asthmatic disease. despite a strong link between mouse exposure and asthmatic disease, the allergic immune response to mouse has been significantly understudied. to date, only one major allergen in mouse, mus m , has been identified and very little is known about the targets of the allergic immune response against mouse. objectives: using a proteomic/transcriptomic approach, we sought to identify t cell targets in mouse allergic and asthmatic patients. results: mouse urine and epithelial extracts were analyzed by d-ige/igg immunoblots using pooled sera from mouse-sensitized donors. mass spectrometry of selected protein spots identified novel antibody reactive proteins. predicted mhc binding peptides from these novel proteins and mouse homologs to mammalian allergens were screened for t cell reactivity in pbmcs from mouse allergic patients. overlapping peptides from the major mouse allergen mus m and its major urinary protein isoforms were screened in parallel. our screen for t cell responses in pbmc from mouse allergic donors demonstrated that major urinary proteins account for > % of the total t cell response but they are not the only target of mouse-specific t cell responses. reactivity to mouse peptides homologous to other mammalian allergens, specifically guinea pig, was also detected. conclusions: in summary, our data demonstrates that the cellular and serological targets of the allergic response overlap, with mus m being the major target for both t cells and antibodies. to the best of our knowledge, this is one of the first comprehensive studies of t cell epitope targets in mouse allergy, which provides important insights into cellular and serological targets. this data may form the basis for the development of a mouse-specific immunotherapeutic approach. introduction: food allergy has a complex etiology with many potential underlying factors proposed to contribute to and modify its development and progression. the use of a databases to collect and analyse all relevant data related to incidents of food allergy is essential to fully understand causal factors and improve treatment. objectives: we developed a database using sql, hibernate and java server pages (jsp) that was designed to allow allergy professionals to easily add and modify patient data, including medical history, reaction details and in vitro/in vivo test results. we then filled this database with clinical data relating to reactions to plant-based foods for patients who visited the allergy service of the regional university hospital of malaga between - . these data were then analysed in various ways. cluster analysis of skin test results was used to search for relationships between different allergens based on similarities between patient sensitisation profiles; descriptive statistics and graphical analysis were performed to search for relationships between food type, age of first reaction, number of reactions and reaction severity. results: cluster analysis placed the different skin test allergens in distinct groups, which generally correlated with the type of allergen. for example, nuts, rosacea plant-food, mites, trees and weeds formed distinct clusters. analysis of patient history data showed that the first reaction occurred most frequently between ages - , with a right skewed distribution. a relationship was also found between age at first reaction and reaction severity, being urticaria and angioedema more common when the initial reaction occurs at a younger age, and anaphylaxis when the initial reaction occurs later in life. oas remained relatively prevalent at all ranges (around a quarter of all reactions in all age groups). we found fruits to be the most frequent triggers, followed by nuts; within fruits peach and banana were the most frequent. conclusions: this preliminary study show the importance and utility of recording patient allergy information in a well-structured and easily managed database. future work is currently underway to collect a new set of patients from the same geographical area and to analyse similar data from a different area in order to identify what results are replicable within our population and which results are generalizable to other areas. introduction: cow's milk allergy is very common in children and its correct diagnosis is important to prevent possible dangerous allergic reactions. the aim of the present work was to evaluate the prevalence of allergic sensitization to both cow's milk and to its main proteins. with medcalc ® . normality distribution of data was evaluated through the kolmogorov-smirnov test. patients were divided into three age groups ( - years, - years- - years). chi-squared test was performed to verify a statistical difference between sensitization to whole milk and to its main proteins and patients' age. introduction: the order fagales represents an important cause of tree pollen allergy, which is ubiquitous in the northern hemisphere. a high degree of allergenic cross-reactivity has been observed among allergens from these plants, mainly represented by pathogenesis-related protein class (pr- ) pr- s, including inhalant and food allergens. conclusions: testing ige reactivity to a panel of pr- s unveils important associations between sensitization profiles and clinical presentation, and allows the identification of novel cluster patterns potentially useful to predict disease severity in patients with pr- allergy. results: patients were included, seven boys and four girls, with a median age at diagnosis of six months. the most common offending foods were cow's milk protein (cmp, n= ) and rice (n= ). other foods were fish, egg, chicken, wheat, carrot and potato. average time of symptom onset was . hours. the most frequent symptoms were vomiting (n= ) and diarrhea (n= ). six patients had a history of hospital admission related to this problem. seven patients had concomitant atopic diseases, being the most frequent allergic comobility atopic eczema (n= ). skin prick tests and/or specific ige to culprit foods were negative at diagnosis, except for one patient with low specific ige to cmp. another patient become sensitized to cmp during follow-up. open food challenges were performed in patients starting from six months of age. resolution was achieved in patients, at a medium age of months. results: a total of cases of immediate-type fa among children were reported, with . % involving patients younger than years of age. the major causative foods were hen's egg ( . %), cow's milk ( . %), walnut ( . %), wheat ( . %), peanut ( . %), soybean ( . %), and shrimp ( . %). the most common causative food in each age group was cow's milk ( - years), walnut ( - years), walnut and hen's egg ( - years), and buckwheat ( - years), respectively. the symptom onset time was less than minutes in %. food-induced anaphylaxis was reported in ( . %) out of cases, and the major causes were cow's milk ( . %), hen's egg ( . %), walnut ( . %), wheat ( . %), peanut ( . %), buckwheat ( . %), and shrimp ( . %). the proportion of anaphylaxis was highest in buckwheat ( . %), followed by walnut and pine nut ( . % each). korean children were hen's egg, cow's milk, walnut, wheat, and peanut, with distinctive distributions according to different age groups. anaphylaxis was reported in . % among immediate-type fa. results: a total of children with a median (inter-quartile) age of . years ( . - . ) were enrolled to the study; (male . %). their ages at diagnosis were . years ( . - . ); follow-up times were . years ( . - . ) and milk specific ige levels at diagnosis were . ku/l ( . - . ). in . % of the children there was only cma; the other children were polyallergic to different foods having most frequently egg white allergy. concomitant diseases were . % atopic dermatitis, . % were asthma, . % were allergic rhinitis. during the follow-up milk tolerance was developed in . %, . % and . % at the ages of , and years respectively. the specific ige level at the beginning of the disease was found to be a risk factor for the persistence of the disease (p<. ). conclusions: cma is frequently present with other food allergies. nearly half of the patients develop tolerance to cm up to the age of years; whereas / becomes tolerant when they are at the age of years. most frequent concomitant diseases are atopic dermatitis and asthma. objectives: two survey tools were used; a questionnaire based on similar surveys done overseas, and the validated food allergy quality of life questionnaire (faqlq). this was distributed throughout paediatric allergy clinics at two metropolitan centres. children and adolescents aged - completed the questionnaire independently, whilst parents assisted with children aged - years. results: surveys have been collected at the time of writing of which were answered by parents for young children. overall, / ( %) reported bullying, with a higher portion in older children and adolescents ( / ; %). of this group, / ( %) reported being bullied or teased because of their food allergies. from parental reports, / ( %) stated that their child had experienced bullying or teasing because of food allergies. for those not bullied, parents mentioned that this may be due to their child having friends at school, being too young for bullying or because other children at school had a good understanding of the severity of allergies and were educated by teachers. the most common location for bullying was "in the playground or sportsground" ( / ). the most common form of bullying involved being "teased, called names or someone has said mean things to me" ( / ). whilst food allergens were involved in bullying in many cases ( / ), there were no reports of children being forced to eat food to which they are allergic. of concern however, two adolescents reported experiencing an allergic reaction as a result of the bullying. the majority reported experiences of sadness from bullying ( / ) while seven stated that it had no effect. conclusions: our current research shows that % of children and adolescents with food allergies experience bullying, and that % ( / ) experience bullying specifically because of their food allergies. this indicates a significant social problem that requires addressing to positively assist those children living with food allergies. introduction: recently we demonstrated that intake of specific foods, types of fat and micronutrients was associated with inflammation and mucosal integrity in adults with eosinophilic oesophagitis (eoe). the current study aimed to compare dietary intake of these patients with dietary guidelines and intakes of the general dutch population to further investigate our hypotheses on the protective or allergy-provoking role of specific nutrients in eoe. results: the total faqlq score was low when assessed by teenagers and children ( . and . , respectively) and moderately low when assessed by parents ( . ). experience of anaphylaxis and having multiple food allergies impaired hrql according to faqlq parent form (p<. ). gender, having prescribed an adrenaline-auto injector, experience of food provocation test, peanut allergy and faim did not contribute to different hrql. hrql in kindergarten and schools were moderately diminished (sum score . in schools and . in kindergartens) (p>. ). perceived disease severity was moderately present with total faim scores being . , . and . , when assessed by children, teenagers and parents, respectively (p>. ). % of participants' reported at least some possibility of dying if child/teenagers would accidently eat a food allergen. after fulfilling faqlq and faim, all participants expressed content, ten children/teenagers decided to approach food provocation tests de novo, employees of children's schools/kindergartens were encouraged in written invitations to assess anaphylaxis training programs, and four families accepted additional psychological support. conclusions: food allergies impair hrql in children and teenagers. allergies to multiple foods and experience of anaphylaxis were associated with more severe impairment of hrql. hrqlq and faim are useful, additional tools to assess and discuss child's/teenager's/parent's fears and obstacles because of food allergy and identify further needs of support. introduction: fruit allergy is the most common cause of food allergy in children older than years and adults. regional variations have been observed in europe but there are few studies in pediatric population. objectives: in the context of a prospective and multicentric study on pollen and vegetable food allergy in spain, we enrolled patients (median age , range - , female %), who had suffered at least two episodes of immediate symptoms after ingestion of fruits and had positive skin test to the implicated fruits. immunocap isac was analyzed in all patients. our aim was to describe the clinical characteristics with the fruits involved and the usefulness of the allergens included in the immunocap isac to improve its characterization. symptoms were categorized into oral allergy syndrome (oas), systemic symptoms (ss) and anaphylaxis. results: a total of patients were included. all of them had symptoms with more than one fruit. patients had pollen sensitization. the main offending food associated with allergic reactions were peach ( %), kiwi ( %), melon ( %), apple ( %) and banana ( %). allergic patients to peach had oas, ss and anaphylaxis, were recognized prup in all patients with anaphylaxis, in patients witch oas and in with ss, also prup associated with abstracts | prup in patients with ss. for allergy to kiwi, patients had oas and ss, were recognized actd in patient with sao and patients with ss. actd in patient with ss. conclusions: in our population, the most prevalent fruit allergy was the peach, as in spanish adults. patients allergic to peach were the ones that presented the most ss and anaphylaxis, followed by allergic to apple. as previously have been reported most of them had sige to its components in isac; being prup the most prevalent ( % had prup ). only patients with ss with kiwi were sensitized to kiwi allergens .the majority of patients allergic to apple, melon and banana were not diagnosed by immunocap isac. introduction: studies have shown that asthma and allergy are prevalent among production workers processing seafood, particularly in workers processing crustaceans. a major ige-reactive proteins is the muscle protein tropomyosin. specific ige to tropomyosin is suggested as a central marker for crustacean allergy, however it is not the only protein characterised as an allergen in crab processing. objectives: the aim of our study was to characterise tropomyosin exposure and prevalence of sensitisation to allergens in workers processing king crab (paralithodes camtschaticus) and edible crab (cancer pagurus) in land based processing plants in norway. results: personal air samplers collected air from the workers' breathing zone during crab processing. workers' blood was collected for ige testing. extracts of both king crab and edible crab raw meat, cooked meat, intestines and shell were made in our lab and used for skin prick testing and immunoblotting. while processing cooked crab yielded highest tropomyosin levels in the edible crab plant, processing raw crab yielded highest levels in king crab plants. ten ( . %) edible crab and ( . %) king crab workers had positive ige test (> . ku/l blood, immunocap systems) to crab. four ( %) of skin prick tested king crab workers and ( %) of skin prick tested edible crab workers had one or more positive reactions to edible crab extracts. more workers reacted to cooked crabmeat extracts than to raw crabmeat extracts. immunoblotting showed ige binding to a large number of proteins in all four extracts of both king and edible crab. binding was found to high molecular weight proteins in all four extracts of the crab tested, and the ige-reactive proteins differed between king crab and edible crab. conclusions: workers are exposed to tropomyosin in their breathing zone during crab processing. both king crab and edible crab workers are sensitised to crab, shown with immunocap specific ige test to crab, as well as positive skin prick tests and immunoblots to four different crab extracts made in our lab. workers processing crab in norwegian processing plants have an increased risk for developing sensitisation to crab. objectives: the aim of the study was to assess frequency of skin symptoms in surgery clinic employees, to evaluate burnout as a predictor of the frequency of skin symptoms, and to determine latexspecific ige in surgery nurses with skin symptoms. results: skin symptoms were significantly more frequent in surgery nurses ( %) than in surgeons ( . %), other physicians ( ), and other nurses ( . %) (v = . ; p=. ). skin symptoms were also significantly more frequent in workers with high/medium than in workers with low emotional exhaustion ( . % vs . %; v = . ; p=. ), as well as in participants with burnout than in subjects without burnout introduction: baker's asthma sensitization pattern is changing due to the introduction of different types of grains and seeds. objectives: a year-old ecuadorian man showing ocular, nasal and pulmonary symptoms when handling grain flours (with or without seeds), while baking for the last years. he tolerated grain flours oral intake, but had oropharyngeal symptoms, rhinoconjunctivitis and dyspnea when eating sunflower and sesame seeds, mustard, and beer with alcohol. he tolerated alcohol-free beer. we performed an allergy study: prick-test with commercial extracts of pollens, dust and storage mite, fungus, animal danders, cereals, yeasts and mustard. prick by prick with patient's products: wheat, multicereals and seeded flour, sunflower seeds, regular and alcoholfree beer spirometry and niox. serial peak flow measurement at and away from work, handling tests with wheat flour and sunflower seeds. laboratory studies: specific ig e to cereals and seeds (cap-isac-microarrays). immunoblot with regular beer (at room temperature and boiled), wheat flour and sunflower seeds, and sequential chromatography. results: skin tests were positive with commercial mustard and all provided products except for the alcohol-free beer. spirometry was normal. niox: ppb. peak-flow monitoring showed a % variability during working period, remaining stable during holidays. handling tests with wheat flour and sunflower seeds were positive. specific ig e was positive for grains, malt, gluten, mustard and sunflower seed. the specific determinants were positive to s-viciline, -s globulin, several prolamins ( s-albumine, alfa-amylase inhibitors and gliadin) and ltp. immunoblot detected a band lower than kda in both regular beer extracts (not detected in alcohol-free beer) identified as barley's ltp, a band of kda in the sunflower seed extract ( salbumine), and two bands lower than kda in wheat flour extract (two kinds of alfa-amylase inhibitors). we present a non-atopic baker with occupational rhinoconjunctivitis and asthma due to prolamins (alfa-amylase inhibitor and gliadin of wheat flour together with s-albumin sunflower seed), and anaphylaxis when eating seeds ( s-albumins, s-vicilin and s-globulin) or drinking beer (sensitization to barley's ltp). it is interesting that the manufacturing process of non-alcoholic beer (high temperature and high pressure) seems to degrade barley's ltp, as suggested by both tolerance to its ingestion and loss of immunoblot band. objectives: the main objective of this study is to evaluate longitudinal change of lung function in workers employed in food preparation and distribution potentially exposed to food allergens. spirometries performed between and as part of medical surveillance of food-handlers workers were evaluated. data about occupational task, work years, smoking habits and diagnosis of atopy, asthma and copd were collected from a clinical database. differences in prevalence were calculated by chi-square test, differences in means were calculated using spirola software referred to european predicted values. results: the majority of workers were females (n= ; . %) and caucasians (n= ; . %). ( . %) subjects were current smokers, ( . %) were ex smokers, ( . %) were atopic and no one reported a diagnosis of asthma or chronic obstructive pulmonary disease. % workers were canteen service employees and % were cookery employees. mean yearly values of the pair-wise within person variation of fev and fvc were respectively À ml and À ml. . % of last observations had a fev below lln and . % of last observations had a fvc below lln. conclusions: this study may help in planning preventive programs and in facilitating early recognition and diagnosis of work-related respiratory diseases. wheat, foods and latex allergens may determine decline in fev and fvc; furthermore, in our study, a significant proportion of workers reported exposure to tobacco smoke. excessive loss in fev over time should be evaluated using a percentage decline ( % plus loss expected due to aging) that we will make afterwards adding more years of follow up spirometries. intervention of smoke avoidance are needed. | prevalence of wood dust sensitization in occupationally exposed workers in germany-what can be tested? objectives: in serum samples from patients with suspiciously allergic symptoms to wood dust overall specific (s)ige-tests with standardized wood-dust extracts coupled to streptavidin-immu-nocaps were conducted. additionally, ccd as known source of non-protein ige-target was evaluated. sensitization rates were calculated for different wood species. most frequently requested wood dust allergens were obeche (n= ), beech (n= ), oak (n= ), spruce (n= ) and pine wood (n= ) followed by - requested sige-tests to mahogany, ash, larch and maple wood. results: overall wood dust sensitization rate was about % (range: - %) with obeche, box wood and kambala as most prominent sensitization sources obtaining each more than % sensitization. no sensitizations were detectable to red cedar and meranti wood in more than requested tests, respectively. in patients at least one sige-sensitization to any wood was measured. there from were additionally tested with ccd resulting in % positive and % negative ige responses to ccd. some wood species were exclusively recognized by ccd-positive subjects: ash, maple, alder, mahogany, teak, mansonia and palisander. whereas other woods were recognized by sige of subjects with / or without sige to ccd: obeche, box wood, spruce, oak, beech, limba, pine and kambala. relevance of wood sensitization next to ccd was investigated in eight double positive subjects (wood + / ccd +). specific ige-binding to wood allergens was completely inhibited by ccd in three samples. these subjects were supposed to have no clinically relevant wood sensitization. whereas in five samples sige-binding to selected wood species was not significantly reduced by ccd. in four of these patients skin prick tests (spt) and challenge tests (bronchial and/or nasal) with corresponding wood allergens were performed. three of four challenge tests were positive with the respective wood extract and all spts with wood extracts whose sige-binding was not affected by ccd inhibition showed positive reactions. here clinical relevance of sige-mediated wood sensitization could be demonstrated. conclusions: in summary, our data demonstrate that standardized wood extracts and ccd tools are necessary for valid in-vitro diagnosis of wood dust sensitization. introduction: respiratory symptoms have been reported frequently among seafood processing workers. since seafood processing workers handle the raw material and participate in processing activities during work, they are exposed to inhalable bioaerosols. this put them at risk of developing respiratory symptoms, asthma and allergy. there is little knowledge about the respiratory health status among fish production workers on board fishing trawlers. objectives: the aim of this study was to assess the respiratory health status among norwegian fish production workers, processing fish on board fishing trawlers. the study population consisted of fish production workers, machinists, support crew members and non exposed controls, all were males. written informed consent was the fish production workers had a significantly decreased fev % predicted compared to the non-exposed control group, b=À . , % ci [À . , À . ], when controlling for age, pack-years and family history of asthma/allergy/eczema. the effect did not change when controlling for doctor diagnosed asthma or after dividing fish production workers by doctor diagnosed asthma. machinists and support crew members showed a similar decrease in fev % predicted, but the difference from the non-exposed control group was not statistically significant. furthermore fish production workers, reported a non-significantly increased prevalence of wheezing and daily morning cough compared to the non-exposed control group. conclusions: fish production workers, processing fish on board fishing trawlers, showed reduced lung function values compared to a non-exposed control group, and this finding is in accordance with previous findings in seafood industry worker populations from our research group. results: study group comprised patients with work-related respiratory symptoms suggesting wra. the research completion with sic allowed to recognise wra in persons ( oa and wea) and to exclude asthma in cases qualified to reference group (gr). workers with wea occupationally exposed do lmw-a manifested the highest level of baseline non-specific bronchial hyperresponsiveness (nsbhr) in comparison to the other groups (table ) . patients with oa exposed to lmw-a more frequently than exposed to hmw-a revealed nsbhr before sic (p=. ) with lower level of median (me) provocative methacholine concentration value causing % fall in fev (pc induced sputum (is) was obtained before and h after sic from patients ( gr and wra). in all gr samples and samples possessed before sic from wea subjects exposed to hmw-a, intermediate profile of is (neutrophils (ne)< % and eosinophils (eo)< %) dominated ( results: eg: in "granulation" exposure is relatively high and the number of different enzymes handled is low; here the risk of sensitization is highest. in contrast in the pilot plants the exposure compared to granulation in general is lower but the number of enzymes handled concurrently is higher. still the sensitization risk is lower than the range for granulation. conclusions: even though this approach may seem crude and not free from bias and potential misclassification, data does not support the hypothesis that the number of enzymes increases risk of sensitization, whereas increasing exposure level seems to be a risk factor. this suggests that each enzyme exposure acts as a risk in its own right and that the "cocktail effect" seems to be of minor relevance. phospholipids. bioinformatic studies of sequence homology conducted prior to this study showed no similarity between the mpla s and known allergens including ves v . however, the common enzymatic activity in ves v and the mpla s might still lead to crossreactivity. the goal of this project was therefore to test for possible cross-reactions between sige towards ves v and three different mpla s. methods: serum from known wasp allergic persons with sige towards ves v spanning from . ku/l to ku/l were used for inhibition studies. from each, ll serum was incubated with ll of either saline solution (negative control), lg/ml alk soluprick solution (positive control) or one of three mpla s, each in three concentrations (either . lg/ml, lg/ml and lg/ml (n= ) or lg/ml, lg/ml and lg/ml (n= )). the level of sige towards ves v was measured using the i immunocap, and a decrease in this level was calculated as %inhibition compared to the sige measured from serum incubated with the negative control. inhibition by mpla s would indicate cross-reactivity. results: the positive control caused . ae . % (n= ) inhibition of sige towards ves v . this was lower than expected but was found to be caused by a few sera where the fraction of sige towards ves v was < % of all sige towards wasp venom. in the remaining sera, %inhibition was . ae . % (n= ). for all three mpla s, no inhibition was found for any serum tested (n= ) at the highest concentration tested with %inhibition being . ae . %, . ae . % and . ae . % respectively. conclusions: no inhibition of sige to ves v was found to any of the three microbial phospholipases tested. this indicates that no cross-reaction is found between the phospholipase a in wasp, ves v , and phospholipase a from microorganisms despite the common enzymatic activity. objectives: the aim of study was to evaluate the prevalence and the impact of polyvalent ige-mediated allergy on the course of ad and the occurrence of allergic symptoms from other organs and systems in infants and young children. conclusions: polyvalent ige-mediated allergy is common in young children with ad and seems to be a risk factor for the severe course of the disease. introduction: non-steroid anti-inflammatory drugs (nsaid) are the second most common cause of drug allergies in childhood. objectives: the aim of the study is to determine the frequency of nsaid hypersensitivity in asthmatic children. results: patients who were being followed up for asthma were included in this study. the mean age of the patients was . ae . years, while . % ( ) were male. % (n= ) of the patients had a reaction history to nsaid (ibuprofen in , flurbiprofen in , diclofenac potassium in , metamizole+acetylsalicylic acid in , paracetamol+acetylsalicylic acid in and ibuprofen+acetylsalicylic acid in ). nsaid sensitivity was confirmed in ( . %; / ) patients who were tested with suspected drugs, while the provocation test was found negative in one patient who described reaction with ibuprofen. of the children who were assessed as a control group, only had a reaction history to acetylsalicylic acid and no reaction developed in the provocation test. conclusions: nsaid hypersensitivity is more common in patients with asthma. thus, these patients should be evaluated for nsaid hypersensitivity. results: from jan to dec , pediatric cases were received by kaers. of pediatric patients, . % were male, . % were female and . % were unknown. these pediatric cases included a total of adr events with an approximate average of . adr events per report. of those cases, . % were in infants (age - years), . % were in young children (age - years), . % were in old children (age - years), . % were in adolescent.(age - years) and unknown were . %. male to female ratio was : . and the mean age was . ae . years. regarding categorical ranking of reported adr agent groups, the most common group were antibiotics ( . %) followed by antineoplastic agents ( . %), vaccine ( . %), antipyretics ( . %), opioids ( . %), sedatives ( . %), antiepileptic drugs ( . %), contrast media ( . %), steroids ( . %). the most common adr symptoms were gastrointestinal system disorder in . %, skin-appendage disorder in . %, abstracts | body as a whole-general disorder in . %, central-peripheral nervous system disorder in . %. regarding seriousness of adrs, events ( . %) had episodes requiring hospitalization and were considered life threatening. of these, cases had anaphylaxis or anaphylactoid reactions. introduction: multiple drug allergy is an adverse reaction to two or more structurally unrelated drugs that appears to occur by immune mediated mechanism. patients with a history of reaction to two or more drugs often apply to allergy clinics. objectives: the aim of this study is to evaluate the test results of the patients who have a history of multiple drug allergies and underwent drug provocation tests. results: during the study period, drug provocation tests were performed in patients ( drug provocation tests). of these patients, ( . %) had a history of drug reactions to or more drugs. the mean age of the patients who had a history of reactions to two or more drugs was . ae . years, and . % (n= ) toms, and autoimmune manifestation in comparison to igm/iga responders (respectively, pneumonia: %, % and %; chronic diarrhea: %, % and %; autoimmunity %, % and %; autoimmune cytopenias: %, % and %). malignancies were found more frequently in the non-responders and igm-only responders groups in comparison to igm/iga responders (respectively, %, % and %). eleven ( %) patients died during the study time. survival analysis according to the igm/iga responder status showed that the -years estimated survival for non-responders vs igm-only vs igm/iga responders was respectively after one year %, % and %; after two year: %, % and %; after three years: %, % and %%; after years: %, % and %; after years: %, % and %; after years: %, % and %. interesting, in our series only two deaths were due to infective complications: five were consequent to malignancies, one to autoimmune cytopenias and three to not-cvid related conditions. between-infusions intervals ( - days) than pid patients ( - days). finally, a small number of patients with anti-cd -related sid was able to discontinue scig replacement therapy after recovery of spontaneous igg production. conclusions: this is, to our knowledge, the biggest single center cohort of scig-treated patients ever described. results suggest that safety and effectiveness of scig is similar in pid and sid, irrespective of the mechanisms underlying igg depletion. moreover, in sid a lower igg dosage is required and ig replacement does not always need to be lifelong, with obvious pharmacoeconomic implications. a | should we screen children with bronchial asthma for primary immune deficiencies? miteva d ; perenovska p ; papochieva v ; georgieva b ; lazova s ; naumova e ; petrova g the patient became febrile and cultures were repeated, being positive to campylobacter jejuni, resistant only to ciprofloxacin (blood) and to campylobacter coli, susceptible only to gentamicin and amoxicillin/ clavulanic acid (stools). treatment was thus switched to amoxicillin/ clavulanic acid ( / mg / h). the patient became apiretic at day and improvement of local inflammatory signs was noticed, treatment was prolonged for six weeks. one week after cessation, skin lesion worsened again in the same location, in association with fever. blood and stool cultures were repeated and gentamicin ( mg/day; iv) and cefixime ( mg / h) were started, in agreement with previous cultures results. curiously, there was no history of diarrhea, but the patient referred a period of recurrent abdominal colicly pain, before cutaneous lesions appear. conclusion: bacteremia with campylobacter species requires specific laboratory workup. diagnosis of campylobacter jejuni bacteremia should be considered in hypogammaglobulinemic patients with recurrent fever, particularly when typical copper color erysipela-like skin lesions occur. campylobacter eradication can only be achieved with prolonged antibiotic therapy guided by antibiogram in cultures. conclusions: in this study, genetic defects of five higm patients have been identified, for other patients further genetic investigation such as next generation sequence (ngs) is required. the study results can help diagnose of the disease more definitively and also can provide valuable information for genetic counseling especially for those who have a history of immunodeficiency in their families and also for prenatal testing. conclusions: mutation analysis of unc d gene can help the families with hlh patients give genetics counseling for carrier detection and prenatal diagnosis. woelke s ; valesky e ; bakhtiar s ; bader p ; schubert r ; zielen s department for children and adolescents, division of allergology, pulmonology and cystic fibrosis, goethe university hospital, frankfurt, germany; department of dermatology, venereology and allergology, goethe university hospital, frankfurt, germany; department for children and adolescents, division for stem cell transplantation and immunology, goethe university hospital, frankfurt, germany introduction: ataxia telangiectasia (a-t) is a devastating multi-system disorder characterized by progressive cerebellar ataxia, growth retardation, immunodeficiency, chronic pulmonary disease and genetic instability with an increased risk for malignoma. as described in other primary immunodeficiencies cutaneous granulomas are a known phenomenon also in a-t. still treatment indication and strategies remain controversial. objectives: from our cohort of classical a-t patients, eight patients in the aged to years presented with granulomas. histopathology of the lesions confirmed the presence of granulomatous inflammation without detection of any microbiological agent in all patients. five patients suffered from cutaneous manifestation, in two patients we detected a bone and in one a joint involvement. both patients with bone involvement (patients and ) as well as one patient with massive skin manifestation (patient ) were treated with tnf inhibitors (infliximab). the patient with granulomas in his finger joint (patient ) was bone marrow transplant (bmt) for other reasons. year led to a total remission for three years now. in patients and treatment with tnf inhibitors led to a partial regression of granulomas. treatment interruptions caused deterioration again. in the course of treatment the effects of infliximab diminished most likely caused by drug antibodies. after changing treatment to subcutaneous adalimumab a further regression could be detected. in patient granulomas totally disappeared with immune reconstitution after successful bmt. partially successful in treatment of granulomas. due to the known immunodeficiency in a-t patients, indication for immunosuppressive therapies as tnfa inhibitors should be held strictly. woelke s ; hess u ; knop v ; krausskopf d ; kieslich m ; schubert r ; zielen s of to years regarding c-reactive protein (crp), liver enzymes, abdominal ultrasound and neurological status (ataxia score). we divided the patients into two age groups of a-t patients aged to years and a-t patients aged years to years. ataxia score (r= . ), although the underlying pathomechanism is unclear. ultrasound revealed nonalcoholic fatty liver disease in only one young patient ( . %) compared to older patients ( . %). one female patient aged years died due to a hcc. conclusions: liver disease is present in almost all older a-t patients. structural changes, nonalcoholic fatty liver disease and fibrosis are frequent findings. there is a considerable risk for hcc. prospective studies are necessary using noninvasive techniques for the assessment of liver fibrosis (eg transient elastography) and to establish the risk of hcc in a-t patients. objectives: in this study, it was aimed to determine the frequency of pollen-food syndrome in children who have sensitization to pollens. results: pollen-sensitized patients were included in this study. the mean age of the patients was . ae . years, while . % (n= ) were male. in . % (n= ) of the patients, allergic rhinitis was concomitant with asthma. . % (n= ) of the patients described symptoms related to pfs. % ( / ) of them had a history of anaphylaxis with suspected food. the mean age of the patients describing pfs was . ae . years and % (n= ) of them were female. in ( . %) of these patients, skin tests performed with suspected food was positive, but in one patient the skin test was negative while specific ige was positive. suspected food was fruit/ vegetables in patients. in patients with pollen allergy, oropharyngeal symptoms related to fresh fruit, vegetables, dried fruits and nuts should be enquired. it should be noted that these patients might experience serious systemic reactions including anaphylaxis. patel nb ; vazquez-ortiz m ; lindsley s ; abrantes g ; bartra j ; dunn galvin a ; turner pj conclusions: there is no evidence that the occurrence of anaphylaxis at fc, and self-treatment with an adrenaline auto-injector device, result in adverse impact on hrql measures. the impact of a reaction at food challenge appears to confer greater benefit on the parent than the child. the relationship between confidence in management and hrql needs further assessment, since it is likely that these outcomes will be affected in different ways following therapeutic interventions. results: fifty-one patients ( females, males) (median age: . years, range - ) with cma were studied. spt to cm was . ae . mm as mean diameter. forty-eight out of fifty-one ( . %) patients underwent dm-opt ( patients refused to underwent opt due to positive spt or s-ige to dm introduction: bovine milk is the most common food allergen in children under years of age. milk allergy is treated by eliminating milk from the diet. the milk elimination diet endangers the child's energy intake and also exposes the child to shortage of multiple nutrients. this study was needed because there are no previous systematic reviews about this subject. objectives: the aim of the present study was to examine if the milk allergy or the other factors associated with milk elimination diet have an influence on child's growth. the present study was conducted according to international guidelines for systematic reviews. results: a total of studies were initially identified, of which three fulfilled our criteria. these three studies included children with cow's milk allergy and control children. in all these three studies, children with cow's milk allergy were lighter than controls. in addition, in two studies, the growth of the children with cow's milk allergy was stunted. in two studies the milk elimination was substituted with special infant formula. also in one study where both the growth and the weight were stunted, no major differences in energy or nutrient intake between cow's milk allergic cases and controls were reported. conclusions: current evidence suggests that milk allergy is associated with stunted growth in childhood, but reasons for this are unclear. in order to clarify the effect of cow's milk elimination diet on growth in childhood and the underpinning mechanisms, more studies need to be conducted. in addition, special attention to the diet and growth of children with cow's milk allergy is needed. results: a total of children were surveyed in this -year period (annual average: ). in , children ( . %) were diagnosed with food allergy, including cases of pfas, cases of egg allergy, and cases of dairy-product allergy. in , children ( . %) were diagnosed with food allergy, including cases of pfas, cases of egg allergy, and cases of dairy-product allergy. over this -year period, the prevalence of pfas increased . fold (from . % to . %). among the pfas cases, the prevalence of rosacea and apple allergy increased . -and . -fold, respectively. the most prevalent was apple allergy ( . %), followed by peach ( . %), loquat ( . %), plum ( . %), pear ( . %), and strawberry ( . %). the prevalence increased significantly for pfas but not for other types of food allergy (egg and dairy-product allergy). in the future, nationwide studies are needed to further elucidate the relationship between pfas and allergic rhinitis. | immune profile after oit in children with cow s milk allergy patients with elimination diet, group : patients with natural tolerance, group : healthy control). in all groups specified laboratory tests were performed at onset and also at month to treatment groups. in desensitization group at month of treatment we evaluated increase in total ige level, sp iga and igg antibody responses, decrease in cow's milk spige levels and an increase in il- , il- , tgf-b cytokine responses without a difference in cd +cd +fox-p % levels. il- levels were similar with pre-treatment levels whereas foxp mrna expression was similar with tolerance group. in elimination group at month treatment, there was a decrease in cow's milk spige whereas there was no change in sp iga levels and a minimal increase in igg levels. there was no change in il- and il- cytokine levels. and an increase in tgf-b cytokine response less than group , decreased il response, a foxp mrna expression differed from tolerance group was identified. objectives: although hyperuricemia has a significant prevalence in the general population, and has been related to exercise-induced asthma, could be related to bronchial asthma and nasal polyposis. hitherto, its possible association with hypersensitivity to nsaids and its convenience as biomarker have not been acquainted. conclusions: in our population, hyperuricemia has not demonstrated to be a reliable biomarker related to nsaids allergy and could not be used as a risk factor for assessing the triad nsaids allergy, asthma and nasal polyps. to study the vas of the total score was seen significant variance in: nsaid-cu ( . pt) and nsaid-pa ( . pt) (p=. ), nsaid-cu conclusions: data support that cutaneous manifestations have a common response with aerd to cox inhibitors. conclusions: this study showed that in a positive drug oral provocation test, respiratory symptoms were accompanied with nitric oxide changes in both nasal and exhaled way. barrionuevo e ; doña i ; salas m ; bogas g ; guerrero ma ; sanchez mi ; cornejo-garcia ja ; torres mj allergy unit, regional university hospital of malaga-ibima, malaga, spain; research laboratory, ibima-regional university hospital of malaga-uma, malaga, spain introduction: non-steroidal anti-inflammatory drugs (nsaids) are the most frequent triggers of drug hypersensitivity reactions, being cross-hypersensitivity reactions (chr) the most frequent. the categories included in chr are nsaids-exacerbated respiratory disease (nerd); nsaids-exacerbated cutaneous disease (necd) and nsaids induced urticaria/angioedema (niua). however, it has been reported patients with chr to nsaids who developed a combination of skin and respiratory symptomatology (blended reactions). objectives: our aim was to analyse the characteristics of patients with blended reactions and compare with those developing symptoms exclusively respiratory (nerd) or cutaneous (niua). episodes of cutaneous and/or respiratory symptoms after the intake abstracts | of ≥ different nsaids included strong cox- inhibitor (acetylsalicylic acid (asa) and/or indomethacin); ii) if they had < episodes of cutaneous and/or respiratory symptoms induced by < different nsaids, a positive drug provocation test (dpt) with asa was required; iii) if patients had respiratory symptoms accompanied or not by cutaneous involvement, a positive nasal provocation test with lysine aspirin (npt-lasa) was required. atopy was assessed by skin prick test using a panel of inhalant and food allergens. objectives: subjects with nsaids hypersensitivity were divided into two groups: a) those from to years and b) those from - years. diagnosis was established by a clinical history and controlled challenge with asa. atopic status was verified with a detailed allergological study including skin testing to inhalant allergens. clinical entities were classified in three categories: urticaria/angioedema, anaphylaxis and respiratory (asthma and/or rhinitis). cases. no differences were observed in the atopic status between both groups. there were significant differences between males/ females (p<. ). when we compared the clinical entities there were more cutaneous manifestations, mainly angioedema, in the group a) and more anaphylaxis in group b) although there were no significant differences due to sample size. conclusions: significant sex differences between hypersensitivity reactions to nsaid occurs with predominance of males in the first group (a). although there are also a predominance of clinical entities, an increase number of cases is needed to establish significance. studies on this direction are in progress. show an increase in all age groups. etiologic analysis was limited as the study was carried out using the icd- code (nhic records) and database of self reporting systems (kaers). so, further study was needed. introduction: genetic variants from the q locus are the strongest known genetic determinant for early-onset childhood asthma, and have also been associated with uncontrolled asthma despite asthma treatment. objectives: the aim of the study was to assess whether there is an association between a single nucleotide polymorphism (snp) in the q locus (rs ) and asthma exacerbations despite the objectives: our hypothesis is that the arg allele is associated with increased use of prescribed asthma medication, over a -year period. to explore this hypothesis, we have undertaken a secondary analysis of breathe, a study of gene-environment associations with asthma severity. breathe data were collected on participants with asthma, aged - years, between and , in tayside conclusions: in children and adults, the homozygous arg/arg status is associated with long-term increased prescribing for asthma medication compared to those carrying at least one gly allele. defining subgroups of individuals requiring more medicines could help predict treatment costs and develop targeted management strategies. objectives: considering the role of ptgdr in allergy, the goal of this study was to analyze the effect of ptgdr expression on cytokine levels in the a cell line. analyze ptgdr expression in a cell cultures. cytokine production assays in the culture supernatant were measured by cytometric bead assay using the bioplexpro tm human cytokine standard -plex, group i. the assays were conducted with bioplex high-throughput fluidics system, powered by the luminex technology. every sample was run at least in triplicate. the ptgdr expression in the transfected cells with the haplotypic variants differed by orders of magnitude relative to control cells (p<. ). we found significant differences in ptgdr expression between ctct and cccc haplotypic variants. the cccc (À c, À c, À c, and À c) introduction: c t polymorphism in the cd gene has been suggested in susceptibility to asthma. cd is a multifunctional receptor endotoxin, which is expressed on the surface of macrophages, monocytes and neutrophils. it is likely to play a role in the inflammation pathway. though data is available regarding association of cd gene with asthma but independent studies are in conflict. objectives: the present study was conducted to examine the association of promoter c t single nucleotide polymorphism (snp) in the cd gene for indian children with atopic asthma. we characterize the c t polymorphism in children with asthma ( ), cohort group ( ) and healthy control group ( ) by pcr rflp. association analysis was performed using v tests. we also analyzed the association of cd (c t) with total ige levels by elisa and foxp expression using flow cytometry. in this snp a base pair (bp) pcr product was generated using the standard primers. after restriction products showed that homozygous c allele was appeared as a single bp band, the homozygous t allele as bands of bp and bp, and heterozygous exhibits all three bands ( , and bp). the or of cc genotype frequency abstracts | was . in study group and . in cohort group and the or of c allele frequency was . in study group and . in cohort group. total ige level were found to be significantly higher in cc genotype compared to ct and tt genotype. foxp level is significantly higher in control group in all genotypes compared to cohort and study group. conclusions: the present study concludes that in cd gene polymorphism cc genotype was not significantly associated with asthma but other factors ie total ige and foxp showed significant association of cc genotype with asthma. on the other hand, there was significant association of c allele with asthma. | the disbalance of tlr , tlr gene expression and cytokines production in children with bronchial asthma svitich oa ; gankovskaya lv ; namazova-baranova ls ; bragvadze bg ; alekseeva aa ; gankovskii va objectives: examined were patients with bronchial asthma aged from to years and healthy children of the same age. cytokines were determined by elisa. determination of mrna expression in scrapings from the mucous membranes of the respiratory tract and in peripheral leukocytes was carried out polymerase chain reaction in real time. results: in scrapings from the mucous in patients with moderate to severe asthma found a significant increase in the gene expression of tlr , times, the gene tlr in times in comparison with the control group. in children with severe asthma also found a significant increase in the gene expression of tlr . times compared to healthy children, p≤. ). indicators of tlr gene expression in this group of patients have a tendency to increase, but not statistically significant. when comparing the indicators of innate immunity in samples with a leukocyte mass in the group of children with severe asthma showed a decreasing expression of tlr compared with the index in healthy children. also decreased the expression of tlr . in children with moderate ba similarly, a significant decrease of tlr gene expression in times. the trend towards reduced expression of tlr remains in this group, but is not reliable. in washings from the nasopharynx shows that patients with bronchial asthma il- is increased . times compared to the norm, to pcg/ml, tnf increased in times and pcg/mg in severe asthma, and . pkg/ mg-for mild, il- increased in times ( pcg/mg), pkg of . / mild blood, il- also increased . -fold and equal to . pkg/mgwith heavier with easy- . pkg/mg, normal À pkg/mg. ie is an increase in proinflammatory and anti-inflammatory cytokines. conclusions: the overexpression of tlr , tlr accompanied by increasing, the production of cytokines. this is a violation of mechanisms of innate immunity at the level of the mucous membrane of the nasal cavity on the role of inflammation in the pathogenesis of tlr. | sustained reduction in risk of experiencing asthma symptoms and using asthma medication in years following grass slittablet treatment-results from the paediatric gap trial were: wheezing, cough (for more than consecutive days), shortness of breath, chest tightness. the odds ratio for having asthma symptoms, using asthma medication, or having asthma symptoms and using asthma medication was significantly lower in the grass slit-tablet group during the followup years. for asthma symptoms, the results were: or= . , p=. days with csms< were defined as "no or minimal symptoms" and days with csms > were defined as severe symptoms. csms score was significant lower in the ilit group than in the placebo group for , and . in mean csms was . roth-walter f ; schmutz r ; mothes-luksch n ; zieglmayreer p ; zieglmayer r ; jensen-jarolim e objectives: here, we investigated whether the immune molecule lipocalin (lcn ) may discriminate between allergic and sensitized individuals, and between responding and non-responding patients. results: lcn -concentrations were assessed in sera of healthy and allergic subjects (n= ) as well as of house dust mite (hdm) allergies that underwent hdm-sublingual immunotherapy (slit) in a randomized, double-blind, placebo controlled trial for weeks. sera pre -, post-slit and at least months after slit were assessed for lcn and correlated with total nasal symptom score (tnss) obtained during chamber challenge at week in patients receiving hdm-(n= ) or placebo-slit (n= ). allergic individuals had significant lower lcn -levels than healthy controls, with women having lower lcn -levels than men in the patient cohort. hdm-allergic patients who received hdm-slit had a significant increase in hlcn months after termination of hdm-slit, whereas in subjects receiving placebo no increase in hlcn was observed. within the hdm-slit treated group, lcn -levels were significantly higher in patients whose symptoms improved during slit in contrast to those in which symptoms became more severe. hence, time-course of lcn in an allergic individual was predictive to assess clinical reactivity to hdm. objectives: here, we present the benefits of treatment in terms of nnt to prevent one additional child from having asthma symptoms and asthma medication use. children treated with grass slit-tablet had a reduced risk of asthma symptoms and asthma medication use during the -year follow-up period compared with placebo (or= . [ . , . ] for sq grass slit-tablet (n= ) vs placebo (n= ), p<. , relative risk reduc-tion= %). the risk reduction was independent of age at treatmentstart. younger children had a higher predicted probability of developing asthma symptoms and asthma medication use than older children. thus, the younger the children were at treatment-start, the greater the percentage was prevented from having asthma symptoms and asthma medication use during follow-up off treatment. for children aged at treatment-start, the risk was reduced from % to % and for those aged it was reduced from % to %. consequently, the nnt to prevent one additional child from having asthma symptoms and asthma medication use during the -year follow-up increased with age, with nnt= for children aged and nnt= for children aged . conclusions: the grass slit-tablet reduced the risk of asthma symptoms and asthma medication use during the -year follow-up period; the risk reduction was independent of age. however, the nnt increased with age as younger children had a higher risk of developing asthma symptoms and asthma medication use, emphasising the importance of treatment-start early in life. results: participants were screened for birch and grass allergy, of whom ultimately met randomization criteria and were treated with either slit-t or placebo for months. treatment was preceded by a successful baseline birch pollen challenge in the eeu where a minimum tnss of was achieved in the first of hours of pollen exposure. participants attended the post treatment challenge in the eeu, also hours in duration. no significant differences were noted in the reduction of birch-induced tnss compared to baseline between the slit-t and the placebo treated participants (the primary outcome measure). adverse events with a minimum % frequency occurred in % of participants in the placebo arm and % of participants in the active arm, with upper respiratory tract infection ( % in active arm and % in placebo arm) being the most common. oropharyngeal itch was the most common adverse event with causality at least possibly related to study medication ( % in active arm and % in placebo). no serious adverse events occurred including no anaphylaxis. objectives: here, we present a pooled subgroup analysis in adolescents from phase ii/iii-iii trials with the hdm slit-tablet ( sq-hdm dose), p in north america and to- - - in japan. results: to- - - was a randomised, dbpc phase ii/iii trial investigating the efficacy and safety of the hdm slit-tablet in japanese adolescents and adults ( to years) with moderate-tosevere hdm ar (n= , of which were adolescents). subjects were randomised to treatment with the hdm slit-tablet in doses of sq-hdm, sq-hdm or placebo for year. p was a randomised dbpc phase iii trial investigating the efficacy and safety of the hdm slit-tablet in north american adolescents and adults (≥ years) with moderate-severe hdm ar with or without asthma (n= , of which were adolescents). subjects were randomised to treatment with sq-hdm or placebo for up to year. in both trials, the primary endpoint was the average total combined rhinitis score (tcrs) during the last weeks of treatment. the pooled analysis was performed on mean values using a linear mixedeffects model. treatment with sq-hdm of the hdm slit-tablet resulted in a statistically significant reduction in the average tcrs of . ( %, p=. ) compared to placebo in the last weeks of treatment. statistically significant differences were seen for both components of the tcrs, the rhinitis medication score (difference= . , p=. ) and rhinitis symptom score (difference= . , p=. ). furthermore, treatment with sq-hdm resulted in a statistically significant reduction of the conjunctivitis symptom score compared to placebo (differ-ence= . , p=. ). treatment was well tolerated. the most frequent adverse events were mild-to-moderate local allergic reactions. the pooled subgroup analysis showed that the hdm slit-tablet ( sq-hdm) was effective in treating hdm allergic rhinitis in adolescents ( - years old). the reduction in the primary endpoint tcrs was statistically significant and comparable to what has been observed in adults. results: at the time of the data-cut for this analysis, a total of european patients were screened ( % male). % of the subjects were aged - , % were aged - , and % were adults. the mean age of the sample was . [sd . ] years, with a minimum of and a maximum of years. in europe were children. many were allergic to foods other than peanut, and most had at least one other atopic condition. even if allergic to multiple foods, patients and their families were nonetheless keen to participate in the trial. the majority of the screened patients were highly sensitive to peanut, reacting to mg (cumulative) or less of peanut protein but a significant proportion of screening failures were due to lack of reactivity to this dose. | efficacy of ir -grass pollen sublingual tablet: improvement in subjects with grass pollen-induced allergic rhinoconjunctivitis based on well days and severe days evaluation objectives: four phase ii/iii dbpc studies, in adults and one in children/adolescents, were conducted worldwide. participants were abstracts | randomised to receive the ir tablet or placebo starting months ( m) prior to the pollen season and continuing for its duration. data from the first season of the trials in adults were pooled. the well days were defined as those with not more than one moderate symptom or mild symptoms of the evaluated symptoms (sneezing, rhinorrhoea, nasal pruritus, nasal congestion, ocular pruritus, watery eyes) and no use of rescue medication. the severe days were defined as either at least one moderate symptom in subjects using rescue medication, or at least moderate symptoms or one severe symptom whether rescue medication was taken or not. for each subject, the proportions of well days and those of severe days were evaluated during the pollen period while on treatment. treatment groups were compared using a wilcoxon -sample test. introduction: the safety of subcutaneous immunotherapy (scit) has been proven in several studies, but the occurrence of side effects (se) remains a concern in daily clinical practice and understanding of their risk factors and avoidance strategies remains limited. objectives: the aim of presented study was to assess the incidence and risk factors of early and late side effects in patients undergoing scit. we conducted a year-long observation of over patients undergoing scit in our outpatient clinic. we recorded detailed information for each administration and screened subjects for both immediate and late reactions. we compiled the records with medical histories to build a database, which was analyzed using multiple logistic regression. casein is a major cow s milk allergen and very resistant to high temperatures. higher levels of ige towards caseins have been reported to associate with persistent cow s milk allergy and higher risk of adverse reactions before and during the milk oit. a follow-up study on oit to milk started in with a six-month built-up phase. seventy-six children (mean age . years) with challenge-verified cma participated the milk oit and their immunological changes were analyzed employing crd. during the year , long-term follow-up report was collected by questionnaires ( %, n= ) and blood samples ( %, n= ). specific antibody responses were characterized before oit and on long term follow up and compared to long-term questionnaire results: milk consumption (yes/no) and side-effects from milk from past months (yes/no). objectives: to define the utility of crd in long-term follow-up after milk oit. results: mean follow-up time was ( - ) years. ten patients ( %) avoided milk completely and patients ( %) reported routine consumption of dairy products. side effects after milk consumption from last months were reported by % of the patients. increased specific ige levels towards caseins were seen among patients who did not consume milk at the long-term (p=. *). there was no significant association between the long-term milk consumption and ige levels to whole milk (p=. ), caseins (p=. ), alpha-lactalbumin (p=. ) and beta-lactoglobulin (p=. ) measured before the oit in this small sample. patients who consumed milk at the longterm follow-up and reported side effects had higher specific ige levels towards caseins before oit (p=. *). conclusions: there was a high incidence of side effects even after eight years of milk consumption, which may indicate desensitization instead of true tolerance. component-resolved diagnostics may corroborate in predicting prognosis, as suggested by higher incidence of side effects among patients with high levels of ige towards caseins also in the long-term follow-up. objectives: retrospective study of patients who underwent subcutaneous ait for allergic rhinitis ( % had concomitant asthma). patients with less than months of treatment were excluded. large local reactions (wheal≥ mm) and systemic reactions were defined according to who grading system. patient's satisfaction was defined by vas score. results: the mean age of patients ( % males) was ae (range - ) years ( %< years).the most prevalent immunizing allergens were house dust mite ( %), olive ( %) mix of grasses ( %) and pets ( %). % of patients were immunized against a single allergen whereas % were immunized with≥ allergens. patients were followed for ae months. following ait the vas score decreased from . ae . to . ae . (p<. ). % of the patients declared that they will recommend immunotherapy to their relatives. systemic adverse reactions ( % class i, % class ii) were observed in introduction: metabolomics, one of the core disciplines of system biology, is a high-dimensional biology method that may allow hypothesis-free profiling of biomarkers, rather than a traditional hypothesis-driven approach. objectives: this study aimed to apply the metabolomic approach to serum to longitudinal alterations during allergy immunotherapy (ait) in dermatophagoides pteronyssinus (der p) sensitized asthmatic children. results: a robust hydroxyeicosatetraenoic acids (hetes) of inflammatory responses was found for discriminating during ait, including -hete, -hete and -hete. -hete and -hete were significantly decreased continuously from through months of ait. moreover, compared with baseline of ait -hete was detected in very low level during and months. the metabolomic profiling could clearly longitudinal alterations biochemical-metabolic profiles in der p-sensitized children during ait. these markers might be involved in asthma pathophysiology but also represent the therapeutic target for ait. background: metabolomics, one of the core disciplines of system biology, is a high-dimensional biology method that may allow hypothesis-free profiling of biomarkers, rather than a traditional hypothesis-driven approach. this study aimed to apply the metabolomic approach to serum to longitudinal alterations during allergy immunotherapy (ait) in dermatophagoides pteronyssinus (der p) sensitized asthmatic children. methods: in this longitudinal study, we recruited der p-sensitized asthmatic children with ait for months. serum samples were analyzed using a metabolomic approach based on mass spectrometry. results: a robust hydroxyeicosatetraenoic acids (hetes) of inflammatory responses was found for discriminating during ait, including -hete, -hete and -hete. -hete and -hete were significantly decreased continuously from through months of ait. moreover, compared with baseline of ait -hete was detected in very low level during and months. the metabolomic profiling could clearly longitudinal alterations biochemical-metabolic profiles in der p-sensitized children during ait. these markers might be involved in asthma pathophysiology but also represent the therapeutic target for ait. we performed desensitization with asa according to the wong protocol (doses of . , . , , , , , , , , mg of asa at intervals of - min). we pre-medicate with cetirizine mg. our patient successfully reached the necessary dose: mg of asa ( . , . , , , , , , and mg) conclusions: approximately % of patients with asthma undergo respiratory symptoms due to exposure to aspirin, meanwhile . % and . % of the population shall undergo hives when exposed to it. desensitization with aspirin is an efficient and safe treatment in patients with hypersensitivity type i, iii and iv. due to the benefits and low toxicity of the wong protocol, we recommend this protocol in order to desensitize patients with allergy to aspirin who undergo rheumatologic or cardiovascular disorders and need antiplatelet treatment. we finally recommend our patients to take mg of asa premedicated with mg of cetirizine every day. we warn that if you interrupt the administration of asa for more than hours, it shall have to be administered again under medical supervision. semedo fm ; cruz c ; reis r ; tomaz e ; in acio f horiuchi t ; takazawa t ; saito s department of anesthesiology, gunma university hospital, maebashi, japan; intensive care unit, gunma university hospital, maebashi, japan introduction: sugammadex is a synthetic c-dextrin derivative that is designed to selectively bind to steroidal neuromuscular blocking agent molecules. although sugammadex has been used in many cases of general anesthesia, there are several reports of anaphylaxis following its use. skin testing is the gold standard for detecting the causative agent of anaphylaxis. however, the test itself sometimes precipitates serious complications, including recurrence of anaphylaxis. hence, development of a novel test that can be performed in vitro without causing such complications is desired. recently, the basophil activation test (bat) has been established as a tool to detect the causative agent of anaphylaxis with high sensitivity and specificity. yet, there are few studies examining the utility of the bat in diagnosing sugammadex-induced anaphylaxis, besides our previous report. although both cd and cd c are currently used as the major markers for activated basophils, which one of them is more suitable for the bat depends on the targeted drugs. objectives: the aim of this study was to investigate whether bat could be utilized to diagnose sugammadex-induced anaphylaxis. in addition, we compared the capability of cd c and cd as markers for activated basophils. seven patients with perioperative anaphylaxis demonstrating a positive skin test for sugammadex were included. furthermore, individuals who tolerated sugammadex and had a negative skin test for allergy to this drug were enrolled as controls. results: the ratios of activated basophils in the patients were much higher than those in controls (mann-whitney u test, p<. ). cd c up-regulation. this was also true for cd . in the case of cd c, the sensitivity of bat for sugammadex was % and specificity was %, while sensitivity and specificity for cd were % and %, respectively. there were no significant differences between cd c and cd in the areas under the roc curve. conclusions: this study showed that bat is a reliable instrument to diagnose sugammadex-induced anaphylaxis. we did not find any difference between cd c and cd as markers for activated basophils in the bat for sugammadex. objectives: we report a retrospective study of patients who were referred to our allergology departments between and with a suggestive history of immediate hypersensitivity to ppis. our purpose was the analysis of the clinical presentations and the allergological investigation performed in order to confirm the diagnosis of drug hypersensitivity to ppis and to study the cross-reactivity among ppis. results: the culprit drugs were pantoprazole (n= ), omeprazole (n= ) and lansoprazole (n= ). the allergological investigation confirmed the diagnosis of hypersensitivity to ppis in patients ( by skin tests and oral challenge). we observed cross-reactions between omeprazole, pantoprazole and esomeprazole (n= ), omeprazole and pantoprazole (n= ), respectively omeprazole and esomeprazole (n= ). in patients the severity and the recurrence of the reaction did not allowed the provocation test with the culprit drug. two oral challenges allowed the use of an alternative ppi (based on the pattern of less cross-reactivity depending on the chemical structure: pantoprazole for a patient who had a grade iii anaphylaxis to lansoprazole and lansoprazole for a patient who had a grade ii anaphylaxis to pantoprazole). conclusions: a complete allergological investigation (skin tests and cautiously, oral challenge) is needed in order to confirm the diagnosis of drug hypersensitivity to ppis and to take a therapeutic decision. the diagnostic approach is limited by the low sensitivity of skin tests and the patient's background (comorbidities and severity of the reaction) which do not always allow the oral provocation test. an ige dependent mechanism may be involved in hypersensitivity reactions to ppis or their metabolites. herrero-lifona l ; muñoz-rom an c hospital quironsalud campo de gibraltar, los barrios, spain; hospital regional universitario de m alaga, m alaga, spain introduction: hypersensitivity reactions to beta-lactams are an important problem to study, especially in children, given that these antibiotics are the gold standard for the treatment of many infectious diseases in the infancy. most hypersensitivity reactions to betalactams in children are due to non-immediate response and to diagnose them is essential to perform a drug challenge test. although hypersensitivity is usually ruled out in children by drug challenge test, it is positive test up to %- %. objectives: a year-old boy is suspected to have experienced two drug reactions after the intake of amoxicillin with and without clavulanic acid for pharyngitis treatment. in the first one, he presented a maculopapular eruption in the back after one day treatment with amoxicillin-clavulanic acid. in the second reaction, two hours after the intake of amoxicillin, it appeared an itching maculopapular eruption in the back that was resolved with symptomatic treatment. in both cases, the patient tolerated treatment with cefuroxime afterwards. results: intradermal test with amoxicillin was negative in immediate and delayed reading. oral drug challenge test with amoxicillin ( mg/kg/day, total cumu- oral drug challenge test with penicillin v (total cumulative dose mg): it was well tolerated and the patient continued taking it for epicutaneous patch testing with amoxicillin in the lesion area and in an unaffected area: in the lesion area, it appeared mild erythema, but it was considered a negative result in both areas. conclusions: we report a case of an amoxicillin-induced multiple fixed exanthema: an unusual non-immediate reaction in childhood. most cases of non-immediate hypersensibility need to be confirmed by drug challenge test, given that skin testing lacks sensitivity both intradermal and patch tests. the patient presents a selective hypersensitivity to amoxicillin, being tolerant to penicillin and cephalosporins. jimenez-rodriguez t ; soriano-gomis v ; gonzalez-delgado p ; cueva-oliver b ; venegas-diaz ij ; fernandez j results: data from patients were analyzed, of which . % ( ) were women. the overall mean age was . ae . years, with no statistical difference between sexes. the . % ( ) of the patients presented symptoms with a single group of nsaids, and . % ( ) with or more different groups. the % ( ) of patients presented a history of atopy. in patients with rhinitis % had symptoms with only one nsaid and % with two or more groups of nsaid, while patients with asthma, % reacted to one nsaid and % to two or more groups. the most frequent clinical manifestations were: urticaria/angioedema in % ( ), pruritus in . % ( ), bronchospasm in . % ( ), other respiratory symptoms in % ( ) and anaphylaxis in % ( ) patients. the most frequently involved nsaids were: metamizole ( . %) and ibuprofen ( . %). skin tests were performed in only patients, of whom ( %) were positive to metamizol. dpt was performed in . % ( ) objectives: fifty patients diagnosed with "dress" ( - ), in a tertiary center were retrospectively analyzed, with cases meeting the regiscar criteria. we collected demographic, clinical, laboratory and therapeutic data from the electronic medical records. results: all cases occurred during hospitalization and in several hospital areas. the mean age was . years ( - ) with . % women and % of caucasian origin. reported clinical manifestations were skin rash ( %), fever ( . %), digestive symptoms ( . %), respiratory ( . %), neurological ( . %), head and neck ( . %), urological ( . %), ophthalmologic ( . %) and musculoskeletal ( . %). the most relevant laboratory findings were eosinophilia ( %), elevated transaminase levels ( %), lymphocytosis ( %), altered coagulation ( %) and altered renal function ( %). virus serology was positive in cases ( . %) involving hhv- , ebv, cmv and hiv. antinuclear antibodies were positive in / cases ( . %). skin biopsy, performed in cases ( . %) revealed findings suggestive of drug induced skin reaction. suspected culprit drugs were antibiotics ( %), nsaids ( %), antiepileptic drugs ( %), and antiparasitic agents ( %). one case was related to the administration of heparins and other to a monoclonal antibody. in % of cases, the episode was not related to a particular drug. treatment was accomplished by the administration of corticosteroids ( %), antihistamines ( %), and immunosuppressant drugs in cases. fluids and other medications were administered attending to symptoms. death occurred in patients, although only in case it was related to dress syndrome. the average time from reaction to death was . months. allergy evaluation, performed in cases addressed the potential role of drugs. skin tests were positive in / patients ( . %) and basophil activation test was negative ( / cases). results: from patients admitted with possible diagnosis of scar, only met the inclusion criteria ( f/ m, age - , average . years-old). they were all admitted to a medicine ward. five patients had diagnosis criteria of dress, of sjs and of ten. as for the drugs related with the reaction, antiepileptic drugs were the most frequent ( patients); allopurinol ( ), betahistine ( ), ciprofloxacin+nimesulide ( ) were the causative drugs in the remaining patients. average time to the beginning of symptoms was . days ( patients unknown). in patient the cause was unknown (he had criteria of ten and also diagnosis of malaria and was transferred to another hospital). there were no deaths. objectives: the objectives of the present study were to determine the efficacy of nfeno to: . establish the diagnosis of rhinitis; and . discriminate allergic rhinitis (ar) from non-allergic rhinitis (nar). material and methods: prospective and controlled study with healthy subjects, which included patients with rhinitis. ar and nar were phenotypically defined according to positive or negative prick test results, respectively; the control group was collected from people without upper or lower respiratory tract disease and the prick test was negative. in all sample included the following measurements were performed: feno and nfeno (novario analyzer) were performed; spirometry; eosinophil counts in blood and nose (by nasal brushing); bilateral nasal endoscopy; and acoustic rhinometry. results: we included cases (ar= , nar= and controls= ), with a mean age of (sd . ) years, % men. the table below shows the results of the variables analyzed by group. patients with rhinitis compared to controls had significantly greater feno production, as well as a higher proportion of eosinophils in blood and nose, but not in nfeno production. however, when the two subgroups of rhinitis were compared, ar patients had significantly higher feno and nfeno than nar, in addition to blood and nose eosinophils. there were no differences in acoustic rhinometry values between groups. conclusions: although nfeno does not appear to identify patients with rhinitis, it may be useful in discriminating ar from nar. in routine clinical practice, it could help guide to identify an ar in cases with inconclusive results of the complementary tests commonly used in its diagnosis. introduction: fractionated exhaled nitric oxide (feno) is used as a marker of eosinophilic airway inflammation in asthma, whereas clinical presentation of nasal no (nno) is unknown. objectives: the objective of this study was to evaluate the factors influencing nno levels. in patients with chronic nasal symptoms, total-nasal-symptom-scores (tnss) were calculated; skin-prick-test conclusions: in conclusion nasal no is useful in allergic inflammation in the absence of sinus obstruction in nasal cavity. however, its value is limited with paranasal sinus ostium occlusion. were recruited across australia and the uk via a patient panel. the aim was to assess which ar treatment attribute(s) drove patient preference. results: table shows the willingness to pay (wtp) for each attribute. all attributes were significant predictors of treatment choice, except administration method. however, patients in both countries showed a considerable preference for treatments that were more efficacious, fast acting and affordable. conclusions: although treatment relief remains of primary concern, time to treatment benefit and cost could dictate treatment preference. these data may be of value in optimizing the acceptability of future ar treatments and informing trial endpoint selection. australia ( izquierdo l; chiriac am; molinari n; demoly p introduction: allergic rhinitis is a frequent disease with an important impact on quality of life. self-administrated control assessment tests can help achieve a better management of this disease. however, none of these tools has been validated in teenagers. test in its original version, following the same protocol as the original study in adults. we designed a multicentre, observational, cross- conclusions: while the number of included patients is low, the first results are promising. indeed, a significant improvement of the rhinitis control score was found between d and d . this led us to the hypothesis that this questionnaire could be used as is to estimate the control of the allergic rhinitis in teenagers. analyses concerning the validation of the questionnaire itself do not reach at the moment the threshold of significance, the recruitment is on-going, to increase its power. objectives: the objective of this study was to evaluate the role of serum vitamin d in patients with symptomatic allergic rhinitis and active asthma during the allergy season and observe the effect of montelukast mg daily as treatment. results: this study included asthmatic and seasonal allergic rhinitis patients following a single-blind, placebo run-in period of - days, patients were randomized to oral montelukast mg (n= ) or placebo (n= ) daily during the -week, double-blind, active-treatment period. the serum vitamin d was also evaluated in both the groups. the serum vitamin d levels were found to be higher in patients taking montelukast compared to placebo after weeks (p<. ). montelukast reduced the daily rhinitis symptoms score: difference between montelukast and placebo (p<. ). similar improvements were seen in daytime nasal symptoms (p<. ) and nighttime symptoms (p<. ). conclusions: montelukast provides significant relief from symptoms of seasonal allergic rhinitis, while also conferring a benefit for asthma, in patients with both allergic rhinitis and asthma. further, it has a beneficial role in improving vitamin d levels. venegas-diaz ij ; jimenez-rodriguez t ; canto-reig vj ; lindo-gutarra m ; soriano-gomis v ; gonzalez-delgado p ; cueva-oliver b ; fernández j allergy section. general hospital alicante. isabial, alicante, spain; allergy section. general hospital alicante. isabial-umh, alicante, spain introduction: local allergic rhinitis is an accepted entity, which only can be recognized by nasal provocation test (npt) in patients with clinical rhinitis with negative skin tests or specific ige (sige). our aim was study this entity in our patients in alicante, spain. objectives: patients with symptoms of rhinitis with skin tests, and sige negative for common aeroallergens were selected, since . half of them ( ) most were young adults, % belonging to the range of age between - years; more than % had family history of atopy; the mean age of onset of symptoms was years and up to . % had had symptoms before the age of years; . % were nonsmokers. regarding comorbidity, . % of the patients presented with concomitant symptoms of conjunctivitis and . % of asthma. symptoms in . % of the patients were persistent and most of moderate ( %) to severe ( . %) intensity. the majority of patients ( . %) presented perennial symptoms and a tpn positive to mites in . %, to salsola pollen in % and to cypress pollen in . %. but patients ( . %) were simultaneously positive to allergens. conclusions: local allergic rhinitis represents an important proportion of patients with clinical rhinitis with negative skin tests and sige. we have to pay attention to identify clinical and demographic factors of ral and to use npt to demonstrate it. objectives: we report the extent of sinus involvement at baseline (bl) in pts with bilateral np refractory to intranasal corticosteroids from a dupilumab phase a study (nct ). ct scans from enrolled pts, adults < years with nasal polyp score of ≥ / , were pooled and analyzed at bl. for opacification, standard lund-mackay (lmk) scoring ( =normal, =partial opacification, =total opacification) in maxillary, anterior/posterior ethmoid, sphenoid, frontal sinuses was used. ten sinus scores plus bilateral ostiomeatal complex (omc) score ( =not occluded, =occluded) were summed to a bilateral total lmk ( - ). zinreich modified lmk score (zlmk), providing more granularity on opacification degree, was evaluated post-hoc; each sinus was given a - score based on opacification % from mucosal thickening ( = %, = %- %, = %- %, = %- %, = %- %, = %); omc results: the prevalence of asthma at the age of years was . %. % of them had an act tm value below , ie uncontrolled asthma, median . (range - ). independent risk factors for uncontrolled asthma at the age of were current doctor diagnosed rhinitis (adjusted or, aor . ; % ci . - . ), wheeze triggered by exercise (aor . ; . - . ) and cat at home (aor . ; . - . ). if at least one of the parents had higher education the risk of uncontrolled asthma was decreased (aor . ; % ci . - . ). six children reported hospitalisation due to asthma during the last months (ie . %) at years of age. hospitalisation was more common in individuals with uncontrolled asthma (or . ; . - . ) or when mites (or . ; . - . ) or pollen (or . ; . - . ) was reported as trigger factors. also, oral corticosteroids (betamethasone), in the last months increased the risk for hospitalisation (or . ; . - . ). to have a parent with asthma ( % compared to %, or . ; . - . ) or higher education ( % compared to %, or . ; . - . ) was numerically less common for children who were hospitalised for asthma but did not reach statistical significance. conclusions: uncontrolled asthma was associated with current allergic rhinitis, having a cat and exercise as trigger factor. at least one parent with higher education reduced the risk. hospitalisation due to asthma was more common in individuals with uncontrolled asthma. abstracts | adolescent asthma in relation to severity and gender-data from a prospective population based cohort study introduction: asthma often debuts early in life, but recent studies show that the development of asthma is a dynamic process with disease turnover throughout child-and young adulthood. objectives: to describe adolescents' asthma with focus on severity and gender. the study population consisted of adolescents participating in the cohort, followed since birth up to years of age with questionnaires and clinical investigations. blood samples from adolescents ( . %), sera analyzed for specific ige against common inhalant allergens. asthma at years was defined as fulfilling at least of the following criteria: symptoms of wheeze and/or breathing difficulties in the last months, ever doctor's diagnosis of asthma and/or asthma medicine occasionally or regularly last months. uncontrolled asthma was based on parental information on symptoms of asthma in the last months prior the -year follow-up, including or features: nocturnal asthma, activity limitation, wheeze times and hospitalization due to acute asthma. we looked into phenotypes; late-onset, defined as asthma at , or , but not at , and years of age and persistent, defined as asthma at , or and , or years of age. severe asthma, defined as asthma as above combined with prescribed and dispensed corticosteroids used within the last months plus uncontrolled asthma and/or lung function (fev < % of predicted). results: at years of age, . % (n= ) fulfilled the study definition of asthma, . % late onset and . % persistent asthma. persistent asthma was more frequent among boys than girls . % vs . % (p=. ). overall ige sensitization was common among adolescents with asthma, . % were sensitised to common inhalant allergens, and equally common in late-onset and persistent asthma ( . % vs . %, p=. ). however, more boys than girls were sensitised ( . % vs . %, p<. ). in total . % (n= ) adolescents had severe asthma, . % (n= ) boys and . % (n= ) girls (p=. ). the overall prevalence of severe asthma in the cohort was estimated to . %. severe asthma did not significantly differ among adolescents with late-onset compared to persistent asthma ( / , / , p=. ). conclusions: among adolescents with asthma, late-onset (age ≥ years) and persistent asthma were equally common. persistent asthma were more common among boys. there were no difference in asthma severity, or proportion of ige sensitization among adolescents with late-onset or persistent asthma. however, data investigating associations with wheeze and asthma in later childhood are scarce. objectives: our aim was to explore the association of maternal milk fatty acid composition with childhood wheezing phenotypes and asthma up to age years. breast milk was collected weeks and months post-delivery in the ulm birth cohort study (n= and n= , respectively). concentrations of - carbon atom chain length fatty acids were measured by high-resolution capillary gas-liquid chromatography. to control for constant sum constraint, concentration data were transformed using the centered log ratio method. compositional biplots and correlation matrices were used to group fatty acids based on within sample correlation. adjusted risk ratios with parent-reported wheezing phenotypes and doctor-diagnosed asthma were computed using a modified poisson regression. results: we observed no straightforward evidence of associations between overall breast milk fatty acid composition and specific wheeze phenotypes or doctor-diagnosed asthma. conclusions: despite our use of sophisticated statistical methodology, our results may have been biased toward the null by several cohort-specific factors associated with breast milk collection and fatty acid composition. to overcome potential selection bias by maternal lifestyle, further research should investigate fatty acid intake during the first year of life including sources other than breast milk among children who were never or not exclusively breastfed. introduction: fall is the most common season for asthma exacerbation. previous studies found that exposure and sensitization to house dust mites (hdms) can exacerbate asthma. the seasonal variation in indoor hdm concentration is highest in the fall, correlating with the incidence of asthma exacerbation. most of the studies conducted to date have focused on the effect of hdm exposure on the incidence of acute asthma exacerbation, but reports about the effect of hdm sensitization are few. thus, we aimed to determine whether sensitization to hdms acts as a risk factor of asthma exacerbation in the fall. in addition, we investigated whether asthma exacerbation in the fall had any distinctive features by comparing levels of various cytokines and chemokines with those in other seasons. objectives: we enrolled children aged - who visited the emergency department because of acute asthma exacerbation from january to december ( . %, males; mean age, . ae . years). they were treated in accordance with the standardized treatment protocol. blood samples were collected from the children during the course of treatment. by using residual sera from the blood samples, we measured the levels of total immunoglobulin e (ige), hdm-specific ige (sige), eosinophil cationic protein (ecp), and various cytokines and chemokines, and classified them according to season. we compared the date divided into fall group (from september to november, n= ) and other season group (from december to august, n= ). ci, confidence interval; or, odds ratio; der f-sige, dermatophagoides farinae -specific immunoglobulin e; der p-sige, dermatophagoides pteronyssinus-specific immunoglobulin e; ecp, eosinophil cationic protein; ige, immunoglobulin e. data are presented as n (%) or as meansaesems and median (range). p value refers to the difference between the fall and "other season" groups and was calculate by the chi-square statistics, fisher's exact test, student's t-test, or wilcoxon rank-sum test. a adjusted for total ige. results: this retrospective study obtained archived nasopharyngeal aspirate (npa) samples from patients aged below years who were hospitalized for acute respiratory illnesses in a university-affiliated hospital during the periods september-november and january-april . their clinical information was retrieved from computerised record. hrv was detected by rt-pcr, and isolates were sequenced to determine the genogroups and serotypes. ninety patients whose npa was positive for hrv and patients being negative for an extended panel of respiratory viruses by multiplex pcr method were identified. mean age of these groups was . years and . years respectively. hrv infection was significantly associated with asthma exacerbation (or . , results: a total of children were included: . % were boys; . % aged months to years, . % aged - years, . % aged - years and . % aged - years; . % were hospitalized, results: the long-term remission (≥ years without treatment) rate years after initiating early anti-inflammatory therapy was . % (intermittent asthma, %; mild persistent asthma, . %; moderate persistent asthma, . %; severe persistent asthma, . %). longterm remission rates improved compared with past asthmatic conva- objectives: the aim of this study is to explore the potential value of feno level for diagnosing chronic cough in children. objectives: in this study, we aimed to compare the efficacy of classical spirometry and impulse oscillometry (ios) in evaluation of late reversibility in children who received treatment with the diagnosis of atopic asthma. we enrolled patients aged - years who were diagnosed with atopic asthma. exclusion criteria were having received asthma treatment during the previous two months, having acute asthma exacerbation findings, having any other respiratory disease or cardiac disease that may affects the lung function test results. allergic sensitization was determined by skin prick test performed according to eeaci guidelines. lung function test measurements were performed at enrollment and after two months of inhaled steroid treatment. conclusions: classical spirometry is more valuable compared to ios in evaluation of late airway hyperreactivity in children with atopic asthma in children older than seven years age. | computer bronchophonographyfrequency analysis of the respiratory cycle. objectives: we performed mct in children with symptoms suggestive of asthma and without respiratory symptoms. after each inhalation step oscillometry and spirometry was performed. parameters analysed for ios were z , r , r , x , x and ax (the integrated impedance reactance at r and above) and fev for spirometry. a fall of % in fev from baseline after mtc was considered as a positive challenge. pc -fev and pc r , x and ax were calculated. results: a total of patients, female, with a mean age of . (ae . ) years were enrolled. had a ≥ % fall in fev after mtc. the mean variation in fev was % (- . %/ + . %), the mean variation in z , r , r , x , x , ax and fres were . % objectives: the objective of our study was to synthesize cationic peptides and study their antiviral activity (aa) in vitro. results: peptides were synthesized by solid phase method with different structures (linear, helical and dendrimeric). cytotoxicity of the peptides was studied by mtt assay using hela cells. objectives: the aim of the study is to evaluate the changes of il- results: subjects aged - years were enrolled in this study, which were divided into groups: patients with diagnosed moderate to severe ba ( st group), ba patients with rvi ( nd group), subjects with rvi only ( rd group) and healthy volunteers ( th group). all patients with ba from group and received inhaled corticosteroids. clinical blood test revealed increase of eosinophils in patients with ba and ba accompanied with rvi up to % and %, respectively. fev was decreased in st and nd groups to % and % compared % and % for rd and th groups, respectively. conclusions: this study is alarming for asthmatic nosocomial hazards in this govt. hospital. identification of ige specific reactive components of predominant fungal allergens and cross-reactivity among each other, delined in this study could minimize the hazard of therapeutic and diagnostic use of these cross-reactive components, in fungal allergen-specific immunotherapy. objectives: we conducted a longitudinal prospective study to examine the development, composition and diversity of the gut microbiota in healthy and allergic children. we followed children from months to years of age with clinical evaluation; specific ige levels and skin prick testing. fecal samples were collected at , , months and years. s rrna sequencing was used to profile the gut microbiome using illumina miseq. the composition and diversity of the gut microbiome were assessed using quantitative insights into microbial ecology (qiime). comparisons between groups were made using the lefse pipeline; non-parametric factorial kruskal-wallis test, unpaired wilcoxon rank test and linear discriminant analyses (lda) with score > . . to assess the interaction effect, the likelihood ratio test (lrt) was applied using r statistical program. p<. was considered significant after correction for multiple testing. results: to achieve our aim we divided balb/c mice into groups: mice with viba ( st group), mice with viba treated with nonspecific sirna against gfp (sigfp) ( nd group) and against il- (siil- ) ( d group). th group was intact mice. groups - were i.p. sensitized on days , , with ovalbumin (ova) mixed with aluminum hydroxide and i.n. challenged with ova on days - . the same mice were i.n. infected with tcid /mouse rsv strain a on day . mice from group and were i.n. treated by sirnas on days - in dose lg/mouse. on day hyperresponsiveness (ahr) to methacholine was measured. on day and lungs were removed for histological analysis. viral rna (vrna) load and il- gene expression were evaluated by qpcr in lungs. bronchoalveolar lavage (bal) was collected for differential cell count by light microscopy. so i.n. administration of siil- suppressed il- gene expression in lungs by % compared to sigfp treated mice. there were no significant changes in body weight and lung vrna amounts between mice received sigfp and siil- . mice treated with siil- demonstrated the tendency to improve lung function compared to mice of group - , that expressed in % reduction of specific resistance of airways and % increase of peak expiratory flow. bal cell count revealed decrease of total cell number, eosinophils and lymphocytes in mice received siil- by %, % and % compared to sigfp treated mice, that indicate reduction of inflammation, that was confirmed by histopathological studies showed % leukocyte reduction. downregulation of il- resulted in -and . -fold decrease of bronchial epithelium metaplasia and hyperplasia. and femur length measurements were collected from routine antenatal screenings. these and derived head to abdominal circumference ratio and estimated fetal weight were converted into z-scores adjusted for gestational age and gender and categorized as "low" (≤ sd below mean), "normal," or "high" (≥ sd above mean). ad cases were children with parent-or pediatrician-report of physician ad diagnosis assessed yearly up to age years and supplemented by clinical diagnoses during dermatological exams at . , , and years. modified poisson regression models were used to compute risk ratios (rr) adjusted for potential confounders. conclusions: these results provide further evidence for a role of fetal growth as an influence on atopic disease outcomes. unlike previous studies, our data suggests several patterns of fetal growth beginning as early as the st trimester may influence ad outcomes. objectives: we aimed to examine the role of eosinophil cationic protein (ecp), eosinophil derived neurotoxin (edn) and total immunoglobulin (ig) e as a bio-marker of disease severity. we examined the difference in level of total ige, ecp and edn between the two groups and whether any correlation existed between disease severity and ecp or edn. objectives: we aimed to identify the subgroup of ad patients with a good clinical response to probiotic treatment. we recruited children who suffered from moderate to severe ad with the scoring ad (scorad) index of or higher. after weeks of washout period, all patients were given lactobacillus plantarum cjlp at a dosage of colony-forming units once a day for weeks. we measured eosinophil counts in the peripheral blood, the proportion of cd + cd + foxp + regulatory t (treg) cells in cd + t cells, serum total ige levels, and specific ige to common allergens before the start of the treatment (t ) and at discontinuation (t ). logistic regression models were used for the statistical analysis. seventy-six patients ( boys and girls) with a mean age of . ae . years completed the study. there were responders and non-responders after probiotic treatment. the median scorad was reduced from . (range . - . ) at t to . (range . - . ) at t in the responder group (p<. ). in multivariable logistic regression analysis, a good clinical response was significantly associated with high total ige levels (aor . , % ci . - . ), increased expression of , and high proportion of cd + cd + foxp + cells in cd + t cells (aor . , % ci . - . ). in responder group, the proportion of cd + cd + foxp + cells of cd + t cells were significantly increased after weeks of treatment (p=. ), while the levels of tgf-b mrna expression were decreased (p=. ). there were no differences in total ige levels between t and t (p=. ) conclusions: the therapeutic effect of l. plantarum cjlp on ad is more pronounced in children with high total ige levels, objectives: the objective of the study was to examine the effect of a specific synbiotic mixture of short-chain galacto-, long-chain fructo-oligosaccharides (scgos/lcfos, ratio : ) and bifidobacterium breve m- v on the severity of ad and correlation to serum chemokines in infants with moderate to severe ad and elevated ige. in an exploratory randomized, double-blind, placebo-controlled trial the effect of extensively-hydrolyzed whey-based formula without intervention. serum obtained prior to start and at the end of intervention were analysed using luminex. six chemokines and nine ratio's thereof were correlated to ad severity (sample size= ). introduction: dyshidrotic eczema is one of the most common skin conditions. contact allergy is often associated with dyshidrotic eczema although the exact impact and the influence of contact allergens in different forms of dyshidrotic eczema remain unknown. hypersensitization to nickel is one of the most common contact allergies associated with pompholyx. the standard of care protocol is to use a medical treatment with topical corticosteroids and calcineurin inhibitors to treat the symptoms, together with occlusive barrier creams to avoid skin exposure to the allergens. after the symptoms have been cleared with the topical treatment, the recommendation is to use occlusive barrier creams to prevent recurrence of the symptoms. objectives: a new emollient with specific metal-scavenging agents and no occlusive ingredients has recently been developed and made commercially available. the aim of this study was to evaluate the effect of such cream to provide relief for patients with dyshidrotic eczema associated with nickel allergy. results: thirty-two subjects with dyshidrotic eczema and a positive patch test ppt (contact sensitized) reaction to nickel were selected. these were divided into two randomized groups, group-a was given nickel-scavenging cream (skintifique creamtm, paris) after medical treatment, (n= ) and group-b followed the standard protocol for pompholyx, (n= ). hand eczema was scored according to the dyshidrotic eczema area and severity index (dasi). dasi scores were evaluated at the beginning of the study (day- ), after the medical treatment (day- ) and two months after the end of medical treatment (day- ). results show a significant difference in the efficacy of treatment between the two groups at day- . a higher percentage of at least % reduction of initial dasi score ( . %) and a higher percentage of total clearance ( %) in patients using nickel-scavenging nonocclusive moisturizing cream was observed as compared to standard-of-care occlusive creams ( . % and %, respectively). objectives: the goal of this study was to investigate whether long-term emollient therapy is associated with alterations of skin barrier function and shifts of the skin microbiome in infants at high risk for developing ad. we prospectively enrolled newborns with a family history of ad to be randomized to either emollient treatment group or control group. at months of age, we tested the skin barrier (transepidermal water loss/tewl, water capacitance/cap, ph) and skin microbiome ( s rdna sequencing of skin swabs from cheek, dorsal and volar forearm). results: the emollient group (n= ) had significantly lower skin ph compared to controls (n= ) (p=. ), but without a statistically significant difference in tewl or cap. the emollient group had higher numbers of different bacterial taxa (chao richness) at cheeks (p=. ), dorsal forearms (p=. ), and volar forearms (p=. ) as compared to controls. both streptococcus pneumoniae and s. salivarius statistically significantly contributed to the observed skin microbiome differences between patient groups. s. salivarius was significantly more abundant in emollient subjects at all sampling sites (p=. ). we then analyzed our previous larger cohort of older children with ad and also observed higher s. salivarius proportions in ad patients with treated and less severe disease (p=. ). objectives: to evaluate the effect of overnight treatment with a temperature-controlled laminar airflow (tla) device in children/adolescents with severe eczema over a -month period. in an open-label study, subjects aged - years (median years) with longstanding severe eczema attended visits during the run-in period lasting - weeks (median . weeks) to optimize eczema management. the run-in was followed by a month treatment period using overnight tla device (airsonett ® , sweden), which included study visits. we used scorad-index results: the median duration of eczema was . months (interquartile range - . ). all subjects were sensitised to ≥ perennial allergen, and had multiple comorbidities ( / rhino-conjunctivitis, / food allergy, / asthma). there were no significant changes during the run-in period in any of the outcome measures. we observed a significant improvement in scorad after the -month tla-treatment period, from . [ . - . ] to . [ . - . ] , p=. . iga improved significantly from a median of [ - ] to [ ] [ ] [ ] , p=. . improvement in symptoms was paralleled by a significant reduction in medication usage. by months, there was a significant improvement in . ] to [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] , p=. ), and an improvement in cdqli (marginal, p=. ). however, we observed no changes in poem (p=. ) . post-hoc cluster analysis of the patterns of changes in scorad over the month treatment period identified two clusters, with participants classified as responders and as non-responders. introduction: intestinal degradation has been shown to determine allergenicity of food allergens. however, it is unclear how allergens are degraded inside pivotal immune cells such as dendritic cells (dc), and how this affects the subsequent immune response to these allergens. in our studies, we determined whether we are able to measure uptake and degradation of allergens inside dc and whether differences in above mentioned factors exist between allergens. objectives: using mouse bone marrow-derived dc and fluorescent-labeled proteins, we studied the cellular uptake of the peanut proteins ara h , , , and . results: first, we observed that dc uptake of ara h was much higher than ara h , and . using blocking reagents and receptor binding assays for various uptake routes in dc, we observed that one of the principal routes of uptake for ara h was the mannose receptor. other uptake routes, and the routes of uptake for ara h , and are currently under investigation. second, using proteins coupled to beads we observed that intracellular protein degradation was higher for ara h and ara h than for ara h and . finally, cd +t cells from ara h , , or sensitized mice were added to matching allergen-pulsed dc. we observed that while ara h , and to lesser extend ara h elicited strong th type responses, ara h did not elicit any t cell responses. conclusions: together, we show that allergenicity of (peanut) proteins may be, at least partly, determined at the level of allergen uptake and breakdown inside the antigen presenting cell. these findings may be relevant to risk evaluation of existing allergens but also of novel or modified proteins. this also illustrates the usefulness of in vitro, cell based assays to examine initial processes of allergenic sensitization to proteins. | sensitising capacity of unmodified and acid hydrolysed gluten through the skin-a comparative study in na€ ıve vs tolerant brown norway rats ballegaard ar; madsen cb; bøgh kl national food institute, technical university of denmark, søborg, denmark introduction: allergic sensitisation to foods may occur in infancy without prior oral exposure to the offending food. this has led to the assumption that food allergy sensitisation may occur through alternative routes, such as the skin, supported by the observed correlation between skin barrier disruption and food allergy. recently, concerns have been raised regarding the safety of use of cosmetic and personal care products containing hydrolysed wheat proteins, since these products have been shown to induce allergy towards acid hydrolysed wheat through the skin, and even to cause an abrogation of the already established oral tolerance against unmodified wheat. objectives: the aim of the study was to compare the sensitising capacity of an unmodified and an acid hydrolysed wheat product via slightly damaged skin, in order to evaluate differences in conditions necessary for skin sensitisation in na€ ıve vs tolerant individuals. brown norway rats were raised and bred on either ( ) a diet free from wheat, resembling individuals with a na€ ıve immune system, or ( ) a conventional wheat containing rat chow, resembling individuals tolerant to wheat. results: in the na€ ıve rats both products were able to induce a statistically significant specific antibody response after application of the products on the slightly damaged skin, whereas in the wheat tolerant rats, only the acid hydrolysed wheat product was able to induce a statistically significant antibody response. for both the na€ ıve and the wheat tolerant rats the response was dose-dependent. in the na€ ıve rats both products were able to sensitise through the skin, inducing a specific ige response, whereas in the tolerant rats only the acid hydrolysed product were able to induce a specific ige response, though this ige response was much lower than in the na€ ıve rats. results from competitive elisas demonstrated that new epitopes had developed as a result of acid hydrolysis, though original epitopes were maintained at the same time. this may explain why only the acid hydrolysed wheat could induce specific antibody responses in the tolerant animals. conclusions: this study showed that the sensitising capacity through the skin of two different wheat products is heavily influenced by the tolerance status of the immune system and the degree of modification of the wheat products. results: using a germ-free c h/hen mouse model of food allergy, we examined the presence of a major peanut allergen, ara h , in the blood after intraperitoneal injection in previously sensitized and control (non-sensitized) mice using an untargeted, quantitative proteomic approach. previously sensitized mice underwent physiological (core temperature decrease, clinical symptoms) and biochemical (mast cell protease increase, ara h specific ige positivity) changes associated with severe allergic reactions. we were able to confidently detect multiple peptides derived from the ara h protein after intraperitoneal injection in both control and ara h sensitized mice. however, the ara h protein was present at - fold higher levels if mice were previously sensitized, suggesting increased transit across the peritoneal mesothelium with sensitization. an untargeted proteomic approach also allowed changes in the blood proteome of mice undergoing a severe allergic response to be examined. we identified proteins with significantly altered quantity in serum between control and sensitized mice and were therefore apparently associated with the allergic response. we demonstrate the applicability of untargeted proteomics to the study of the allergen transport and proteomic changes which co-occur with a resultant allergic reaction. the transit of allergens into the bloodstream is heavily dependent upon previous sensitization. we are continuing this work to examine the specificity of observed increases in trans-mesothelial transport and to address transport of allergens after intragastric challenge. | iga to cow's milk differs between breast milk and serum for its epitope specificity objectives: we sought to assess whether the profile of epitopespecific iga differs between mother's serum and bm. we also examined how infants' food epitope-specific iga develops in early infancy and the relationship of iga epitope recognition with development of cow's milk allergy (cma). results: . we measured iga specific to an array of overlapping peptides in major cow's milk allergens (alpha s -, alpha s -, betaand kappa-caseins and beta-lactoglobulin). diversity of peptide-specific iga (ie epitope diversity) was determined in paired maternal and infant sera as well as breast milk samples in mother-infant dyads within the first postpartum months utilizing peptide microarray. microarray data was converted to z-scores and filtered for noise. peptide epitopes were determined based on jaccard distance between neighboring peptides, and intra individual correlation between sample types was estimated using phi coefficient. comparisons between groups and individuals was done using non-parametric tests. we noted marked discordance in epitope recognition in paired breast milk and maternal serum samples. at least one shared epitope was recognized by both milk and serum samples ranging from % of mothers for alpha-s casein to % for kappa-casein. epitopespecific iga was detectable in infants' sera starting at less than months of age. sera of mothers with a cma infant had increased binding of epitope-specific iga to cow's milk proteins compared to those with a non-cma infant (p<. for all five proteins). conclusions: these findings support the concept that mothers' milk represents a product of the mucosal immune system that has an antibody repertoire distinct from that of peripheral blood. results: multiple ige-binding proteins were detected in the different wn preparations and many of which were dissemblance in dblotting. profiles of detectable proteins (peptides) of raw, roasted and boiled wn extracts were profoundly different in emi analysis. introduction: consumption of tree nuts is on the rise due to their beneficial health effects. however, tree nuts can led to severe allergic reactions in sensitized patients. thermal processing can modify the structure and function of food proteins and may alter (increase or decrease) their allergenic properties. knowledge about the effects of thermal processing on tree nuts such as cashew or pistachio is rare and based on traditional in vitro immunoassays. objectives: to elucidate the influence of thermal treatments (boiling and heat / pressure) on the ige reactivity of cashew and pistachio proteins, by means of traditional in vitro immunoassays and mediator release assays (mra). results: the allergenicity of untreated and treated cashew and pistachio nuts was evaluated by ige-elisa, ige-immunoblot and elisa inhibition assays using sera from spanish patients with clinical allergy to cashew and pistachio. rat basophilic leukaemia cell line transfected with the a-chain from the human high-affinity ige receptor fceri, was sensitized with a pooled sera and used for mra. sensitized cells were stimulated with untreated and treated protein extracts, in order to investigate the capability of untreated and treated cashew and pistachio proteins to cross-link ige on effector cells. the results showed that heat and pressure treatment at the harshest conditions considered in this study produced a higher decrease of the ige-binding capacity of cashew and pistachio proteins than boiling without pressure or soft conditions of heat and pressure. interestingly, although the treatments of heat and pressure seemed to affect cashew allergens to a greater extent than pistachio allergens (evaluated by ige-elisa and elisa inhibition), the results of mra using the cell line rbl- indicated that cashew proteins treated with heat and pressure, still retained some capacity to cross-link ige. introduction: previous research has indicated an important role for dietary non-digestible oligosaccharides in decreasing the incidence of atopic dermatitis in children at risk of allergy. it is assumed that these prebiotics promote colonization of beneficial bacteria in the gut. children with atopic dermatitis receiving a diet of galacto-and long chain fructo-oligosaccharides (scgos/lcfos) with bifidobacterium breve m- v had enhanced serum galectin- levels. galectin- has ige-binding capacities and can hereby suppress degranulation of mast cells and basophils. next to their function in the gut, oligosaccharides may also affect other immune cells directly, since they were found in plasma and urine. objectives: we investigated whether non-digestible oligosaccharides or galectin- can have a direct effect on immune cells, by determining the effect on basophil degranulation in peanut-allergic patients. whole heparinized blood samples were collected from peanut-allergic adult patients and incubated for hours with either a mixture of . % : scgos/lcfos or scfos/lcfos, or galectin- ( or lg/ml) at °c in the presence of il- ( . ng/ml). after hours, a basophil activation test (bat) was performed. basophils were stimulated for minutes at °c with increasing concentrations of whole roasted peanut extract or human anti-ige. degranulating basophils were determined as cd + cells and calculated as percentage positive cells. results: in each patient, the concentration of anti-ige or peanut extract that induced maximal degranulation in the untreated control sample was used as reference value to compare degranulation of the samples pretreated with scgos/lcfos, scfos/lcfos, or galectin- . pre-treatment of whole blood with scgos/lcfos resulted in an average decrease in degranulation of approximately %, while a significant reduction of % was observed after pre-treatment with scfos/lcfos (p<. ). pre-treatment with lg/ml galectin- decreased basophil degranulation with %, whereas lg/ml galectin- caused a significant decrease of % (p<. ). no differences were observed in the ec , indicating that the basophils are not becoming less sensitive to the peanut extract or anti-ige. the prebiotic mixture scfos/lcfos and galectin- can contribute to decreased degranulation of basophils in a igemediated bat assay using whole blood. further analysis is warranted to define the exact working mechanism of these oligosaccharides. introduction: the intestinal mucosa plays a key role in the development of food allergies. we studied the interaction between intestinal epithelial cells (iecs) and pbmcs of peanut-allergic patients in a transwell co-culture model. exposure of iecs to a mixture of galacto-and/or long chain fructo-oligosaccharides (scgos/lcfos) in combination with synthetic cpg dna (tlr ligand),modulated the cytokine response of activated pbmcs, driving away from the allergic phenotype. objectives: our aim was to compare the efficacy of scgos/lcfos with a scfos/lcfos mixture and to evaluate these effects in an allergen-specific co-culture model. iecs (ht- , human colon adenocarcinoma) were grown on transwell filters until confluence. iecs were apically exposed to . % : scgos/lcfos or scfos/lcfos either or not in combination with . lmol l À cpg dna to mimic presence of dna of beneficial bacterial in the gut. these iecs were co-cultured with basolateral pbmcs from peanut-allergic patients, either activated with anti-cd /cd ( hours) or peanut-extract (pe, days).cytokines ifn-c, il- , il- and tnf-a were measured in the basolateral supernatant and t-cell polarization of the pbmcs was determined (th , th , treg and tfh). results: apical exposure of iecs to cpg dna increased basolateral ifn-c and il- production by anti-cd /cd activated pbmcs (p<. ), and was enhanced by both oligosaccharide mixtures (p<. ). cpg exposure in transwells with pe stimulated pbmcs also increased ifn-c and il- production, which was further enhanced by scfos/lcfos (p<. ). in this pe-specific model, percentages of th and treg cells increased upon cpg exposure of iecs, and th frequency was increased by scfos/lcfos (p<. ). cpg dna exposed iecs suppressed il- and tnf-a production by anti-cd / cd activated pbmcs. both scgos/lcfos and scfos/lcfos reduced tnf-a production in combination with cpg dna (p<. ). tfh cells can produce il- , inhibiting class-switching to ige . upon cpg exposure of iecs, we observed an increase in tfh cells (p<. ) and similar tendency for cd + il- + cell frequency in anti-cd / cd activated pbmcs. conclusions: epithelial exposure to both scgos/lcfos and scfos/lcfos enhances the cpg dna induced th and regulatory il- response in an anti-cd /cd co-culture model, whereas only scfos/lcfos was effective in an peanut-specific co-culture model. introduction: in areas of spain with high level of grass pollen exposure, % of grass allergic patients were sensitized to profilin, and most of them developed severe profilin mediated food reactions. this specific population of patients constitute an ideal model to study the relation among respiratory and food allergy objectives: our aim here was to analyze the links between epithelial barrier integrity and inflammation in oral mucosa. methods: allergic patients and controls were included in the study. allergic patients were stratified into mild or severe according to their clinical history and response to profilin oral challenge test. immunohistochemistry (ihc) for cd c, cd , cd , claudin- ; and dapi nuclear staining were performed in formalin-fixed, paraffin embedded sections of oral mucosa biopsies. rt-pcr was performed to analyze il b and il gene expression and the number of circulating cd + cells in pbmc was measured by flow cytometry. additionally, basophil activation test was carried out in whole blood samples upon profilin stimulation and the ec was calculated. results: regarding epithelial barrier integrity, claudin- expression resulted inversely proportional to pollen-associated food allergy severity. furthermore, by dapi staining, we noticed a lower number of epithelial cells in allergic patients than in non-allergic, and the gene expression of il b and il resulted significantly increased in oral mucosa from severe group. as for immune response in oral mucosa, the number of cd c and cd + cells resulted significantly higher in severe group. in allergic patients, double ihc for cd c-cd showed an increase colocalization of t cells and apcs in the interface between epithelium and connective tissue. a decrease in blood circulating cd + cells was detected in allergic patients compared to non-allergic. as for the basophil sensitivity, ec in severe patients was -times lower than in mild. our results show that damage in oral mucosa epithelium, probably induced by high grass pollen exposure, might allow profilin to penetrate inside oral mucosa and induce inflammation with local recruitment of immune cells. furthermore, analyzing the immune response developed by effector cells, basophils from severe group result more sensitive to profilin as they react to a lower allergen concentration. these data explain the differences in food allergy severity between mild and severe group and propose oral mucosa as a new sensitization route. introduction: th cells producing the hallmark cytokines il- , il- and il- have been found to constitute the majority of the allergen-specific th cell responses in allergic diseases. subpopulations of the th responses have been described with an early primed th subtype characterized by production of il- and il- , and a highly differentiated th subtype, which in addition produce at least il- . objectives: we aimed to investigate the polarity of tree nut and peanut allergen-specific th cells in subjects with confirmed tolerance or allergy to multiple nuts, and hereby detect differences in allergenspecific th cell responses within the same study population. we also wanted to stress the question whether a th phenotype dominates in asymptomatic sensitization. methods: pbmcs from donors all assessed for clinical reactivity to hazelnut, walnut, cashew nut, pistachio nut and peanut was stained with cfse and stimulated ( cells/ml) with and without whole nut extracts ( - lg/ml) for days. allergen-specific cd + t cell phenotypes and cytokine release was analyzed with flow cytometry and luminex, respectively. the allergen-specific th cells of the allergic donors showed a trend of more highly differentiated il- +il- + th cells and higher abstracts | release of il- than in the tolerant donors. unexpected, except in the cashew nut stimulated cells, no difference was found in the relative percentage of the less differentiated th cells (single il- + allergen-specific cd + t cells) when comparing allergic with tolerant donors. when subdividing the tolerant donors into asymptomatically sensitized or ige-negative (< . kua/l), increased frequency of highly differentiated il- +il- + allergen-specific th cells were found in asymptomatically sensitized compared to tolerant-ige-negative donors. interestingly, a positive association of the allergen-specific ige level and the frequencies of allergen-specific il- +il- + and il- + th cells were found in hazelnut, pistachio nut and cashew nut but not in walnut and peanut allergic subjects. conclusions: an overrepresentation of allergen-specific highly differentiated il- +il- + th cells and an elevated il- production were observed in allergic subjects compared to subjects that tolerated the nuts. we furthermore found a trend that subjects asymptomatically sensitized to nuts differed from tolerant-ige-negative subjects by having relatively more highly differentiated il- +il- + allergen-specific th cells. introduction: it remains largely unknown which features of food proteins that render them allergenic vs tolerogenic. however, it has been suggested that the protein-chemical features affects protein uptake in the intestine, and that protein uptake route may impact on the risk of sensitisation. objectives: the aim of this study was to investigate the interplay between protein-chemical characteristics, the allergenic vs tolerogenic properties and the intestinal uptake of two protein products. the allergenic vs tolerogenic capacity of a heat-treated whey product, consisting of partly denatured and aggregated proteins, was compared to an unmodified whey product in: ( ) results: though this study showed that both unmodified and heattreated whey had immunogenic, sensitising and eliciting capacities as well as tolerance inducing capacity, significant differences between the two products were observed. the heat-treated product was found to have a lower allergenicity combined with high tolerogenicity compared to the unmodified product. competitive igg elisas indicated that heat-treatment of whey induced de novo epitopes while the original epitopes were maintained. newly established methods to study in vivo intestinal uptake were successfully applied to compare the uptake kinetics of the two products in different small intestinal tissues and serum. collectively the in vivo and in vitro uptake experiments suggested that uptake kinetics and the major intestinal uptake route differed between the heattreated and unmodified product. conclusions: this study showed that heat-treatment, which induces partly protein denaturation and aggregation, changes the immunological properties and intestinal uptake of a whey protein product. the heat-treated product was found to have a lower allergenicity combined with high tolerogenicity compared to the unmodified product, which highlights this products promising potential for induction of cow's milk tolerance. objectives: in this study, we enumerated tregs in esophageal tissue of patient with eoe, gerd and normal controls. ten patients with eoe, patients with gastroesophageal reflux disease (gerd), and patients with normal endoscopy and normal esophageal tissue were included. tregs were enumerated in paraffin embedded esophageal biopsy blocks, using immunohistochemistry assay. tregs were identified as foxp +, cd + cells. results: tregs were counted in high power fields (hpf, ) for patients and the average of hpf was recorded. the number of tregs in esophageal tissue of patient with eoe (mean . cells/ hpf) was significantly more than gerd(mean . cells/hpf) and control groups(mean . cells/hpf) (p value <. ). conclusions: there is an increase in number of regulatory t cells in esophagus of patients with eoe in comparison to gerd and control groups. the presence of these cells might be due to eosinophilic inflammation and help controlling the inflammation. objectives: to evaluate whether anti-cd (daratumumab) treatment results in a reduction of total and specific ige levels. results: samples from patients with relapsed/refractory multiple myeloma, treated with daratumumab monotherapy or daratumumab plus lenalidomide-dexamethasone in the umc utrecht between april and august , were tested for total ige levels as well as presence of specific ige against common inhalant allergens. in patients with detectable ige at baseline, the total and specific ige levels were evaluated during treatment up to weeks. of eight patients receiving treatment, four had detectable ige levels at baseline. one patient demonstrated sensitization to common inhalant allergens. for this patient, levels of total ige gradually decreased during weeks of treatment (from to ku/l; %), as well as specific ige against timothy grass ( . - . ku/l; %) and house dust mite ( . - . ku/l; %). a second patient, not sensitized to common inhalant allergens but with ige levels of ku/l at baseline, also demonstrated a decrease in ige levels, to ku/l ( %). the last two patients had total ige levels < ku/l at baseline, which dropped below detection limit after eight weeks of treatment. conclusions: this proof of concept demonstrates that (specific) ige depletion occurred during treatment with anti-cd (daratumumab). anti-cd could potentially play a role in the management of severe ige-mediated diseases. objectives: following individual and assessment, patients established and stable on omalizumab have been commenced on home therapy. training and education in self-administration has been provided. a service assessment has been carried out to review the ongoing safety, quality and patient experience of the service. results: to date, over doses of omalizumab have been self administered in the community with no adverse events or incidents related to home therapy. conclusions: self-administration of omalizumab at home by patients offers the potential to improve quality of life while also providing efficiency savings. introduction: chronic idiopathic/spontaneous urticaria (csu) is a chronic urticarial subtype, defined as itchy hives that last for at least weeks, with or without angioedema, and that have no apparent external trigger. although csu is more frequent in adult populationup to . %- %-, it can affect children and generally has a prolonged duration and has a detrimental effect on patients' quality of life. before the fda and ema approval of the anti-ige monoclonal therapy omalizumab for adults and children years and above, nonsedating h -antihistamines were the only agents licensed for use in patients with csu. however, a majority of patients did not respond to these drugs, even when they were administered at three to four times their licensed dose. objectives: we present pediatric patients (≥ years old) with csu non-responding to antihistamines, treated with omalizumab. results: at the diagnosis of csu, the patients were , , years old, respectively. a trial with non-sedating h -antihistamines, administered up to three to four times their licensed dose, were performed for all patients, without clinical efficacy. omalizumab was started at , , years, respectively. before anti-ige therapy, the urticaria activity score (uas) was , , respectively, indicating poor symptom control. omalizumab therapy was administered every weeks for months at the dosage of mg s.c. after month of therapy, all patients were symptom free with uas ; the patients remained asymptomatic for all the months of duration of monoclonal therapy and antihistamines were discontinued. by now, after , , months respectively from discontinuation of omalizumab, all patients are asymptomatic with uas . introduction: mepolizumab is a humanized monoclonal antibody directed against il- , and is licensed for the treatment of severe asthma in patients aged > years (eu only adults) with an eosinophilic phenotype as an add-on treatment. we were interested to know whether the substance has an antiallergic effect, too. objectives: here, we report the case of a year old man (non- results: in march he was switched from omalizumab to mepolizumab ( mg/month) weeks after the last omalizumab because of two asthma exacerbations under omalizumab in the last months and eosinophils/ll blood under mg prednisolone/day. after two injections of mepolizumab his fev increased from % to % pred., the act from to points, feno decreased from to ppb and the amount of prednisolone from mg to mg/day. but -the patient reported new nasal symptoms after the nd injection of mepolizumab, mainly blocked nose which has not been observed under omalizumab. he agreed to be challenged in the mobile gae²len exposure chamber* with house dust mite allergen for min. the total symptom score increased from to points after min exposure time remaining stable till the end, the positive nasal inspiratory flow decreased from to l after min and l after min, the fev decreased from % to % pred. following the inhalation of salbutamol the fev reversed. conclusions: mepolizumab has an anti-asthmatic effect but the anti-allergic efficacy seems to be small or absent. methods: all patients treated with omalizumab for severe allergic asthma or chronic spontaneous urticaria at the department of respiratory medicine and allergy at aarhus university hospital (n= ) were grouped after their home municipality. the number of omalizumab treated patients/inhabitant in these municipalities was correlated to the distance to the treatment centre at aarhus university hospital. results: mean distance to the treatment centre was . km for all inhabitants in the central region, while patients treated with omalizumab lived in average . km away. we found a negative linear correlation between the number of patients treated with omalizumab/inhabitant and the distance from the municipality to the treatment centre (slope: À . %ci: À . to À . ), p=. , n= ). conclusions: patients living at long distance from the treatment centre are less likely to be offered omalizumab treatment for severe allergic asthma or chronic spontaneous urticaria. objectives: demographics, clinical characteristics, and response to mepolizumab, were evaluated for atopic and non-atopic subgroups. sensitization to any one of the following; house dust mite, dog dander, cat dander, alternaria, or cockroach was considered as atopic, as assessed by specific serum ige of ≥ . ku/l. mensa (nct ) was a gsk sponsored study. results: of the severe asthma patients, ( %) were considered atopic, ( %) were considered non-atopic and atopic status was missing for ( %) patients. the majority of atopic patients (n= ) were sensitized to ≥ antigens. compared to the non-atopic sub-group the atopic sub-group was younger with a mean age of vs years of age, had a longer mean duration of asthma ( . vs . years), and a higher total baseline ige level ( u/ml vs u/ml). mean number of exacerbations in the months prior to the study was similar in the atopic and non-atopic subgroups ( . vs . ) as was the mean baseline peripheral blood eosinophil level ( cells/ll vs cells/ll). with mepolizumab an % reduction in eosinophils was achieved by week irrespective of atopic status and maintained throughout the treatment period. mepolizumab reduced the rate of exacerbations relative to placebo by % in the atopic subgroup and by % in the non-atopic subgroup. conclusions: the mensa study recruited an equivalent portion of atopic and non-atopic severe asthma patients. the atopic population was younger and had a longer duration of asthma than the non-atopic subgroup. while the baseline total ige level was > times greater in the atopic subgroup, the pharmacodynamic and efficacy response to mepolizumab treatment was similar. introduction: a treatment goal in the management of oral corticosteroid (ocs) dependent severe asthma is to reduce daily ocs use due to the side effects associated with long term use. anti ige treatment is used in atopic patients to reduce daily ocs. this analysis characterizes ocs reduction and asthma control in the sub-set of atopic and non-atopic ocs-dependent severe eosinophilic asthma (sea) patients from the -week sirius ocs reduction study. objectives: sirius study participants (n= ) were sub-grouped by atopic status in a post-hoc analysis; demographics, clinical characteristics, and response to mepolizumab were evaluated. sensitization to any one of the following; house dust mite, dog dander, cat dander, alternaria, or cockroach was considered as atopic, as assessed by specific serum ige of ≥ . ku/l. sirius (nct ) was a gsk sponsored study. results: of the ocs-dependent sea patients, ( %) were considered atopic ( % female), ( %) were considered non-atopic ( % female), atopic status was missing for patients ( %). compared to the non-atopic sub-group, the atopic sub-group was younger; mean age of vs years of age, while the mean duration of asthma was the same irrespective of atopic status ( years). the mean ocs daily dose and acq- score at baseline were similar between subgroups ( . mg vs . mg and . vs . , in the atopic and non-atopic subgroups respectively). the mean baseline peripheral blood eosinophil level was comparable in both subgroups ( cells/ll vs cells/ll) while the total ige level was higher in the atopic subgroup ( u/ml vs u/ml). mepolizumab lead to a ≥ % reduction in eosinophils by week irrespective of atopic status and eosinophil reduction was maintained throughout the study. mepolizumab reduced the ocs dose in the atopic group and non-atopic subgroups (odds ratio of a greater ocs reduction category of . ( % ci . , . ) and . ( % ci . , . ), respectively) and led to improvement in asthma control with a change in acq- of À . ( % ci À . , . ) in the atopic subgroup and À . ( % ci À . , . ) in the non-atopic subgroup. in an ocs dependent sea population mepolizumab reduced eosinophils independent of ige level and atopic status. in this limited post-hoc analysis, mepolizumab was an effective ocs sparing agent while improving asthma control in both atopic and non-atopic patients. patients who responded to retreatment had a similar mean time to response between the st dosing period ( . weeks) and nd dosing period ( . weeks). of all patients who were retreated (n= ), symptom control (uas ≤ ) after two doses was achieved in % ( st period) and % ( nd period) of patients; complete response (uas = ) occurred in % ( st period) and % ( nd period) of these patients. omalizumab was well-tolerated during both dosing periods. conclusions: omalizumab retreatment is safe and effective in patients with ciu/csu who respond to initial treatment and relapse after withdrawal, with most patients regaining symptom control after a nd course of omalizumab. : total ige reactivity of the grass allergoid formulation was diminished compared with native unmodified extracts. a difference in igg profiles was observed and indicated enhancement of accessible reactive igg epitopes across size distribution profiles of the grass allergoid formulation. detailed analysis of the epitope specificity showed retention of six lol p igg binding epitopes in the grass modified extract. all epitopes were mapped on the solvent exposed area of lol p homology model accessible for igg binding. one of the epitopes was identified as an "immunodominant" lol p igg binding epitope ( -ifkdgrgcgscfeik- ) and classified as a novel epitope. lastly, lol p igg antibodies showed functional capacity to block up to % of ige binding sites which provides evidence in protective function of immunotherapy induced antibodies against native allergens. the structural and immunological changes which take place following the grass allergen modification process were further unravelled revealing distinct igg immunological profiles. the results from this study support the concept that modification not only enhances the safety profile of scit but allows shorter-course objectives: design targeted sirna delivery system into liver cells. results: liposome surface was modified by lactose derivatives with different structures: lac(c ) and (lac) lac(c ) . the basic physicochemical and biological properties of the carriers have been examined. it is shown that glycoconjugate introduction has no effect on the physico-chemical characteristics. however the carbohydrate modification of the liposomal surface leads to increasing in transfection efficiency on a specific cell line hepg . moreover, the introduction of mono-carbohydrate derivative increases the transfection efficiency better than using a branched derivative of lactose. in the pharmacokinetic study target effect also was shown. unmodified liposomes start to be detected in the liver at minutes after administration, whereas modified liposomes were detected at minutes after administration. similarly, the excretion of modified liposomes from the liver was more slowly. also worth noting the high concentration of modified liposomes in the liver. furthermore liposomes modified by carbohydrates reduces the intensity of its accumulation in the lung. conclusions: it was shown that increasing attraction of drugs to the liver cells can be achieved by using liposome modification with lactose derivative. | sialylated fetuin-a is a candidate predictive biomarker for successful grass pollen allergen immunotherapy objectives: to identify new biomarkers of ait efficacy, pre-treatment sera obtained from grass pollen allergic patients responding or not to sublingual ait were differentially assessed by d-dige or label-free mass spectrometry. the role of fetuin-a in allergy physiopathology was studied by using gene silencing in a mouse asthma model, human dendritic cell stimulation assays and surface plasmon resonance. results: using comparative proteomics, we provide evidence for an increased o-linked sialylation of fetuin-a in sera collected before treatment from patients exhibiting clinical responses, when compared with low responders. whereas feta may either inhibit or promote chronic inflammation, no specific role in allergy had been ascribed to it until now. in ovalbumin-sensitized mice, silencing of the fetuin-a gene increased airway hyperresponsiveness and th responses. fetuin-a, but not its non sialytated counterpart, synergizes with lps and grass pollen or mite allergens in a tlr -dependent pathway to enhance the proallergic profile of human monocyte-derived dendritic cells. conclusions: quantification of sialylated fetuin-a glycoforms in the blood before treatment allows to identify patients more likely to benefit from grass pollen immunotherapy. validation of the hypothesis that this marker associated with "an inflammation status" can be used to predict ait efficacy is ongoing in larger cohorts of patients. introduction: kawasaki disease (kd) is a vasculitis that mainly affects small to medium-sized vessels, particularly the coronary arteries, and is a leading cause of acquired heart disease in children. previously, we found that the development of kd is associated with an elevation of both th and th immunity. gene hypomethylation is abstracts | an important form of epigenetic regulation, which results in increased gene expression. because m macrophages are associated with inflammation and th immunity while m macrophages are associated with immune regulation and th immunity, we hypothesize that kd is associated with hypomethylation of both m and m macrophage related genes. objectives: our objective was to investigate the methylation profile of m and m related genes in patients with kawasaki disease. twenty-four patients with kd and age-matched healthy controls (hc) were included in this study. in patients with kd, blood was sampled hours before ivig therapy (kd ) and days after ivig therapy (kd ). after dna extraction, samples were analyzed using human methylation bead chip (illumina) to examine the methylation ratios of genes related to m macrophages ( genes, cpg sites) and m macrophages ( genes, cpg sites). cpg sites with more than % difference in methylation levels and a pvalue less than . between groups were considered significant. objectives: primary aim of the study is the identification of differentially expressed genes (deg) associated with allergic rhinitis (ar) by using genome-wide transcriptomics data from blood immune cells. this set of candidate genes will then be used to define gene networks relevant for onset, severity and potential treatment outcome of house dust mite associated ar. with different ethnicity or populations exposed to a different environment is currently in preparation. introduction: allergic patients display abnormal immune responses to harmless antigens, leading to various symptoms from hay fever to life-threatening conditions. these responses include abnormal type immunity polarization and induction of allergen-specific memory t and b cells, resulting in development of allergy instead of immune tolerance. allergen-specific immunotherapy (ait) is currently the only causative treatment of allergic disorders. yet, in depth understanding of the underlying differences in allergen-specific cd + t cell and treg responses between allergy and tolerance and their changes during immunotherapy is lacking. objectives: we investigated whole-genome transcriptomics of circulating birch (bet v ) and grass (phl p a)-specific cd + t cells in allergic patients before and at , , and months of ait, as well in non-allergic healthy controls in corresponding seasonal time points. detailed immunophenotyping with flow cytometry and cd + mhc class ii tetramer staining with low rna/single cell next generation sequencing were performed. results: at baseline, out of the pollen season, there were more allergen-specific cd + t cells in allergic patients than in controls. at this time, over genes were significantly changed in allergenspecific as compared to total cd +t cells in patients, yet we found substantial differences in signal transduction and inflammatory response gene expression when compared to healthy controls. during ait we noted significant increase of allergen-specific cd + cells in patients with subsequent gene expression changes in the immune tolerance pathways. finally, we found increase in allergen-specific treg cells in patients upon ait, but not in tolerant controls in corresponding seasons. of interest yet, at early ait time points, allergenspecific treg cells displayed gene profiles suggesting their insufficient suppressive functions. conclusions: in summary, in vivo allergen exposure causes profound changes in the transcriptomic profiles of allergen-specific t cells. these gene profiles seem to be deficient at baseline in allergic patients, but ait is skewing them into the tolerant controls levels. introduction: the variability of the pharmacological response to beta (b )-agonists may be due to the polymorphism of the gene of results: singled out statistically significant differences of the genotype distribution. the gly/gly homozygous allele was discovered twice as often in the group with an insufficient response to b -agonists than in the group with a good response ( vs %, p<. ), while the distribution of heterozygous allele was detected the opposite pattern ( vs %, p<. ). in the arg/arg genotype distribution, there were no considerable differences in both groups ( % in each group). in the subgroups of children, receiving the high doses of the inhaled glucocorticoids, there was a trend for the prevalence of gly/gly homozygous allele prevalence. we have discovered the association of the gly/ gly genotype of the adrb gene with an insufficient effect of broncholytic therapy by means of short-term b -agonists; we also revealed the participation of the gly allele in the phenotype formation with the severe run of bronchial asthma and tolerance towards the therapy both by b -agonists and inhaled glucocorticoids. mckenna oe ; posselt g ; lackner p ; schmitt a ; h€ ollbacher b ; briza p ; wessler s ; gadermaier g ; ferreira f universit€ at salzburg, salzburg, austria; georg august-universit€ at g€ ottingen, g€ ottingen, germany introduction: an excess of million people worldwide have a reported allergy to birch pollen. proteases in such allergen sources have been suggested to contribute to primary sensitisation and exacerbation of allergic disorders. until now the protease content of betula pendula, a species endemic to the northern hemisphere, has not been studied in detail. hence, we aim to identify and characterise pollen and bacterial derived proteases found within betula pendula pollen. objectives: birch pollen transcriptome was constructed via de novo transcriptome sequencing. reads were assembled using the trinity software suite.. analysis of the birch pollen proteome was achieved via mass spectrometry and use of zymographic gels with the embedded substrates gelatinase and casein, which enabled visualisation of proteolytic activity. further to this, protease activity was quantified using a fluorescently labelled casein substrate protease assay. results: by using mass spectrometry, we were able to identify up to proteases within birch pollen. we could cluster the proteases into specific families based on their distinct proteolytic activities. further comparative analysis of the proteome and transcriptome revealed the relationship between transcript levels and the proteins they encode. zymographic methods enabled distinct visualisation of proteolytic activity for both casein and gelatin substrates. using fluorescently labelled casein, the birch pollen protease activity was quantified as . lg/ml when compared to a trypsin standard curve. additionally, bacterial isolates of the birch pollen were identified, and the proteolytic activity analysed. we report successful discovery of pollen and bacterial derived proteases endogenous to betula pendula. whilst none of the known birch pollen allergens have been recognised as a protease, we aim to investigate the role of tight junction degradation within epithelial cells and further enhance understanding of proteolytic activity on immune-polarization. objectives: to investigate the frequency and reasons of shortand long-term reintroduction failure in adults after a negative fc. method:: these are preliminary results of an ongoing prospective study. after a negative fc, patients receive standardized aftercare consisting of an introduction scheme to introduce the food at home and consultation by phone for advice and support hours, - weeks and months after the fc. short-term data about the frequency that patients failed introduction, defined as not completing the introduction scheme or patient-reported allergic complaints repeatedly during introduction, was obtained using a telephone interview. long-term data ( - months after negative fc) about frequency and reasons of reintroduction failure in daily diet, defined as not eating the food or only eating products with traces of the food, was obtained using a patient-reported questionnaire. results: from until now patients were included (mean age: years, male: %), who underwent a total of fcs with: hazelnut ( %), other nuts ( %), fruit ( %), composite meals ( %), fish and crustaceans ( %), cow's milk ( %), hen's egg ( %) and other ( %). in ( %) of the negative fcs, introduction using an introduction scheme was advised. in %, patients did not receive standardized aftercare for different reasons, eg negative fc with a composite meal. in %, introduction with an introduction scheme failed. long-term information was available for fcs. introduction failed in fcs ( %), including patient that even avoided traces of the food. patient-reported reasons for introduction failure were (n= ): symptoms after ingestion of the food (n= ), fear for allergic reactions (n= ) and not like the taste of the food (n= ). conclusions: short term introduction with an introduction scheme failed in %. however on the long-term in almost one third of the negative fcs, patients failed to reintroduce the food in daily diet, despite careful aftercare. it is recommended to give these patient even more intensive and tailored support. introduction: in order to help allergic patients manage often severe symptoms, food manufacturers are required to list allergens on labels and take precautions to avoid inadvertent contamination of foods with allergens. existing tools using generic immunoassays do not provide precise identification or quantification of specific food allergens. furthermore, existing elisa immunoassays are not able to be run simultaneously and are often unreliable. objectives: our goal was to develop and validate an accurate, sensitive and high throughput immunoassay that would enable simultaneous quantification of multiple allergens in foods. fluorescent beads coupled to allergen specific monoclonal antibodies were used to develop a multiplex array for simultaneous quantification of major allergens from peanut (ara h ), milk (bos d ), egg (gal d ), and shrimp tropomyosin (pen a ). target allergens were detected using biotinylated antibodies and streptavidin conjugated fluorochrome. the array was quantified using highly purified natural allergens as standards. allergen content was measured in various samples including samples spiked with purified allergen and allergen incurred food matrices. the results were compared to elisa. a multi laboratory validation was performed to validate the performance characteristics of the assay. results: there was a high correlation between the multiplex array and allergen specific elisa. the limit of detection of the array was as low as pg/ml. no significant cross reactivity was observed between the various food allergen assays. the recovery of allergen from spiked samples was generally between and %. inter and intra assay variability was observed to be less than %. in conclusion, an accurate, sensitive and reliable multiplex array for major food allergens was developed and validated. the flexibility of the microsphere technology allows for further expansion to produce a comprehensive array for the most important food allergens. this quantitative multiplex array may help to reduce the risk of inadvertent contamination of food. objectives: our aim was to create a food allergy web-based educational program for both schools and restaurants professionals. results: an interactive platform that hosts a free learning program, conclusions: the program and the toolkit are currently available online and are being implemented in schools at the north of portugal. we expect that fac program will give us an important insight on the professionals' knowledge about food allergy. additionally, acting as free integrated service and awareness effort, this program could be an educational tool easily adapted and disseminated, which may improve professionals 'commitment and skills to deal with food allergy in the community. | development of parallel reaction monitoring (prm) methods for soy and milk detection: consideration of allergen-derived ingredients chen s ; krawitzky m ; yang ct ; downs m university of nebraska-lincoln, lincoln, united states; thermo fisher scientific, san jose, united states introduction: the presence of undeclared food allergens poses both regulatory and health risks. in order to assess the magnitude of these risks, accurate quantitative detection methods are required. for some allergenic foods, the food industry uses not only the allergenic source but also a number of source-derived ingredients. some detection methods (both immunoassays and mass spectrometry methods) may fail to accurately detect and quantify these allergen-derived ingredients if they are not taken into consideration during development. objectives: the objective of this work was to select peptide targets for parallel reaction monitoring (prm) mass spectrometry methods that are suitable for detecting a variety of soy-and milk-derived ingredients. six soy-derived and six milk-derived ingredients were obtained for this study. the ingredients were extracted ( mmol l À tris-hcl, ph . , with mol l À urea, mmol l À dtt, and % pvpp) and subjected to in solution trypsin digestion. discovery proteomics analysis was conducted by lc-ms/ms using a q exactive tm plus orbitrap tm running in top data-dependent acquisition mode. peptides were identified using proteome discoverer . and relative, labelfree quantification was conducted on high-confidence (fdr< . ) peptides. selected peptides were subsequently analyzed in a targeted prm mode. results: the relative abundance of identified peptides varied among both the soy-derived and milk-derived ingredients. in the case of soy ingredients, for example, there were particularly marked decreases in the abundances of numerous peptides, across different proteins, in a hydrolyzed soy protein isolate. in the milk ingredients, variation in peptide abundance could be more directly attributed to differences in product protein fractionation (eg a decrease in abundance of whey proteins in a sodium caseinate product), although some peptides and proteins maintained consistent abundance across ingredients. after applying specificity and performance criteria, peptides from soy proteins and peptides from milk proteins were selected for further analysis in a targeted prm method. conclusions: peptide abundances vary widely among ingredients derived from allergenic foods. consideration of these peptide differences during ms method development by incorporating discovery proteomics may lead to more versatile and widely-applicable quantitative detection methods for food allergens. introduction: milk and its derivates are usual ingredients in many food products, which must be excluded by cow's milk allergic (cma) patients. oit protocols in patients with cma appear to be safe and effective in inducing desensitization and milk introduction in the diet. objectives: we conducted a survey in cma patients after successful completion of an oit programme, to assess their dietetic profile after introduction of fresh milk and dairy products (unrestricted diet) we considered cma patients (pts), males and females, age - (median . ), who successfully completed the oit protocol. these patients were on an unrestricted diet for milk and derivates, and they had been recommended to assume at least ml of fresh milk or yogurt every day. patients were given an ad hoc questionnaire to assess the milk/dairy products intake at least months after oit completion. results: from our investigation all of the pts have been assuming milk protein everyday without significant reactions after oit. % of the interviewee ( pts) referred to be drinking fresh milk at least three times a week, in a quantity of ml or higher. of note, % have to add cocoa powder ( pts) or coffee ( pts) to mask milk taste. dislike of milk taste was the cause of the refuse to take fresh milk in pts (over patients that didn't take milk at all); pts who didn't drink milk had at least ml yogurt instead, almost every day. fresh cheese was eaten at least once a week by % of all the pts; hard cheese was eaten as main course almost once a week by %. % of patients consumed biscuits and sweet baked products containing milk/derivates at least once a week, % every day. pizza was also present in the diet of the majority of pts ( %), once a week/month. ice cream was appreciated by all the patients and regularly assumed especially during the summer time. conclusions: taste seems to be the main factor that directs the daily choice of milk derivates or milk containing products. all pts easily consume baked products containing milk/derivates, and the majority of them accept fresh milk as advised in order to maintain unresponsiveness. our survey confirms that oit is effective in expanding food choice, but for some patients the change of dietetic habits is hampered due to taste reasons. a more detailed, qualitative and quantitative analysis of the milkunrestricted diet will derive from the -days food diary given to these patients. | frozen-defrosted dried skimmed milk is a suitable product for sublingual immunotherapy for cow's milk allergy introduction: sublingual immunotherapy (slit) is a promising treatment for cow's milk allergy (cma) due to its favourable safety profile. however, its efficacy is limited-probably due to the small volumes and doses that can be delivered sublingually, especially in children. milk products with preserved allergenicity that allow higher protein concentrations in smaller volumes might potentially improve the efficacy of slit for cma. dried skimmed milk (dsm) could fulfill these characteristics. in addition, once dsm is reconstituted, freezing individual vials from the same batch for further administrations could increase dose-consistency throughout the treatment, which would help ensure safety. however, little is known about whether processing to produce dsm, and further freezing-defrosting, may alter its allergenicity. objectives: to evaluate the allergenic protein composition of dsm, including once frozen-defrosted, in comparison to fully-allergenic usually consumed fresh milk. methods: sodium dodecyl sulfate polyacrylamide gel electrophoresis (sds-page) followed by silver staining was performed following the laemmli method to determine the soluble protein composition of the following products: fresh pasteurized milk (friesland campina, amersfoort, the netherlands), dsm (marvel, the premier foods group ltd, london, uk) and frozen-defrosted dsm to identify all protein bands present. western blot with anti-whey and anti-casein antibodies was performed to identify the specific allergenic proteins. results: no significant differences were found amongst the milk products tested, with sds-page displaying all the bands corresponding to the major allergenic proteins in milk (alpha-lactalbumin, beta-lactoglobulin and alpha-, beta-and kappa-caseins) and the western blot showing recognition to all proteins with similar intensity. the major allergenic proteins present in unprocessed milk are well-preserved in dsm, even after freezing-defrosting, making it a convenient product for sublingual immunotherapy. results: nineteen children were randomized into the low dose group (n= ) and the elimination group (n= ). there were no significant differences in background between these groups. after weeks of therapy, the rate of passing the oral food challenge test with / th of a whole egg was significantly higher in the low dose group ( / ( %) vs / ( %), p=. ). ovomucoid-specific ige levels in the low dose group after weeks were significantly lower than those at baseline. adverse events associated with both therapies did not occur during the study period. conclusions: these results show that low dose ingestion of egg is safe and effective for tolerance or desensitization induction in children with egg allergy, without the need for dose elevation. | another brick in the wall: toward a national food allergy strategy for canada introduction: the world is experiencing an apparent epidemic of food allergies. with rising prevalence and increasing global spread, basic scientists continue to search for causes while clinical and social scientists continue to study the consequences. these include life-long chronic illness, fear and anxiety, social exclusion and stigma, all of which are underscored by inequalities across vulnerable groups (eg, low income families, immigrants, indigenous peoples). concomitantly, consumer organizations and patient support groups attempt to influence policy in order to maximize choice and minimize risk for individuals and families affected by food allergy, both directly and indirectly. this includes food labeling legislation, food safety regulations, and policies and practices in public places such as schools, restaurants and transportation modes (eg, airplanes). objectives: in canada, with the support of + years of science undertaken by the allergy genes and environment (allergen) networks of centre of excellence in allergic disease, we are leading a national team that aims to establish the building blocks for a national food allergy strategy. conclusions: the greatest challenges to building a national food allergy strategy are not those related to the basic or clinical science, but rather the activities and commitment of individual stakeholders. while gaps remain in the science, the challenges of transdisciplinary integrated knowledge translation hinder progress. we present lesions learned regarding culture shifts that will facilitate the progress we need to maximize choice and minimize risk for canadians affected by food allergy. | component resolved diagnostics reduces diet restrictions by half among finnish school children savolainen j ; mascialino b ; pensamo e ; hermansson l ; silvan m ; borres mp ; korhonen k university of turku, turku, finland; department of allergology, uppsala, sweden; thermo fisher scientific-immunodiagnostics, turku, finland; university of turku, uppsala, sweden; thermo fisher scientific-immunodiagnostics, lieto, finland introduction: there are - special diets because of food allergy in finnish schools. the finnish allergy program - was launched to reduce problems and costs induced by allergies. one of the special aims was to reduce diets caused by food allergy will by %. the h€ ark€ atie social and health care service region schools have required doctor's certificates for diets for over abstracts | years. all diets are listed in a register and checked on a regular basis. objectives: the purposes of this study were to evaluate whether it is possible reduce the special diets when the special diet system appears to be working well and to assess the added value of immu-nocap ® isac allergen component diagnostics in the intervention. results: there were children attending the schools in the h€ ark€ atie region. there were children with diet due to food allergy. children were recruited to study from the diet register and contacted by a nurse's phone interview. there were children who refused the study leaving children for the assessment of the diet. children were not following any diet and in children the diet was not regarded necessary by the study nurse. children agreed to take part in the study and were referred to laboratory tests for food specific ige and isac. children dropped out leaving children in the study. after the food specific ige results were available, children were contacted by physician. based on the results and/or interview a free diet was allowed for children. children were eating small amounts of the food and were encouraged to increase the use of the foods. children were advised to avoid the foods only if they caused symptoms. only children were advised to continue diet. after the results of isac were available, children conclusions: the study confirmed that it is possible to have diets decreased over % in accordance to the finnish allergy program. additionally, the study showed that food allergic children can benefit from the use of component resolved diagnostics. | omalizumab treatment for severe food allergy caused by lipid transfer protein: a preliminary case series mari a; zennaro d; ferrara r; bernardi ml; alessandri c caam-centri associati di allergologia molecolare, rome, italy introduction: lipid transfer proteins (ltp) are allergens from plantderived foods causing symptoms ranging from oas to anaphylaxis. ltp are present in almost all kind of plant species used for human feeding. ltp allergic patients suffer of reactions to a broad variety of foods, with a very personal reactivity profile which can involve few or many foods. in addition, patients who start to record severe reaction to several foods begin to be afraid of eating any other related or non-related food, leading to a poor diet. omalizumab (ozm) has been documented to be effective in treating food allergies with sensitization to other allergens. objectives: to document the approach for recruiting, studying, monitoring ltp allergic patients, and do a preliminary evaluation of the clinical impact of ozm therapy. results: six adult patients with documented reactions to plantderived foods in the last months and diagnosed to be ige positive to multiple ltp by using multiplex testing, namely isac at the beginning and faber during the follow up, were recruited. ozm was offered as an off label treatment adopting an open label study design. a questionnaire was submitted to each patient before, during and after the treatment. foods listed as "no more eaten" where considered for reintroduction, starting from those excluded because of fear, going for those with an increasing risk of reactions. re-introduction was done at home after receiving detailed instructions, having all rescue medication at hand. the allergist was connected real time with the patients using one or more ict tools. one patient dropped out because was not complying with the scheduled reintroduction. three patients completed the treatment with a successful re-introduction of all or almost all excluded foods, in two cases peach was reintroduced. the last two patients reintroduced %- % of the excluded foods, including some of those previously causing reactions. the attempt of re-introducing the most risky foods failed causing local allergic reactions promptly controlled by the therapy. all foods re-introduced were tolerated once the treatment was stopped. conclusions: ozm seems to be a promising treatment for severe ltp allergics, improving their qol. starting from the recruitment phase to the re-introduction, the overall procedure looks quite complicated and deserve much resources. ige sensitization to ltp, carefully defined before treatment, can be monitored during the ozm course as the drug doesn't interfere with faber test ige detection. | oral immunotherapy with peach-juice in lipid transfer protein (ltp) allergy: is it possible to reach tolerance? introduction: food allergy to rosaceae fruits and nuts, due to sensitization to lipid-transfer protein (ltp), is frequent in the mediterranean area countries. based on milk allergy oral immunotherapy (oit) protocols, a study is proposed to obtain an oit regimen in patients allergic to ltp. objectives: we included patients with anaphylactic reactions due to ltp-food allergy, from january/ to october/ . skin prick test (spt) was performed with a food and inhalant battery, ltp bial-aristegui ® ( . mg/ml), prick by prick (pbp) with a specific commercial peach-juice (dilutions to endpoint), and determination of pru p ige levels (immunocap). the presence of pru p protein in the peach-juice, was confirmed by sds-page and elisa method, and quantified with anti-pru p . we elaborated an oit guideline with progressive administration of peach-juice, - - - drops ( drops= . ml), sublingually, starting concentration chosen according to the endpoint spt results, up to ml daily dose. the dose reached at the allergy service, was continued at home, daily, for - weeks. all the increasing doses were performed at the allergy service, after pbp with peach-juice and ltp control spt. after a time, an oral challenge up to ml peach-juice was performed. patients were instructed on the importance of maintaining regular intakes and avoiding cofactors. results: patients started this protocol ( male/ female), aged - (media . ). peach-juice analysis in agarose gel electrophoresis, showed a kda band quantified as . lg/ml of ltp. there was no difference between wheal diameter on spt for ltp bial-aristegui ® and pbp with commercial peach-juice along all the study. average concentration on pbp to endpoint: / ( ), / ( ), / ( ). pru p ige level average: . ku/l. none anaphylactic or serious reactions during the oit protocol appeared. only five patients ( %) reported mild occasional symptoms (oral pruritus and mild located urticaria). patients reached ml daily dose ( . %), and of them ( %) completed oral food challenge with peach-juice up to ml, with good tolerance. this pattern also allowed us to reintroduce withdrawn foods from the diet due to previous reactions, with good tolerance. results: children (age - years) sensitized to dog dander extract (median . ku a /l), with or without known dog induced allergic airway disease, were included. nasal provocation testing with dog dander extract was performed. measurement of ige to dog dander extract and to can f -can f was performed with immunocap. an ige level ≥ . ku a /l was considered positive. among all children sensitization to can f ( %) and can f ( %) was most frequent. corresponding numbers for can f , can f , can f and can f were %, %, % and % respectively. based on the results from the nasal challenges three groups were identified; no (n= ), mild (n= ) and strong reaction (n= ). the median ige levels to dog dander and to all allergen molecules were higher in the strong reaction group than in the mild and the no reaction group. among children with a strong reaction, ige to can f was found in % ( / ) compared to % ( / ) among children with no reaction (p=. ). ige to can f showed a similar pattern (p=. ). % ( / ) of the children with a strong reaction were sensitized to can f compared to . % ( / ) of the patients with no reaction (p=. ). no associations were found between the ige levels to can f , can f and can f and the no reaction or strong reaction groups. using multiple regression analysis, with all allergens in the model, sensitization to can f showed a statistically significant difference between the groups. conclusions: molecular allergology may improve diagnostics of dog allergy in children. sensitization to the lipocalin can f was significantly associated to a strong positive nasal reaction implying its usefulness as a marker of clinically relevant dog allergy. tsolakis n ; malinovschi a ; nordvall l ; janson c ; mattson l ; lidholm j ; borres m ; alving k uppsala university, women's and children's health, uppsala, sweden; uppsala university, medical sciences, uppsala, sweden; thermo fisher scientific, uppsala, sweden introduction: cat allergy is common worldwide and a major trigger of asthma in many countries. molecular patterns of cat sensitisation vary between individuals but their relationship with allergic inflammation has not been extensively studied. objectives: the aim was to investigate the prevalence of ige to different cat allergen components and their relationship to type- inflammation and bronchial responsiveness in young asthmatics. conclusions: ige sensitisation to cat serum albumin (fel d ) and cat lipocalins (fel d , fel d ) , but not to secretoglobin (fel d ) or cat dander extract, were independently associated with feno and b-eos count. we suggest that cat serum albumin and cat lipocalins can be used as markers for increased risk of type- inflammation in young asthmatics, as shown in multiple regression analyses. | complete sequence and recombinant production of horse dander allergen equ c lidholm j; lundgren t; larsson h; mattsson l thermo fisher scientific, uppsala, sweden introduction: horse dander is an increasingly important cause of respiratory allergy. equ c was one of the first horse allergens to be recognised but only a small part of its amino acid sequence has been reported. objectives: the aim of this study was to determine the complete sequence of equ c and express it as an immunoreactive recombinant protein. methods: equ c was purified by size exclusion, hydrophobic interaction, anion exchange and reversed phase chromatography. recombinant equ c was expressed as a hexahistidine tagged protein in e. coli and purified by immobilized metal ion affinity and ion exchange chromatography. ige antibody reactivity to natural and recombinant equ c and other horse dander allergens was determined in sera of subjects allergic to horse. results: a putative equ c sequence predicted from genomic data revealed a lipocalin protein of amino acids with a highest sequence identity among known lipocalin allergens of % to can f . n-terminal sequencing and mass spectrometric analysis of purified natural equ c confirmed . % ( / residues) of the predicted sequence. recombinant equ c displayed ige antibody binding activity comparable to that of purified natural equ c (r=. ). of the horse allergic subjects studied, ( %) showed ige antibody binding to equ c , ( %) to equ c , ( %) to equ c and ( %) to equ c . the complete sequence of equ c was established. as a fully immunoreactive recombinant protein, it represents an important addition to the panel of allergens useful in the diagnosis of allergy to horse. | component resolved diagnosis using guinea-pig allergens elucidates allergen sensitization profiles in allergy to furry animals objectives: to identify major guinea-pig allergens and to evaluate their potential as reliable markers for a specific ige-diagnosis in comparison to dander extracts. results: forty-three patients with a clinical history of allergy to guinea-pig and patients allergic to cat and/or dog were recruited for the study. major guinea-pig allergens were identified by ige-immunoblot and n-terminal sequencing of ige-reactive proteins. corresponding cdnas were cloned and allergens were expressed as recombinant proteins in e. coli. specific ige to animal dander, fel d and can f were determined, specific ige to fel d , can f and to guinea-pig allergens were quantified by elisa. two new guinea-pig lipocalin allergens, cav p and cav p , were identified in guineapig dander. the combination of guinea-pig allergens, the new allergens and the previously isolated lipocalins cav p and cav p , enabled the identification of out of patients sensitized to guinea-pig. the vast majority of the patients had specific ige to cav p ( %). cav p shares % sequence identity with fel d and can f and was found to be cross-reactive with these cat and dog allergens. in the group of cat and/or dog allergic patients, % had also specific ige to guinea-pig dander. nearly half of those ( %) had ige to cat serum albumin fel d or to fel d ( %) and to can f ( %), explaining the high degree of cross-reactivity to guinea-pig dander. only % of the cat/dog allergic patients with a positive isle test to guinea-pig dander had specific ige to any of the non crossreactive guinea-pig allergens cav p , cav p or cav p . however, none allergen has been characterized from mongolian oak. objectives: in this study, we tried to characterize a major allergen from mongolian oak. results: a molecule homologous to pathogenesis-related protein , a putative que m , was cloned by rt-pcr and its recombinant protein along with que a , an allergen from white oak (q. alba) was produced. cloned que m sequence shares . %- . % amino acid sequence identity ( . %) with pr- -like allergens from various plants. allergenicity and diagnostic value of recombinant que m abstracts | , que a and bet v proteins were compared by elisa using sera from oak sensitized subjects. specific ige to recombinant que m , que a , and bet v were detected in . %, . %, and . % of serum samples from korean tree pollinosis patients. recombinant que m was able to inhibit ige reactivity to que a and bet v , indicating its strong cross-reactivity. activation pattern of basophils from five patients was similar in terms of cd c expression and protein concentration of challenged bet v and que m . objectives: over the course of one year, all patients who were seen at our immunoallergology clinic for the first time underwent spt with our standard series, to which four olive tree cultivar extracts were added (arbequina, blanqueta, hojiblanca e picual). we then recorded wheal size diameters, considering a wheal > mm to correspond to a positive test. we recorded individual sessions of spts, in which presented at least one positive result. two hundred and thirtysix of these patients ( . %) had a positive spt for olive tree pollen, only one of them being monosensitized. when looking only at pollen-sensitized patients, twenty-two patients ( . %) tested positive solely for olive tree pollen. in all allergic patients, the most frequent cultivar sensitization was to the cultivars hojiblanca ( . %) and arbequina ( . %), followed by the cultivars picual ( . %) and blanqueta ( %). twenty-six patients ( % of all olive pollen sensitizations) had a positive spt for the conventional extract and negative spt for the cultivars; patients ( . %) had a positive spt for both. we noted that . % (n= ) of patients sensitized to olive tree pollen had a negative spt with the conventional extract and positive with one of the cultivar extracts. the cultivar hojiblanca was the most frequent in this group ( . %, n= ), followed by the arbequina cultivar ( . %, n= ). in the group as a whole, there was a positive correlation between the results of the spts with the conventional extract and each of the cultivar extracts. this correlation was weaker with the cultivar hojiblanca (r=. ). conclusions: some patients, sensitized only to the pollen of certain olive tree cultivars, are not identified with the conventional extract. spt with the hojiblanca cultivar could identify most of these patients in our country, and therefore should be considered in patients with a history of pollinosis and a negative spt for the common extract of olive tree pollen. | structural and immunological comparison of heat treated pru p and art v , the non-specific lipid transfer proteins of peach and mugwort pollen wildner s ; stock l ; regl c ; alessandri c ; mari a ; huber c ; stutz h ; gadermaier g objectives: recombinant art v . and pru p . were expressed in e. coli rosetta-gamib plyss and purified using cation exchange chromatography. proteins were analyzed in gel electrophoresis and mass spectrometry. proteins were incubated at °c in time intervals up to min using buffers at ph . and . . physico-chemical properties of native and heated allergens were analyzed by circular dichroism spectroscopy, dynamic light scattering and size exclusion chromatography (sec). using sera from italian patients sensitized to pru p and art v (n= ), ige binding to native and heat-denatured allergens was investigated in elisa. results: highly pure recombinant pru p and art v were obtained as non-tagged proteins from e. coli. identity and formation of disulfide bonds was verified by mass spectrometry. circular dichroism showed high thermal stability of both proteins at acidic ph. the alpha-helical fold of art v was lost upon heating for min at ph . while pru p was already altered after min. purified pru p and art v are monomeric molecules with a hydrodynamic radius of . and . nm, respectively. structural relaxation is observed upon heat treatment which is not attributed to protein aggregation as determined by sec. the ige reactivity to both allergens was largely unaffected upon heating at ph . . notably, ige reactivity to art v was already significantly decreased upon min heating and was completely abrogated to both proteins after min denaturation at neutral conditions. conclusions: even though the fold of pru p is more compact compared to art v , susceptibility to structural changes upon thermal treatment at neutral conditions are more pronounced which do however not directly translate to lower ige binding capacities. particularly the buffer environment needs to be considered when formulating ltp-containing products which undergo heat treatment. objectives: we sought to determine the ige binding capacity and potential diagnostic value of a recombinant hybrid molecule. results: the codon-optimized nucleotide sequences of a hybrid molecule comprising the full sequences of blo t and der p at the amino and carboxyl ends respectively, here named bp- , was cloned into a plasmid vector and expressed in escherichia coli as a xhis tag protein. two hundred and thirty three sera from colombian (n= ) and cuban (n= ) allergic patients were tested by elisa for ige reactivity. thirty seven sera from non-allergic subjects and negative skin test (spt) to mites were used as controls. all subjects provided written informed consent to their participation in this study. hdm allergy was diagnosed on the basis of clinical symptoms in combination with mite extract spt. potential diagnostic value of bp- specific ige was determined by receiver operating characteristic (roc) analysis and area under roc curve (auc) calculated. positive serum ige values to hybrid molecule were defined as optical density (od) higher than . (mean od plus standard deviations in nonallergic subjects). in respiratory allergic patients, the overall frequency of positive ige reactivity to bp- was . %, in non-allergic subjects the frequency was %. serum ige levels to bp- were positively correlated to spt to b. tropicalis (spearman r=. , p=. ), and to d. pteronyssinus (spearman r=. , p=. ). using spt to mite extracts as gold standard, the sensitivity and specificity of serum ige levels to bp- were . % and . % respectively, with an auc of . ( % confidence interval . - . ). conclusions: these data suggest that bp- could be a useful reagent for identifying allergic patients sensitized to b. tropicalis and/or d. pteronyssinus. | igg, ige and igg specific antibodies to molecular allergens of aspergillus fumigatus introduction: in clinical allergy, alongside with skin prick tests, in vitro determination of specific ige for a particular patient contributes to the diagnosis and helps to estimate the risk associated with different food allergens. however, with commercial methods of specific ige antibodies detection (component-resolved diagnosis, crd), the clinician is typically limited by the list of the available allergens. objectives: to overcome this limitation, we developed two component-resolved diagnostic tests for food allergy in which natural extracts can be used. in the first developed method, the crd is performed using immunoaffinity capillary electrophoresis (iace) coupled with matrixassisted laser desorption/ionization mass spectrometry. meanwhile, the second method is based on in-tube immunomagnetic separation (ims) with mass spectrometry identification (mass spectrometry or peptide mass fingerprinting). in both techniques, magnetic beads coated with antihuman ige antibodies are used to extract the ige antibodies from the blood serum of the allergic patient. then, the immunocomplex, obtained on the magnetic beads, is used to quantify the total ige level or to probe the ige binding with standard allergens or natural allergenic extracts. afterwards, the identification of the extracted proteins, ie potential allergens, is performed by mass spectrometry with or without ce separation. after optimisation, the proposed methods have been successfully applied to a commercial blood sample of a patient with a known allergy to cow's milk, with results confirmed by standard tests. as a proof-of-concept, the sensitization profile of a patient suffering from protein contact dermatitis to the cow's whey fraction has been determined. we confirmed the presence of circulating ige antibodies binding lactoferrin and bovine serum albumin. cross-reactivity tests were also performed using goat and sheep milk and revealed the patient sensitivity to serum albumins from these two milks. such approaches open the possibility for direct identification of ige-bound allergens molecular mass and structure. these methods allow the discovery of yet unknown allergens and could be useful for precise personalized allergy diagnosis, allergens epitope mapping, and cross-reactivity studies. objectives: the objective of this study was to investigate the validity of cord blood ige for predicting atopy at years of age. methods: a total of children born in participated in the longitudinal investigation of global health in taiwanese schoolchildren (lights) cohort. total ige was measured in umbilical cord blood at birth. perinatal history was collected from medical records in the chang gung memorial hospital, taiwan. total and specific serum ige and questionnaires were carried out at years of age. receiver-operating characteristic (roc) curves were used to determine the validity of cord blood ige for predicting atopy at years of age. logistic regression models were applied to assess the association between cord blood ige and atopy at years of age. results: cord blood ige levels was significantly associated with total serum ige level at years of age (r=. , p<. ). the cord blood ige levels in atopic children aged years (meanaesd, . ae . ku/l) were significantly higher than those in nonatopic children ( . ae . ku/l) (p<. ). the area under the receiveroperating characteristic (roc) curve of cord blood ige for predicting atopy at years of age was . . the sensitivity, specificity, and positive and negative predictive values of cord blood at the optimal cutoff of . ku/l on the roc curve for predicting atopy were . %, . %, . %, and . %, respectively. higher cord blood ige levels (≥ . ku/l) was associated with a higher likelihood of atopy at years of age (or= . ; % ci: . - . ; p<. ). our results indicate that cord blood ige is a potential predictor of atopy at school age, with an optimal cutoff of . ku/l. bogomolov a vinnitsa national pirogov memorial medical university, vinnitsa, ukraine introduction: allergen sensitization is being diagnosed by commonly available methods in clinical practice-skin prick tests (spts) and specific immunoglobulin e test (sige). recently, a new thermographic (th) method for the assessment of spt was developed, and it was demonstrated that the th measurements of forearm temperature distribution during spt, supported by a mathematical model, offer a new quantification method of allergen-induced skin reactions. objectives: the aim of this study is a comprehensive comparison of the th method with spt and sige techniques. the group of patients who were participated in this study consist of patients. among them were patients ( . %) with allergic rhinitis and patient ( . %) with asthma, . % of them were men and . % were women aged - years (mean age . ae . years). spt and sige testings were performed by the standard techniques. for th analyses, set of thermograms of both forearms were acquired after prick and analyzed with the use of developed software. all results were converted into categorized scale for comparison. after counting patients who were true positive (tp), true negative (tn), false positive (fp), and false negative (fn), the sensitivity, specificity, and accuracy were calculated according to the following formula using the results of spt as the standard; sensitivity=tp/(tp+fn), specificity=tn/(tn+fp), and efficacy=(tp+tn)/(tp+tn+fp+fn). the results showed high correlation coefficients between the methods equal to . - . . the sensitivity and accuracy of the th assessment in respect of both the classical methods is at a good level ( . - . ). the acceptable level of specificity . - . was also achieved for the majority of allergic reactions. the best accordance was observed between th and sige results (r=. ), while th-spt was the most divergent pair r=. . in case of particular allergens, the biggest correlation was . , while the smallest value amounted to . . the results of diagnostic indicators of thermographic measurement of skin reactivity in comparison with the classical methods of determining the sensitivity to allergens show the prospect of using the method in routine practice. the main advantages of this method are its higher measuring ability and objectivity, by which the possibility of making error in diagnosis is significantly reduced. introduction: chronic urticaria symptoms may be worsened by factors such as temperature, exercise, hormones and stress. a salicylate rich diet has been reported to worsen symptoms in these patients. the mechanism by which natural salicylates do this is unclear but, like aspirin, is thought to be due to their ability to interfere with the arachidonic pathway via cyclooxygenase inhibition. studies have shown that low dose aspirin increases serum il- levels in patients with antiphospholipid syndrome. il- is important in basophil and mast cell function, inducing mediator release and cd c upregulation in the absence of ige stimuli. objectives: the gold standard for diagnosing salicylate exacerbated chronic urticaria is by challenge testing. there is no in vitro laboratory test approved for routine diagnosis. this study investigated whether il- levels are raised in patients with chronic urticaria and if these levels were affected by salicylate intake. we aimed to find an optimum method of measuring il- levels by comparing levels in serum and salivary samples. the quantikine human il- enzyme linked immunosorbent assay (elisa) was validated and used on both saliva and serum of patients with chronic urticaria and normal controls. this was a case control study of medicated patients with chronic urticaria and controls at university hospital southampton, to see whether there were any correlations with il- , and degree of salicylate intake (based on a questionnaire). introduction: since the introduction of molecular components in allergy, a big challenge of allergy diagnostics is to connect clinical symptoms with optimal test use and correct interpretation of results. objectives: the aim of the study was to ( ) develop an algorithm that would meet that need, and ( ) to evaluate the effect of introduction of algorithm to clinical practice. the algorithm was developed which groups clinical symptoms into six categories: rhinoconjunctivitis/ asthma, oral allergy syndrome (oas), urticaria/angioedema, eczema, anaphylaxis, and a combination of symptoms and combines them with knowledge of possible allergen specificity. this information is combined with two basic allergen mixtures (panels), reflex testing of selected food molecular components and accompanied by interpretative comments. the introduction of our algorithm led to less inhalation screenings, more food screenings and an increase in the requested molecular components. the oas was seldom recognized or used as a symptom by specialists. the reduction in costs, by using the possibility that the disease presentation may be a consequence of an relatively not dangerous oas, was therefore not achieved. all pr- positive proteins in various allergen sources showed also positivity for birch antigen. the screening based on this algorithm has potential to enable clinicians/general practitioners with a tool to increase the pre-test probability of allergy for the most frequently occurring allergens. allergy diagnostics may be more efficient if pr- component of birch (r bet v ) is included in early screening and can help in early recognition of oas. helbling a department of otorhinolaryngology-head and neck surgery | clinical and immunological evolution of patients who failed milk-oral immunotherapy there is lack of evidence on evolution among failures. objectives: to analyze clinical and immunological evolution of patients who failed milk-oral immunotherapy. data were obtained from medical records of a cohort of patients who failed moit in the past years in hospital infantil universitario niño jesus ( %) patients failed during build-up phase [ ( %) due to adverse events (ae) and ( %) to family decision. failed during maintenance phase: ( %) due to eosinophilic esophagitis, ( %) to family decision, to psychiatric disorder and (range - ). the most frequent aes were cutaneous and gastrointestinal symptoms. / ( %) patients underwent a second moit and was successful in . the second moit was performed between and years after the first one. there was no statistical differences between specific ige(ku/l) levels at baseline and months after the moit end portugal introduction: fish allergy is common in countries where consumption is high. parvalbumins present in fish muscle are the major allergens. allergy to multiple fish species is caused by parvalbuminspecific cross-reactive ige. cross-reactivity with parvalbumin from baltic cod retrospective study of patients with fish allergy followed in our immunoallergology department. fish tolerance acquisition was evaluated by oral food challenge. statistical analysis was performed using spss version (descriptive statistics, student test results: pts were included ( male, female), children and adults (age ae years). ( %) had previous history of rhinitis, ( %) of asthma and ( %) of eczema age of first contact with fish averaged . ae . months (min , max ) and the possible types of contact were: oral in ( %), cutaneous in ( %) and inhalation of cooking fish vapours age of first clinical manifestation (excluding the pts who developed allergy in adulthood) was at ae months (min , max ) the clinical manifestation of the reaction was: angioedema/urticaria ( %), gastrointestinal symptoms ( %), eczema ( %), respiratory symptoms ( %), oral allergy syndrome ( %), cardiovascular symptoms ( %) age at the first immunoallergology out-patient clinic consult averaged ae years (min . , max ) and time from first symptom to first thermo-fisher) was evaluated before and after acquisition of tolerance to at least fish. before tolerance, sige (ku/l) averaged roc curve (area under curve . ) showed that, for gad c ku/l, pts had a sensitivity of . % and specificity of . % that they would have a negative oral food challenge to a fish an sige< . ku/l had sensitivity of % of a negative challenge ku/l had specificity of . % of a positive challenge. conclusions: fish allergy is a common allergy in early childhood however, acquisition of tolerance is possible. rgad c appears to be a good marker for fish tolerance and could help allergologists as to when start testing for fish tolerance key: cord- - ubhd vf authors: abraham, louis; b'ecigneul, gary; scholkopf, bernhard title: crackovid: optimizing group testing date: - - journal: nan doi: nan sha: doc_id: cord_uid: ubhd vf we study the problem usually referred to as group testing in the context of covid- . given $n$ samples taken from patients, how should we select mixtures of samples to be tested, so as to maximize information and minimize the number of tests? we consider both adaptive and non-adaptive strategies, and take a bayesian approach with a prior both for infection of patients and test errors. we start by proposing a mathematically principled objective, grounded in information theory. we then optimize non-adaptive optimization strategies using genetic algorithms, and leverage the mathematical framework of adaptive sub-modularity to obtain theoretical guarantees for the greedy-adaptive method. lacking effective treatments or vaccinations, the most effective way to save lives in an ongoing epidemic is to mitigate and control its spread. this can be done by testing and isolating positive cases early enough to prevent subsequent infections. if done sufficiently regularly and for a sufficiently large fraction of individuals at risk, this has the potential to prevent a large fraction of the infections a positive case would normally cause. however, a number of factors, such as limits on material resources as well as on work force, necessitate economical and efficient use of test resources. group testing aims to improve properties of tests by testing groups of items simultaneously. we wish to leverage this framework to improve covid- testing. one needs to differentiate between two different settings: adaptive and non-adaptive. in the former, tests can be decided one at a time, taking into account previous test results. in the latter, one has to select all tests before seeing any lab result and could thus run them in parallel. one can also imagine a semi-adaptive setting in which tests are selected in small batches between each lab evaluation. a simple example of a semi-adaptive group test is to first split n samples into g groups of (roughly) equal size, pool the samples within the groups and perform g tests on the pooled samples. all samples in negatively tested pools are marked as negative, and all samples in positively tested pools are subsequently tested individually. this strategy has recently been validated for covid- pcr tests [schmidt et al., ] . non-adaptive group testing. most of the existing research on non-adaptive group testing is concerned with identifying at most k positive samples amongst n items, which is referred to as non-adaptive hypergeometric group testing [hwang and sós, ] . this assumption yields asymptotic bounds on the number of tests needed to recover the ground truth [knill et al., , indyk et al., , cheraghchi et al., , chan et al., . however, these are of limited practical relevance when constructive results on small numbers of samples are required. a different problem formulation. we formulate the problem differently: given n people and m testing kits, the characteristics of the test and prior probabilities for each person to be sick, we seek to optimize the way the tests are used by combining several samples. for simplicity, samples are assumed to be independent. [mazumdar, ] considers these assumptions as well, for the non-adaptive setting. however, his results are also asymptotic, i.e., valid for large n. adaptive group testing. in the adaptive setting, subsequent test designs may take into account earlier test results. by leveraging the framework of adaptive sub-modularity initially developed for sensor covering by [golovin and krause, ] , we prove near-optimality of the greedy-adaptive strategy. our contributions are as follows: • we provide a mathematically grounded objective function to optimize when designing a strategy, leveraging information theory. • we implement different strategies, both non-adaptive and adaptive, which can readily be used in a web browser to know (i) which tests to run and (ii) how to interpret the outcome. • we provide a guarantee of near-optimality of the greedy-adaptive strategy which is based on the mathematical objective we proposed. • software is available at https://louisabraham.github.io/crackovid/crackovid.html. intuition. our mathematical objective is designed such that the mixture tests it proposes to run in the lab will maximize the amount of information we gain on the ground truth once their lab results are revealed − in expectation, over the randomness of both imperfect tests and prior probabilities of infection per individual. notations are progressively introduced throughout, but also all gathered in appendix a. denote the number of patient samples by n, and the number of tests to run by m. tests are assumed to be imperfect, with a true positive rate (or sensitivity) tpr and true negative rate (or specificity) tnr. patient sample i is infected with probability p i ∈ [ , ] and we assume statistical independence of infection of patient samples. denoting by a ' ' a positive result (infection), the unknown ground truth describing who is infected and who is not is a vector of size n made up of ' 's and ' 's: we call this the secret, denoted as s ∈ { , } n . a design of a test d ∈ { , } n to run in the lab is a subset of patient samples to mix together into the same sample, where d i = if patient sample i is mixed into design d and d i = otherwise. note that the outcome of a perfect design d for a given secret s can simply be obtained as , a test result is positive if there is at least one patient i for which d i = (i is included in the sample) and s i = (i is infected). recall that the secret s is unknown. however, since we assume initially that patient sample i is infected with probability p i and that patient samples are independent, this yields a prior probability distribution over the possible values of s. we hence represent the random value of s as a random variable (r.v.) , denoted by s, with probability distribution p s (s) := pr[s = s] over { , } n . let us now recall the definition of the entropy of our random variable, representing the amount of uncertainty that we have on its outcome, measured in bits. it is maximized when s follows a uniform distribution, and minimized when s constantly outputs the same value. as we perform tests, we gain additional knowledge about s. for instance, if a test pools all samples and returns a negative result, then our posterior probability that all patients are healthy goes up, i.e., p s (( , . . . , )) increases, governed by bayes' rule of probability theory. more generally, we may perform a sequence of tests of varying composition, updating our posterior after each test. our goal will be to select designs of tests so as to minimize entropy, resulting in the least amount of uncertainty about the test outcome for all individuals. note that since tests are imperfect, for a given pool design d ∈ { , } n and a given secret s ∈ { , } n , the boolean outcome t (s, d) of the test in the lab is not deterministic. if tests were perfect, we would have t (s, d) = d,s > . to allow for imperfect tests, we model t (s, d) as a r.v. whose distribution is described by pr since the secret s is also unknown (and described by the r.v. s), the outcome t (s, d) has now two sources of randomness: imperfection of tests and unknown secret. in practice, one will not run one test but multiple tests. we now suppose that m tests of pool designs are run and let their designs be represented as a multiset d ∈ ({ , } n this leads us to the following question: given an initial prior probability distribution p s over the secret, how should we select pool designs to test in the lab? we want to select it such that once we have its outcome, we have as much information as possible about s, i.e. the entropy (uncertainty) of s has been minimized. since we cannot know in advance the outcome of the tests, we have to minimize this quantity in expectation over the randomness coming from both the imperfects test and unknown secret. this requires the notion of conditional entropy. conditional entropy. given pool designs d, we consider two random variables s (secret) and t := t (s, d) (test results). the conditional entropy of s given t is given by: in this formula, the joint probability pr[s = s, t = t] has been computed with the conditional probability formula pr[s = s, t = t] = pr[s = s] pr[t = t|s = s], and the posterior distribution is computed using bayesian updating, i.e., where it represents the amount of information (measured in bits) needed to describe the outcome of s, given that the result of t is known. mutual information. equivalently, one can define the mutual information between s and t as: it quantifies the amount of information obtained about s by observing t . a well-motivated criterion for test selection. since h(s) does not depend on d, selecting the pool design d minimizing the conditional entropy of s given the outcome of d is equivalent to selecting the one maximizing the mutual information between s and t (s, d). we now have a clear criterion for selecting d: this criterion selects the pool designs d whose outcome will maximize our information about s. expected confidence. we report another evaluation metric of interest called the expected confidence. it is the mean average precision of the maximum likelihood outcome. the maximum likelihood outcome it defined by: which yields the following definition of expected confidence: ml is of particular practical interest: given test results t, a physician wants to make a prediction. in this case, it makes sense to use the maximum likelihood predictor. the interpretation of confidence is straightforward: the probability of the prediction to be true (across all possible secrets). updating the priors. both scoring functions described above compute the expectation relative to the test results of a score on the posterior distribution p s|t =t (s). after observing the test results, we are able to replace the prior distribution p s by the posterior. by the rules of bayesian computation, this update operation is commutative, i.e., the order in which designs d and d are tested does not matter, and compositional in the sense that we can test {d , d } simultaneously with the same results. thus, we can decompose those steps and make different choices as we run tests (see the adaptive method below). (a) compare two outcomes: ( ) the posterior is concentrated on two points s ∈ { , } n , taking the values . and . . ( ) it is concentrated on three points, taking the values . , . , . . the entropy is higher, but maybe we still prefer ( ) since the margin to the second best explanation is larger? foreword. non-adaptive methods have the benefit over their adaptive counterparts that they can be run in parallel. on the flip side, they describe a strictly more restrictive class of algorithms, since any non-adaptive method is an adaptive one ignoring the information obtained adaptively. moreover, non-asymptotic (i.e., for small values of n) performance guarantees are harder to obtain than for adaptive methods. given numbers n & m, test characteristics tpr & tnr as well as prior probabilities of sample infection p i , the best multiset d of m pool designs is the one maximizing some score, like i(s, t (s, d)) or confidence(s, t (s, d)). the tests are order insensitive, which gives a search space of cardinality n +m m . evaluating the score of every multiset separately takes o ( n+m ) operations. hence, brute-forcing this search space is prohibitive even for small values of n and m. we resort to randomized algorithms to find a good enough solution. our approach is to use evolution strategies. we apply a variant of the ( + λ) es with optimal restarts [luby et al., ] to optimize any objective function over individuals (multisets of tests). detailed description. we maintain a population of individual between steps. at every step of the es, we mutate it in λ ∈ n + offsprings. in the standard ( + λ) es, each offspring is mutated from the population, whereas our offsprings are iteratively mutated, each one being the mutation of the previous. these offsprings are added to the population, and the best element of the population is selected as the next generation of the population. we initialize our population with the "zero" individual that doesn't test anybody. our mutation step is straightforward: flipping one bit d i of one pool design d, both chosen uniformly at random. our iterative mutation scheme allows us to step out of local optima. after choosing a basis b proportional to n × m (which is approximately the logarithm of our search space), we apply restarts according to the luby sequence: this sequence of restarts is optimal for las vegas algorithms [luby et al., ] , and our es can be viewed as such under two conditions: (i) that the population never be stuck in a local optimum, which can be achieved in our algorithm using λ = n × m (note that much smaller constant values are used in practice); (ii) the second condition is purely conceptual and consists in defining a success as having a score larger than some (unknown) threshold. the fact that our algorithm does not use this threshold as an input yields the following result: theorem . under condition (i), the evolutionary strategy using the sequence of restarts illustrated in eq. ( ) yields a las vegas algorithm that restarts optimally (as defined by [luby et al., ] ) to achieve any target score threshold. future improvements would consist in (i) initializing the population with random pool designs (following randomized testing methods from the literature), (ii) design new mutation rules and (iii) a dynamic restart strategy based on the detection of lack of progress. foreword. adaptive methods have the clear advantage over their non-adaptive counterparts to be more efficient in the number of tests, although they require waiting for the lab results after each sequential test run. although searching the space of all possible adaptive strategies would yield a prohibitive complexity of Ω( m ), it turns out that a simple adaptive strategy can yield provably near-optimal results. detailed description. we describe our adaptive method as algorithm which greedily optimizes the criterion defined in eq. ( ). leveraging the framework of adaptive sub-modularity [golovin and krause, ] , and the fact that the criterion defined by eq. ( ) is adaptive sub-modular and adaptive monotone, algorithm has the guarantee below. we prove it in appendix b. . algo, the expectation being taken over all m outcomes of lab results. denote by 'optimal' the best (unknown) adaptive strategy. if we run algorithm for m tests and optimal for m tests, we have: where α is defined as follows: assume that our priors p i are wrong, in the sense that there exist constants c, d with cp i ≤ p ′ i ≤ dp i for i ∈ { , ..., n}, with c ≤ and d ≥ , where p ′ i denotes the true prior: we set α := d/c. remarks. theorem states that algorithm is (i) robust to wrong priors and (ii) nearoptimal in the sense that the ratio of its performance with that of the optimal strategy goes to exponentially fast in the ratio of the numbers of tests run in each algorithm. for α = and m = m , this yields − /e ≃ . . there exists recent work applying group testing to covid- : [seifried and ciesek, ] report using mini pools of patient samples of size yielding no error in the prediction of healthy patients, over a set of patient samples; [yelin et al., ] report the possibility of mixing up to patient samples together, with a false positive rate of %; [jeffay, ] made a press release about the possibility of reliably testing mixtures including as many as patient samples; [kadri, ] mentions simple mathematical methods to approach the problem; [deleforge, ] published a blogpost with appealing illustrations vulgarizing the mathematics of group testing. we have discussed some interesting special cases using relatively restrictive assumptions. while theoretical results often require such assumptions, our implementation can in principle be generalized into various directions... we have used the number of tests and samples as given, and then optimized a conditional entropy. however, from a practical point of view, other quantities are relevant and may need to be included in the objective, e.g. the expectation (over a population) of the waiting time before an individual is "cleared" as negative (and can then go to work, visit a nursing home, or perform other actions which may require a confirmation of non-infectiousness). semi-adaptive tests. instead of performing m consecutive tests, one could do them in k batches of respective sizes m , ..., m k satisfying m + ... + m k = m. adaptivity over the sequence of length k could be handled greedily as in algorithm , except that instead of selecting a single pool design d * , we would select m i designs at the i th step. we named this semi-adaptive algorithm the k-greedy strategy. pool size optimization. one could analyze the simple setting of [schmidt et al., ] , i.e., what is the best pool size given an average prior probability. "best" here could mean something different than in our setting. one might want to take into account the number of tests kits used as well as the number of people which are "cleared" as negative after a given time duration. pool allocation. how do we allocate people to the (first round) pool designs in this setting if prior probabilities are non-uniform? this will naturally arise if we apply group testing as per [schmidt et al., ] every day for part of the workforce of a company, in which case a negative result for a person on a given day would imply a low prior on the next day. one could also wonder how to allocate people to the pool designs in the presence of correlations between patient samples. one initial guess could be to place correlated people into the same pool in order to minimize the expected number of what one might call false pool alarms, i.e., cases where a person ends up in a positively tested pool even though they are personally negative. further practical considerations. a good practical strategy could be to perform one round of pooled tests to disjoint groups every morning as individuals arrive at work, being evaluated during work hours. those who are in a positive group (adaptively) get assigned to a second pool design tested later, which can consist of a non-adaptive combination of multiple designs, tested over night. they receive the result in the morning before they go to work, and if individually positive, the enter quarantine. if the test is so sensitive that it detects infections even before individuals become contagious (which may be the case for pcr tests), such a strategy could avoid most infections at work. dependencies between tpr, tnr and pool size. the reliability of tests may vary with pool size. in our notation, the outcome of the tests is a random variable that need not only depend on whether one person is sick ( d,s > ) but it may also depend on the number of tested people |d| and the number of sick people d, s (cf. footnote ); it could even assign different values of tpr and tnr to different people. the tpr may in practice be an increasing function of the proportion of sick people d, s /|d|. estimating prior infection probabilities. currently, we start with a factorized prior of infection that not only assumes independence between the tested patients but is also oblivious to the individual characteristics. we could, however, build a simple ml system that estimates the prior probabilities based on a set of features such as: job, number of people living in the same household, number of children, location of home, movement or contact data, etc. those prior probabilities can then be readily used by our approach to optimize the pool designs, and the ml system can gradually be improved as we gather more test results. prevalence estimation. similar methods can be applied to the question of estimating prevalence. note that this is an easier problem in the sense that we need not necessarily estimate which individuals are positive, but only how many. ethical considerations. we identify two families of concern to address. the first family concerns the accuracy of the tests. indeed, when the number of tests and patients are equal, it is natural to compare the tpr/tnr of the individual test to the tpr/tnr of the individual results in our grouped test framework (obtained by marginalizing the posterior distribution). in some situations with unbalanced priors, the marginal tpr/tnr of some people in the group could be lower than the test tpr/tnr, even if the test will be more successful overall. however, reporting the marginal individual results gives doctors a tool to decide whether further testing should be needed; hence we cannot rule out that individuals might be worse off by being tested in a group. the second family of concerns, directly resulting from the first, is the responsibility of the doctor when assigning the people in batches and giving them prior probabilities (using another model). the assignment of people in batches should be dealt with in a future extension of our framework, while the sensitivity of our protocol to priors should be studied in more depth. in particular, the adaptive framework is more robust with respect to the choice of priors than the non-adaptive one. • h(p s|t =t ) : f (e(π, Φ), Φ); • h(s | t ) : f avg := e[f (e(π, Φ), Φ)]. this allows one to define, following definition of [golovin and krause, ] , the conditional expected marginal benefit of a pool design d given results t as: it represents the marginal gain of information obtained, in expectation, by observing the outcome of d at a given stage (this stage being defined by p s , i.e. after having observed test results t). adaptive monotonicity holds if ∆(d) ≥ for any d. adaptive sub-modularity holds if for any two sets of results t and t ′ such that t is a sub-realization of t ′ , for any pool design d: the below lemma concludes the proof. lemma. with respect to ∆ defined in eq. ( ), adaptive monotonicity and adaptive sub-modularity both hold. proof. adaptive monotonicity is a consequence of the "information-never-hurts" bound h(x | y ) ≤ h(x) [cover and thomas, ] . moreover, as mentioned in lemma of [guestrin et al., ] , sub-modularity also follows directly from this bound. in this section, we show how our program (available at https://louisabraham.github.io/crackovid/cra can be used for practical applications. suppose a doctor already made some pooled tests. our program can compute the posterior distribution and report the most probable diagnosis, its confidence as well as the marginal probabilities for each person to be sick. in our numerical example, tpr= . , tnr= . , we test persons with tests. the i-th test is applied to everybody but the i-th person. we can then enter the results of each test. the input of our program is thus i.e. there exist d and d ′ such that t (s, d) = t, t (s, d ′ ) = t ′ and d ⊂ d ′ . nonadaptive group testing: explicit bounds and novel algorithms graph-constrained group testing elements of information theory the maths of group testing: mixing samples to speed up covid- detection adaptive submodularity: theory and applications in active learning and stochastic optimization near-optimal sensor placements in gaussian processes non-adaptive hypergeometric group testing efficiently decodable nonadaptive group testing to ease global virus test bottleneck, israeli scientists suggest pooling samples enhancing the number of lab tests with a 'poisoned wine' approach non-adaptive group testing in the presence of errors optimal speedup of las vegas algorithms nonadaptive group testing with random set of defectives fact -frankfurt adjusted covid- testing -a novel method enables high-throughput sars-cov- screening without loss of sensitivity pool testing of sars-cov- samples increases worldwide test capacities many times over evaluation of covid- rt-qpcr test we use upper case letters exclusively for random variables (r.v.), except for mutual information i and entropy h. • n: number of patient samples • m: number of tests to run in the lab } n : the secret to unveil, with s i = if and only if patient sample i is positive over possible values of s whose law describes the current information we have about s } n : a pool design, with d i = if and only if patient sample i belongs to pool design d } n ) m : random multiset describing the pool designs output by the strategy } m : lab result of a list of m tests • t : r.v. over possible values of t describing lab results • tpr: true positive rate, sensitivity, hit rate, detection rate, recall • tnr: true negative rate, specificity, correct rejection rate, selectivity a]: probability of event a to happen ) is both adaptive monotone and adaptive sub-modular. direct respective correspondence between our notations and that of • set d of selected designs : set e(π, Φ) of selected items by policy π gary bécigneul is funded by the max planck eth center for learning systems. subject to privacy considerations with [results] a binary code representing the test observations. if the results are , the program indicates that with very high probability nobody is sick: most probable diagnosis: confidence: . marginals: . e- . e- . e- if the results are , the program predicts that the first person is sick and the other two are healthy: most probable diagnosis: confidence: . marginals: . . . interestingly, we observe error correction when the results are (an impossible outcome with perfect tests) as the program still infers that nobody is sick: most probable diagnosis: confidence: . marginals: . . . e- this mode, given prior probabilities of people to be sick and a number of tests, finds a pooling scheme to optimize the expectation of some score on the posterior probabilities, eg minimize the entropy or maximize the confidence.in fact, the framework we applied above is optimal as suppose that instead of testing people, we want to test people. a possible return value of our randomized algorithm is: as . = . < . , grouping people together gives much more accurate results than dividing then in two groups of people. key: cord- -chwk bs authors: nan title: abstracts: poster session date: - - journal: ann neurol doi: . /ana. sha: doc_id: cord_uid: chwk bs nan an immune etiology has been postulated for acute cerebellar ataxia of childhood (acac) since it frequently follows viral infections. we analyzed serum and cerebrospinal fluid (csf) from acac patients for antibody cross-reacting with cerebellar neurons. serum and csf were obtained within days of onset of pancerebellar ataxia from subjects aged . to years. varicella infection preceded cases. results of enhanced cranial ct scans were normal; csf demonstrated - cells/mm with sterile cultures. serial dilutions from : of serum and undiluted csf were screened for antineuronal antibody by indirect immunofluorescence (iif) using frozen, unfixed normal human cerebellum. serum ( : ) was examined further for antineural antibody by western immunoblotting using purified cerebellar neuronal extracts as antigen. serum from age-matched, neurologically normal pediatric inpatients served as the control group for iif and immunoblot experiments. in acac patients, no antineuronal immunoreactivity was observed by iif. immunoblots demonstrated no consistent pattern of immunoreaction when comparing acac to controls, though patient exhibited distinct bands at kd (neurofilament protein) and kd. although antecedent infection suggests an immune etiology for acac, our preliminary results do not support a humoral mechanism for this disorder. ingrid taff; joseph zito, robert gould, and steven pavlakis, great neck and manhasset, ny in a -month period we studied patients between the ages of weeks and years with magnetic resonance angiography (mra). studies were performed on a . t magnet (siemens magnetom sp) with a circular polarized head coil. a three-dimensional time-of-flight technique was utilized. occasionally, images were obtained after gadopenetate dimeglumine infusion. two-dimensional projection images were calculated using a maximum intensity projection algorithm and recorded on laser film. sixty-seven patients also had routine mri. a sampling of vascular lesions was demonstrated. nineteen patients had clinical and mri evidence of stroke. mra revealed intracranial vascular occlusion in patients, diminished focal cerebral flow in the affected area in , and generalized ipsilateral underdeveloped cerebral circulation in . a moya-moya vascular pattern was found in and sickle-cell vasculopathy was found in patient. seven mras were normal. seventeen vascular hamartomas were demonstrated including vene of galen malformations, arteriovascular malformations, and venous angiomas. three aneurysms were found. thirty-one mras were normal. we find m u to be a valuable adjunct to routine mr imaging in the evaluation of pediatric patients with potential cerebrovascular disease. it demonstrates a spectrum of pathology, is noninvasive, and allows for serial follow-up examinations. angiography in pediatric cerebrovascular disease p . thalamic change in acute encephalopathy of adult rats. twelve weeks after grafting, clinical and histological studies were performed. we developed a protocol for evaluating functional deficits that follow spinal cord injury in the rat. the survival, growth, differentiation, and parenchymal integration of the graft were documented histologically on semi-thin section. animals that received the transplants demonstrated qualitative and quantitative improvements in several parameters of locomotion. donor tissue integrated most often with the host spinal cord at interfaces with host gray matter; however, some implants also exhibited sites of fusion with damaged host white matter. we suggest embryonic rat spinal cord transplantation may be a useful treatment of spinal cord injury and a possible therapeutic strategy in human spinal cord injury and amyotrophic lateral sclerosis. the basic neuropathophysiology of hemineglect after unilateral cerebral lesions is still not clear. one theory holds that degraded perceptual processing occurs in the damaged hemisphere due to intrahemispheric deficits. another holds interhemispheric interaction at fault, with the intact hemisphere actively inhibiting spatial cognitive processes in the damaged one. we tested adult macaca fascicuhris with acute neglect on a task in which the whole visual surround was restricted to degrees from central fixation, and a second in which an opaque lens occluded the eye either ipsilateral (ipsi) or contralateral (contra) to the lesion. using paired t tests, in the first task there were no differences in reaction time to the ipsi and contralesional hemifields. in the second, there was no change in extent of the ipsilesional field (obtained with the contralesional eye occluded), as compared to its extent without occlusion. the contralesional field, however, improved significantly ( p < . ) with the ipsilesional eye occluded. since reducing sensory input to both hemispheres leads to no worsening of hemineglect, but reducing sensory input to the intact hemisphere alone leads to improvement of hemineglect, we conclude that adverse interhemispheric interactions play a major role in the pathophysiology of hemineglect. we assessed the sensitivity and applicability of a new, cornbined cognitive and mood screening battery for multiple sclerosis (ms). sixty consecutive, untreated clinically active ms patients, each relapsing-remitting and chronic progressive, underwent the battery and head mri upon entering concurrent treatment trials. the battery combines the faust-fogel brief cognitive screen and visual analogue dysphoria scale, both previously validated in other neurological diseases. cognitive domains tested were immediate and delayed sentence and word-pair recall, verbal fluency, and conflicting response suppression. patients marked ''usual mood" along a "happy-sad" cartoon continuum. relapsing patients were program and abstracts, american neurological association younger ( . vs . yr mean), with shorter ms durations ( . vs . yr), and had lower kurtzke disability scores ( . vs . ). modified qualitative mri grading (lesion burden, confluence, localization) was compared. half as many relapsing patients ( % vs %) scored ''abnormal'' cognitively, despite similar "sadness" rates ( % vs %). subjective dys-~ phoria in both groups correlated with denser periventricular lesion burdens. the battery was well tolerated and easily administered within minutes without special equipment. this combined cognitive and mood screening battery is sensitive and convenient for clinically active ms. alternate forms of the battery are needed for repeatability. questionnaires may be reliable and valid supplements to laboratory tests for brain-damaged patients, as they can be applied to situations for which laboratory testing is not possible. we investigated the usefulness of informant-based data in alzheimer's disease (ad) by comparing caregivers' subjective evaluations of probable a d patients' performance on an abbreviated version of the memory self-report questionnaire to objective evaluations derived from an extensive battery of neuropsychological tests and to clinicians' evaluations. similar information was obtained from healthy agematched controls. caregivers' subjective appraisals of patients' memory correlated significantly with objective measures of secondary memory, with all cognitive variables, measures of activities of daily living, and clinicians' evaluations of dementia staging. scores were independent of clinical indicators of depression. the abbreviated memory questionnaire showed good reliability, internal consistency, and external validity. its positive predictive value is . and its negative predictive value is close to %. results suggest that ( ) informant-based questionnaires may be useful for obtaining valid information on cognitive ability outside of laboratory settings; ( ) the scale reflected more than just memory functions; and ( ) the scale may be promising for screening cognitive difficulties in epidemiological or clinical settings. although neglect along the horizontal dimensions of extrapersonal space is well recognized, there are only a limited number of observations documenting neglect along the vertical and radial spatial dimensions. we report an investigation of neglect along the principal dimensions of extrapersonal space in a patient with bilateral mesial temporo-occipital infarctions. neglect was assessed by asking the patient and controls to bisect lines of lengths oriented in directions with respect to the body: horizontal, vertical, and radial. our patient showed significant neglect of upper vertical and far radial space, as well as neglect of left hemispace. his line bisection errors were consistently in a direction opposite the slight directional biases shown by controls for all line orientations ( p < . ). the magnitude of the patient's bisection errors increased by moving the lines toward the neglected sectors of -dimensional space. neglect of upper vertical and far radial space was also evident on line cancellation tasks. our results suggest that following focal brain injury, neglect may be observed along all dimensions of extrapersonal space. these findings provide further empirical support for functional specialization within inferior and mesial temporooccipital regions for attending to upper vertical and far visual space (previc, ) . p . posterior cortical atrophy: degenerative disease with primary visuospatial and visuosemantic deficits a. kertesz, m . polk, and a. kirk, london, ontario, and saskatoon, saskatchewan, canada posterior cortical atrophy is a recent, and heidenhahn's disease is an old, label for a miscellaneous group of patients with imaging or pathological and clinical evidence of visuocognitive deficits and cortical atrophy localized to the posterior cortex. the extent of this cortical localization and the nature of the pathological findings are not fully agreed upon, but spongiform degeneration and alzheimer pathology have been described. detailed examination of patients who are representative of the problem and have uniquely specific deficits is presented. one patient had visual associative agnosia, prosopagnosia, and transcortical sensory aphasia. lexicosemantic experiments of categorization, word retrieval, and comprehension of auditory and visual stimuli showed a specific impairment of visuoverbal semantics. a striking preservation of phonological, orthographic and visual structural input, and intercategory dissociations was demonstrated. consistency of errors argued for specific loss of semantic knowledge. another patient with apraxia, primary visuospatial deficit, agraphia, and amnesia at the beginning had predominantly right-sided posterior cortical atrophy, demonstrating further fractionation of the entity and the striking specificity of visuospatial function. the behavioral specification of degenerative disease is clinically and theoretically important. permanent neurological deficits after ischemic stroke are mainly determined by the location and size of the infarct. clinical recovery also depends on the functional state of adjacent brain tissue, where both neuronal loss and deactivation without gross morphological damage may affect flow and metabolism to a varying degree (g. mies et al, stroke ; - ) , and where the ability to respond to stimulation by appropriate neuronal recruitment may be impaired. therefore, degree of resting hypometabolism and of responsiveness to functional activation may provide a measure of prognosis. in patients (age . . yr) with aphasia consequent to ischemic stroke of the dominant hemisphere, regional cerebral metabolic rate of glucose (rcmrgi) was measured at rest and in of them also during spontaneous speech, using positron emission tomography (pet) of -(f )-fluoro- -deoxy-~-glucose (fdg). the pet study and a standardized neuropsychological test battery to assess the main aspects of language were performed around the fourteenth day after the stroke, and the language functions were assessed again to months later. performances in various dimensions of language weeks and to months after stroke were related to rcmrgl in topographically meaningful areas at rest and during activation using wilcoxon-rank program and abstracts, american neurological association sum test and multiple regression analysis. severity of aphasia was assessed by the token test, which showed a bimodal distribution to slight and severe, and a lower representation of moderate cases. global and all regional cmrgl at rest and during activation were significantly correlated to scores in token test at first and second examination, with the highest correlation coefficients ( - . to - . ) for broca's, wernicke's, and left temporoparietal regions. for performance after to months, the relationships were still significant with lower coefficients. verbal fluency also was correlated to kmrgi, but with lower coefficients that slightly increased for the recovery state. language performance at different stages in the course after ischemic stroke was significantly related (r = . for token test, r = . for verbal fluency). however, there exists a high variability in recovery that may be explained by stepwise regression of metabolic values. significant effects were observed only for cmrgl of the left hemisphere outside the infarct (partial r' = . ) at rest and for cmrgl within the infarct ( . ), the contralat-era mirror region ( . ), and broca's region ( . ) during activation, with a sum of all partial weight factors of . at rest and . during activation. our results furnish indicators for recovery of aphasia: the resting metabolism of the left hemisphere outside the infarct, and the activated metabolism in residual tissue within the infarct and in languagerelated areas. although the hemispheric metabolism at rest might be related to neuronal loss and thereby to the brain's reserve capacity, the extent of metabolic activation indicates neuronal recruitment and the capability of neuronal networks for functional recovery. heparin therapy for acute myocardial infarction: the timi-i pilot and randomized trial combined experience m . a. sloan, t . r. price, m . l. tevrin, and s. forman for the timi investigators, baltimore, m d of , myocardial infarction (mi) patients treated with rt-pa and heparin, ( . %) developed ischemic cerebral infarcts (ci). all ci patients had detailed neurological evaluations and ( %) had c t scans. age range was to years (mean yr), were male, and were caucasian. electrocardiographic location of mi was anterior in ( %) and nonanterior in ( %). six cis occurred within hours; between and hours; between and hours; between and hours; during the second week; and others distributed over the weeks after study entry. six of cis did not involve cerebral cortex; ( %) had multiple cis. of cis thought to be embolic in origin, had at least cardiac abnormality (mural clot, wall motion abnormality, aneurysm, or transient atrial fibrillation) known to be associated more specifically with embolism than just the diagnosis of myocardial infarction. eight of ( %) with ct scans had hemorrhagic conversion of varying degrees. the time of occurrence and sites of ci after rt-pa and heparin therapy for acute mi are similar to those reported in the prethrombolytic area. nancy futrell andjeanne m. riddle, detroit, m i photochemical irradiation of the carotid artery of rats has been used to induce endothelial damage, producing a nonocc h i v e thrombus (that apparently embolizes spontaneously) thrombi and emboli and multiple cerebral infarcts. evidence for embolism generally has a presumptive component. to document further that cerebral infarcts in this model are indeed due to embolism, we studied the ultrastructure of the carotid thrombi and the presumed cerebral emboli using scanning and transmission electron microscopy (sem, tem). the right carotid artery of wistar rats was irradiated with a laser ( nm, mw/cm , min) following the injection of the photosensitizing dye photofrin , . mgikg. rats were sacrificed from to hours later. endothelial damage with formation of a fragmenting thrombus, composed mainly of platelets and erythrocytes (with no fibrin in most areas), was present in the carotid arteries of all rats by sem. sem was done on cerebral vessels, containing peripheral blood elements, with single ( ) and aggregated ( ) platelets (causing occlusion in ), single ( ) and aggregated ( ) erythrocytes (without occlusion), and single ( ) and aggregated ( ) leukocytes (without occlusion). tem demonstrated that the platelet aggregates did not adhere to the cerebral endothelium. the endothelial surface of all cerebral vessels was normal, which provided additional evidence that the mechanism of cerebral infarction in this model is embolism. model of repetitive ischemia: this effect is significantly enhanced when combined with mild hypothermia ashfaq shuaib and elisabeth sechocka, saskatoon, saskatchewan. canada there is considerable evidence that glutamate release resulting in activation of postsynaptic receptors (especially nmethyhaspartate) is a major mechanism of ischemic neuronal injury. in vivo experiments have shown that a more severe release of glutamate may be responsible for the excessive damage seen with repeated ischemic insults. we have shown that in cell cultures the effect of brief repeated insults is more severe than a single insult of similar duration. in the present study, we tested the protective effects of cgs- in a cell culture model of single ischemic and multiple-insult paradigm. in the multiple-insult paradigm, in some cultures cgs- was combined with mild hypothermia to see if this would offer additional protection. cgs- offered a dose-dependent protection in cell cultures exposed to a single ischemic insult. cgs- was protective to cultures exposed to repeated ischemic insults. the protective effects were enhanced significantly when they were combined with hypothermia, resulting in almost complete protection of the cultures. the combination of therapies appears to be a valuable strategy in neuronal protection during cerebral ischemia. toby i. gropen, i . prohovnik, t . k. tatemirhi, z. sharif; and m. hirano, new york, n y although a rare syndrome, mitochondria encephalomyopathy, lactic acidosis, and stroke (melas) may offer a unique insight into stroke mechanisms. we report novel observations in a patient with melas studied with serial and quantitative cerebral perfusion after stroke using """tc-ceretec spect and ' ixe rcbf. a -year-old man with melas presented with left-sided headache, generalized seizures, fluent aphasia, and right hemianopia. serial ct and mri showed infarction of the posterior left hemisphere in a multiterritorial distribution. spect performed days after stroke showed to % greater flow in the infarct than in normal brain, which reversed days after stroke. quantitative rcbf (m isi, reflecting mostly gray matter), when corpatients died. we recommend ct evaluation in all patients who have a seizure or lose consciousness during the peripar-tum period. despite intensive management, mortality is high. seizures should not be attributed to eclampsia without careful neurological assessment. when prenatal care is sought, women should be counseled about the dangers of cocaine to themselves as well as to their babies. changes in circulating blood volume following stephan a. mayer, matthew e. fink, laura lenniban, louise m. klebanoff; auis beckford, lsak prohounik, william young, and robert a. solomon, new york, n y reduction of blood volume (bv) has been implicated as a risk factor for delayed cerebral ischemia (dci) due to vasospasm after aneurysmal subarachnoid hemorrhage (sah). volume expansion guided by target filling pressures has gained popularity as a means of preventing or reversing dci; however, the adequacy of central venous pressure (cvp) as a reflection of bv in this setting remains unclear. we measured bv and cvp concurrently in patients ( males, females; mean age yr) day after craniotomy (mean . days after sah) and an average of . days later. the mean bv (mllkg) measured using chromium '-labeled red blood cells (rbcs) fell from . to . (normal range - ), a reduction of % ( p = . , paired student's t test). despite this, mean cvp (mm hg) remained unchanged ( . vs . ). similar reductions of plasma volume ( %) and rbc volume ( %) accounted for no change in mean hematocrit ( . vs . ). bv fell . % among grade iiiliv patients (n = ) compared to . % among grade / patients (n = ). a moderate correlation between bv and cvp ( r = . , p = . ) was found only with the first set of measurements. time-related alterations in venous capacitance, myocardial contractility, or systemic vascular resistance may explain our findings. axel rosengart, louis r. caplan, michael s. pessin, atherostenosis of the extracranial vertebral artery (ec-va) has rarely been studied systematically in series of patients with acute vertebrobasilar strokes or transient ischemic attacks. we identified by conventional angiography and neuroimaging (ct, mri, ultrasound, mr angiography) patients with ec-va disease among patients with posterior circulation ischemia. patients with cardiac sources of emboli were excluded. the probable etiologic mechanisms were: group a: vertebral artery origin (vao) atherostenosis with embolism- patients; group b: vao atherostenosis with hemodynamic spells- patients; group c: patient with vao atherostenosis and both intra-arterial embolism and hernodynamic spells; group d: ec-va dissection- patients ( unilateral, bilateral); patient had perioperative compromise of the ec-va with presumed intra-arterial embolism; group e: vao disease in addition to other distal vascular lesions- patients ( with intracranial va and with basilar artery [baf occlusive disease). ec-va disease is not always benign. vao atherostenosis and dissection of the ec-va are sources of intra-arterial emboli. hemodynamicrelated ischemia occurs with bilateral and unilateral va disease but is often transient. vao atherostenosis is often accompanied by severe occlusive disease of the intracranial va and ba. program and abstracts, american neurological association sebastian e. ameriso, vicky l. y. wong, andvas gruber, hidemi ishii, and mark fisher, los angeles and la jolla, c a , and kanagawa, japan hemostasis abnormalities are associated with ischemic stroke. these changes typically are demonstrated in antecubital venous blood samples and may not necessarily represent changes within the vasculature of the brain. the purpose of this study was to identify potential differences in hemostatic profile from samples of cranial versus noncranial venous sites in patients with acute ischemic stroke. eight patients were studied within days of acute brain infarction. some patients were studied on separate days. blood was drawn from the external jugular vein and immediately thereafter from an antecubital vein without the use of tourniquet. we measured hematocrit, leukocyte count, platelet count, fibrin d-dimer (cross-linked fibrin fragment), plasminogen activator inhibitor- (pai- , an important antifibrinolytic protein), and anticoagulant proteins thrombomodulin and activated protein c. a jugular-to-antecubital ratio was calculated for each paired blood sampling. thirteen paired samples were obtained from the eight patients. external jugular-to-antecubital ratios (mean to-antecubitat ratio for pal was significantly different from ( p < . ), with higher concentrations in jugular samples. in conclusion, levels of hemostatic proteins measured from cranial venous blood may differ from antecubital samples in patients with acute ischemic stroke. in animal models of transient cerebral ischemia, the effects of repetitive insults are more severe than a single ischemic episode of similar duration. we used the cell culture model of ischemia to determine if the effects of repetitive ischemia are similarly more severe in this model of ischemia. for cell culture, we used fetal mice cortical astrocytic and postnatal cerebellar (glutamatergic) granular neurons and cerebral gamma-aminobutyric acid (gaba)ergic cells. lactic dehydrogenase (ldh) (activity per gram protein) release in the medium was used as a measure of cellular damage. compared to a single insult, there was a large increase in ldh release during repetitive ischemia in astrocytes ( vs , p < . ) and granular cells ( vs , p < . ) (highly significant) and a modest (but significant) increase in the cortical neurons ( . vs . p = . ). the demonstration that repetitive ischemia produces more severe damage in cell culture would suggest that the mechanisms are not predominantly vascular. cell culture could prove useful to study the mechanisms of neuronal damage with repetitive ischemia. we studied the spontaneous recovery of neurological function after acute ischemic stroke using a standardized stroke nih stroke scale scale ( n i h stroke scale) to assess the extent of improvement, differences in stroke types, and early predictors of later outcome. we performed serial neurological assessments on admission; , , and hours after admission; and to days and > days after admission. twenty-six patients had presumed embolic occlusion of the middle cerebral artery (mca) and had a clinical diagnosis of lacune. admission score was better in the lacune group compared to the mca group. the mean scores for all patients improved by the to -day and the > -day examination, but the degree of improvement was greater in the mca group than in the lacune group at > days ( p < . ). the degree of change at to days correlated with the change in score at hours ( r = . , p < . ) and hours ( r = . , p < . ). most patients improve after acute ischemic stroke, but to variable degrees and at different rates. david w. desmond, thomas k. tatemichi, miguel figueroa, dew'itt t . cross, and yaakov stern, new yovk, n y to investigate the effects of lacunar infarction (li) on cognitive function, we examined li patients months after stroke (age = . ? . yr; education = . . yr) and stroke-free nondemented control subjects (age = . k . yr; education = . k . yr) with a battery of neuropsychological tests. li was defined as a presenting infarct of cc and a mean volume of any additional subcortical infarctions of cc on ct scan. using multiple regression analyses, with significance set at p < . to minimize the risk of type i error, we considered the role of li as a correlate of performance in multiple cognitive domains. controlling for the effects of demographic factors, vascular risk factors, alcohol use, and depression within the multivariate models, li was a significant independent correlate of deficits in memory (( = -. , p = . ), verbal (p = -. , p = . ), visuospatial (p = -. , p < .oool), abstract reasoning (p = -. , p = . ), and attentional skills (p = -. , p < . ). we further investigated the effects of infarct number, volume, and location, as well as atrophy, on global cognitive function within the li group. the only significant independent correlate of global cognitive performance was a preponderance of left-hemisphere infarctions (p = -. , p = , ). these results suggest that li may produce dysfunction in multiple cognitive domains, particularly when the left hemisphere is differentially involved. p . increased intracranial atherosclerotic stroke in hispanics and blacks from northern manhattan ralph l. sacco, christina zamanillo, t . shi, andj. p. mobr, new york, ny intracranial atherosclerosis has been found to be more frequent in blacks compared to whites, whereas hispanics have rarely been characterized. among consecutive patients from northern manhattan over age hospitalized at the presbyterian hospital from to , cerebral infarction occurred in whites, blacks, and hispanics. all patients had at least one c t scan, % had duplex doppler, % transcranial doppler, and % angiography. strokes were classified as atherosclerotic (ath), cardioembolism, lacunar, and as infarcts of undetermined cause. ath was further subdivided into extracranial (eath) or intracranial (iath) . overall, the frequency of ath was similar in the three racelethnic groups (white , black ' , hispanic ) . the distribution of the atherosclerosis, however, was different in whites compared to blacks and hispanics. whites had more eath stroke than blacks and hispanics (white %, black % , hispanic lo%), while iath was similar in blacks and hispanics and greater than in whites (white , black , hispanic %). nonwhites have more iath stroke than whites. the similarity in the distribution of atherosclerosis between blacks and hispanics argues for shared environmental risk factors, rather than genetic differences. ethnic differences in stroke risk factors may help explain differences in infarct subtype. we studied mild to moderate alzheimer's disease (ad) patients with a series of " water bolus positron emission tomographic (pet) activation studies, and compared them to similar studies in age-matched normal controls. for each group, pet images were mapped onto the subjects' mri scan, and results of a particular activation condition were averaged across the group. naming a series of pictures (line drawings of animals) minus counting abstract designs as a baseline produced strong activation of the anterior cingulate gyrus only in the ad group. silent reading of words minus viewing a baseline series of "xs" similarly showed strong activation of the anterior cingulate gyms in the ad subjects but not the normals. naming block (activation condition) of % unnamed pictures, minus a second block (baseline) of easily named pictures, demonstrated much greater cingulate activation in the ad patients, for naming of the more difficult pictures. we conclude that this cingulate activation may reflect the greater involvement of an attentional network (of which the anterior cingulate is a part) in tasks requiring a higher degree of "mental work" on the part of ad patients. dementia in alzheimer's disease j. w. pettegrew, k. panchalingam, w. e. klunk, and r. j alzheimer's disease (ad) predominantly affects the brain, resulting in the loss of multiple cognitive abilities. some studies suggest the membranes of peripheral cells are involved in the disease. to investigate erythrocyte membrane molecular dynamics in ad patients and age-matched controls, we investigated erythrocyte membrane molecular motion at the surface (fluorescamine), aqueous-hydrocarbon interface (dppe-ans), and hydrocarbon core ( j-as; ppc-dph) by steady-state fluorescence anisotropy measurements of probable ad patients ( males; females) and ( males; females) age-matched controls. cognitive function was assessed by the mini-mental, mattis, and blessed scales. we found that intergroup comparisons revealed decreased motion at the surface ( p = . ) and aqueous-hydrocarbon interface ( p = . ) and increased motion in the hydrocarbon core ( p = . ) of the moderately to severely impaired ad patients compared to the controls. in the ad patients, there were significant correlations between decreasing membrane surface motion and worsening blessed scores (males p = . ; r = . ; femalesp = . ; r = . ). these findings suggest that molecules are being produced in the brain of ad patients that gain access to the circulation. these molecules insert into the erythrocyte membrane and secondarily alter erythrocyte membrane molecular motion. the production of these molecules correlates with the dementia and could contribute to the molecular pathophysiology of the disease. parkinson's disease (pd) and alzheimer's disease (ad) are common disorders of old age and may therefore coexist. the prognosis in demented pd patients is poor and early recognition of such cases is therefore desirable. the objective of this study was to identify characteristics that distinguish pd + ad from pd patients during early stage. all patients were clinically evaluated over a -year period . clinical diagnosis of dementia was made only when unequivocal clinical evidence of progressive decline in memory and cognitive function was documented, and pathological diagnosis of ad and pd was made using standard criteria. twentysix patients who had only pd or pd + ad were identified; had no dementia and at autopsy had pd. six patients had clinical evidence of parkinsonism and dementia and at autopsy had distinct pathological findings-pd and ad. these cases could be classified as having simultaneous or sequential evolution of pd + ad. those with sequential onset had pd before age years but were inexplicably functionally disabled early on, whereas those with simultaneous onset manifested pd after age years. pd + ad patients had rapid disease progression, shorter survival, poorer drug response, and more side effects of levodopa than pd patients. to study the prevalence ofwhite matter lesions in the general elderly population, and to investigate whether white matter lesions were relatively frequent in subjects with classic vascular risk factors and with hemostatic risk factors, magnetic resonance scans were obtained of participants, aged to years, of the rotterdam elderly study. the subjects for the imaging study were a random sample from the general population, stratified by age and gender. t -weighted images were obtained in the axial plane. white matter lesions were considered present when moderate or severe periventricular hyperintensities or when more than small focal lesions or focal confluent lesions were found. overall, % of subjects had white matter lesions. the prevalence and severity of le-program and abstracts, american neurological association sions increased with age. history of stroke or myocardial infarction, presence of peripheral arterial disease, factor viic activity, and fibrinogen level were each significantly and independently associated with the presence of white matter lesions. significant relations with actual systolic as well as diastolic blood pressure, with a history of hypertension, and with plasma cholesterol were observed only for subjects between and years. this study suggests that white matter lesions in the elderly may be related not only to the classic cardiovascular risk factors. but also to hemostatic factors. joan m. swearer, paula nelligan, hanno muelher, beatrice woodward, and david drachman, worcester, ma although behavioral disturbances occur frequently in alzheimer's disease and other dementing disorders, little is known about the factors that predict their development or predispose to their occurrence. in the present study we examined sets of possible predictive/predisposing factors retrospectively for behavioral disturbances in mildly to severely demented, community-dwelling patients. the factors examined included: individual distinguishing features (age, gender, age of onset, premorbid personality traits, prior psychiatric history) and dementia severity (dependence in activities of daily living [adls) and self-care, duration of dementia, global disease severity). spearman correlations and t tests were used to assess the relative influence of these factors on the occurrence of types of aberrant behaviors: aggressive behaviors, disordered ideation, and motor abnormalities. forty percent of the patients exhibited aggressive behaviors, % exhibited disordered ideation, and % had motor abnormalities. neither a prior history of psychiatric disorders nor premorbid personality traits were associated with the occurrence of the target behaviors. dependence in adls and self-care and greater global severity were associated ( p < . ) with the frequency and severity of aggressive behaviors, disordered ideation, and motor abnormalities. these results suggest that severity of dementia is a consistent and reliable factor in the development of aberrant behaviors, whereas preexisting personality traits are not. dementia of the alzheimer t y p e w. j. burke, a. ranno, w. h . roccafrte, s. p. wengel. b. l. bayer, and n . k. willcockson, omaha, ne l-deprenyl is an irreversible inhibitor of mao-b that has been reported to cause modest improvements in short-term memory and behavioral symptoms in persons with dementia of the alzheimer type (dat). thirty-eight subjects meeting research criteria for mild d a t were enrolled in a placebo-controlled, double-blind trial of r-deprenyl at a dose of mg twice a day. subjects underwent extensive clinical and neuropsychological assessments at entry, and at and months. after months, subjects taking both l-deprenyl and placebo showed a significant decline in their scores on the mini-mental state examination, the clinical dementia rating (cdr) scale, and the sum-of-boxes score derived from the cdr. when the change in scores on these clinical measures was examined across the groups, there was no significant difference. there were no significant differences within or between groups on several behavioral measures including the brief psychiatric rating scale and the cornell rating scale for depression in dementia. neuropsychological testing demonstrated no significant differences berween groups based on mean score change. l-deprenyl did not affect cognition or behavioral symptoms of dat in this -month study. k. marder, m-x. tang, r. ottman, l. cote, y. stern, and r. mayeux, new york, n y the etiology of dementia in parkinson's disease (pd) is probably multifactorial but there may be a shared susceptibility for p d and alzheimer's disease (ad). reliable risk factor interviews were conducted with informants of nondemented p d patients (pd-d) and demented p d patients (pd + d) enrolled in a longitudinal community study of pd. p d + d were older ( . yr) than pd-d ( . yr) and had later age at onset of motor signs ( . yr) than pd-d ( . yr) ( p < , ). the frequency of smoking, alcohol use, head injury, and family history (fh) of pd did not differ but fh of ad was significantly more frequent in the pd + d group (or . , ci . - . ). using stepwise logistic regression, only age of onset of motor signs (or . ), education < years (or . ), and the interaction of age of onset of motor signs and fh of a d (or . ) were independent predictors of dementia in pd. to address variable years at risk for development of dementia, life table analysis revealed the cumulative risk of a d to age in first-degree relatives of p d + d was . , and . in pd-d relatives ( p < . ). cox proportional hazards analysis controlling for the differences in ages of the relatives of both groups yielded a rate ratio of . (ci . - . ) for the development of a d among p d + d compared to pd-d relatives. we conclude that a genetic susceptibility to a d may raise the risk for dementia in patients with pd. differentiated from alzheimer's disease? john c. mowis, elizabeth grant, rita canfield, eugene rubin, and daniel mckeel, jr, st louis. mo vascular dementia (vd) is believed to account for to % of all us cases of dementia; however, pathologically confirmed cases are quite rare. this discrepancy suggests that current diagnostic criteria lead to the clinical overdiagnosis of vd. twenty v d subjects (mean age . yr; men, women) were diagnosed solely on the basis of the presence of dementia, a history of stroke(s), and a documented relationship of stroke to onset andlor course of dementia; ischemic scores (is) and neuroradiographic findings were not used for diagnosis. compared with subjects (mean age . yr; men, women) with dementia of the alzheimer type (dat), there were no significant group differences for comparable clinical dementia rating stages of dementia for measures of language, activities of daily living, or general cognition. the vd group scored significantly higher than the dat group on the modified is (f [ , ] = . , p < , ). all autopsied d a t subjects had verified alzheimer's disease (ad); also had cerebral infarctions. the autopsied v d subjects had , , and cc of brain tissue affected by stroke; ( cc) also satisfied histological criteria for ad. we conclude that ( ) the clinical features of vd and a d overlap considerably; ( ) diagnostic criteria based on the temporal association of stroke with dementia may have predictive value for vd; and ( ) the frequent coexistence of a d and strokes indicates that refinement of criteria is needed to distinguish "mixed" and "pure" vd. clinicopathological correlation remains essential for any study of putative vd. left-handedness has been proposed as a marker for decreased survival in the general population, but possible effects of handedness on longevity in alzheimer's disease (ad) have not been examined. we hypothesized that left-handed ad patients would evince more rapid deterioration and therefore die at an earlier age than right-handed patients. subjects were demented patients consecutively confirmed at autopsy to meet nincds-adrda criteria for "definite" ad. handedness was determined from structured interviews with primary caregivers and validated for most subjects with the edinburgh inventory of handedness. age at onset of dementia symptoms retrospectively determined by caregivers was used to calculate the duration of illness at the time of death. because of reported gender differences with regard to longevity, we first partialled out effects of gender before using hierarchical regression procedures to test the hypothesis. four of men and of women with definite ad were left-handed. the mean age at onset did not differ significantly between handedness groups (f [ l,loo] = . ), but the mean duration of symptoms ( alterations in the optical properties of brain can be used to detect pathological changes in patients with alzheimer's disease (ad). using time-resolved spectroscopy (trs) and phase-modulation spectroscopy (pms), we measured the absorption (ua) coefficient, scattering (us) coefficient, and mean photon pathlength (pl) of red light directed through the base of the frontal lobes of patients with ad and age-matched control subjects. the measured values and the asymmetry index (ai) (an indication of the symmetry of the measurements between the left and right side of the brain) were correlated with the severity of disease as determined by mini-mental state score. there were significant differences between the ad and control group for ua, us, pl, and the standard deviation of ai. there was no correlation between the mms score and ua, us, or pl. however, the highest asymmetry index values were seen in moderately impaired patients , which suggests that the asymmetrical nature of the pathological process detected by optical spectroscopy is most marked during this stage of the illness. this noninvasive technique may provide a convenient method to detect and monitor the pathological changes that occur in the brain of patients with ad. disease p . memory impairment in very mild alzheimer's a memory impairment is often the earliest indication of alzheimer's disease (ad). we investigated components of disease learning and recall to determine which aspect of memory function is impaired the earliest in incipient ad. using the mayo clinic alzheimer's disease patient registry, which is a longitudinal prospective project on ad and normal aging, we identified patients with very mild ad (i.e., with a mini-mental state score of or greater) and age-and sex-matched controls. we assessed performance on memory measures: the rey auditory verbal learning test and the buschke free and cued selective reminding test (fcsrt). the parameters evaluated included a measure of acquisition, total learning over trials (tl), and delayed recall (dr). on the fcsrt, an index of facilitation of performance with semantic cues (sc) was assessed. results indicated that all indices, tl., dr, and sc, were capable of separating the mild ad group from the controls ( p < , ). using a linear discriminant analysis with stepwise variable entry, the measure that assessed the patient's ability to use semantic cues (sc) was the most sensitive parameter for separating the groups ( f = . , p < . ), and the acquisition parameter (tl) was also useful at adding some additional predictive power (f = . , p < . ). the delayed recall measure, however, did not add anything to the previous measures. it appears that very early ad can be detected using appropriately structured memory tasks, and these procedures can be helpful in identifying at-risk individuals. alzheimer's disease (ad) has an insidious onset that is difficult to date reliably. we developed a standardized interview to provide objective criteria for dating the onset of different symptoms (memory complainr, performance problems, language deficits, disorientation, depression, behavior problems, and psychosis), yielding an estimated disease onset date. inrerrater reliability (icc = . ;p < , ) and interinformant reliability (icc = ; p < . ) for the onset of first symptom was high. interrater agreement for the order in which symptoms appeared was high (icc = . - . ) as was interinformant reliability for all symptoms except memory complaint. the interview was administered to patients with ad. mean estimate duration of illness was . years k . years and correlated significanrly with problems in instrumental activities of daily living. sixty-six percent had memory complaint and % had performance problems as their initial symptom. this technique provides a reliable characterization of disease onset. longitudinal studies will determine if particular onset symptoms differentially predict disease progression. the purpose of this study was to determine whether there is an excess of white matter disease (wmd) in alzheimer's disease (ad). brun and englund ( ) reported an excess of wmd in brains of patients with ad vs age-matched controls. there have been reports both confirming (bowen et al, ; fazekas et al, ) and refuting (leys, ) these findings using ct and mri in patients with clinically diagnosed ad. postmortem t -weighted mri scans and program and abstracts, american neurological association neuropathology were graded on brains of pathologically confirmed ad subjects and brains of age-matched neuropathologically normal controls. white matter lesions were scored on a to scale (none, mild, moderate, severe) separately for periventricular (pvl) and deep white matter (dwm) areas in mri scans and lux fast blue (lfb)-stained brain sections. correlations between mri and neuropathology were good ( r = . for pvl, r = . for dwm). pvl scores were higher in ad than in normal subjects on mri (ad: . l . vs controls: . rfr . ; p < . ). on pathology the difference in scores did not reach significance (ad: . . vs controls: . * . ; p = . ). similarly, dwm scores were higher in ad subjects than normals on mri, but not neuropathology. in conclusion, ad brains have a significant excess of wmd on mri compared to controls. although the pvl and dwm scores for pathological sections are not different in the groups, mri is much more sensitive than lfb-stained sections for wmd. thirteen autopsy cases of progressive supranuclear palsy (psp) were investigated for clinical-neuropathological correlations and heterogeneity. we reviewed clinical records of men and women aged to years (mean age yr) with disease duration ranging from to years. most patients had classic features of psp including ophthalmoplegia, postural instability, and extrapyramidal signs. dementia was eventually observed in of the patients ( %). six of patients ( %) on whom adequate initial documentation was available presented with memory loss or behavior change. five of the patients ( %), including with an initial presentation of memory loss, were diagnosed clinically as having alzheimer's disease (ad) rather than psp; neuropathological diagnoses in these cases varied: i had combined ad-psp; had ad-psp combined with parkinson's disease (pd) changes; had psp-pd; and had "pure" psp. the patients with concomitant pd changes showed lewy bodies in the substantia nigra, locus coeruleus, nucleus basalis, and neocortex. the remaining patients were clinically diagnosed as having psp; neuropathological diagnoses in these cases included with "pure" psp and with psp that also met neuropathological criteria for ad (psp-ad). these findings emphasize the clinical and neuropathological heterogeneity in psp. the neuropsychological battery developed for the consortium to establish a registry for alzheimer's disease (cerad) is currently used in many research studies to index the cognitive impairments of alzheimer's disease. in spite of its widespread use, normative informarion on the battery, important for interpretation of performance, has not been available. we report norms for the cerad battery based on a large sample of elderly control subjects (n = ; white men and women; ages - yr) enrolled in the national study of cerad. performance on the neuropsychological measures was examined separately for subjects with high ( yr) and low (< yr) education. distribution of scores and basic descriptive information (means and sd) for each measure were determined. significant age and sex effects were observed on most cognitive measures in the highly educated group. in contrast, no significant age effects were observed in the low education group. effect of sex was not explored in this group due to the limited sample size (n = ). further exploration of cerad performance in normal controls from underrepresented groups including minorities, residents of rural communities, and individuals with low education is in progress. intraneuronal inclusions of cytoskeletal proteins appear in several neurological diseases; for example, the neurofibrillary tangles of alzheimer's disease contain a cytoskeletal protein, tau. because the previously described slowing of axonal transport in aged animals might lead to accumulation of cytoskeletal proteins in nerve-cell bodies and axons, we assessed the abundance of major cytoskeletal proteins in brain tracts of rats at age months or months. immunoassay was performed with monoclonal antibodies to alpha and beta tubulin and to nf-l (the core neurofilament protein) by published methods. samples were dissected in a standardized fashion and -mrn pieces of the following tracts were assayed: optic nerve, corticospinal tract (medulla), superior cerebellar peduncle, l dorsal root, and l ventral root. between months and months, the nf-l content approximately doubled in each brain site. tubulin substantially increased at of aged rats all sites except the fimbria-fornix. in contrast, tubulin did not change in the spinal roots. nf-l increased slightly in the ventral but not the dorsal root. this tendency of senescent brain neurons to accumulate cytoskeletal proteins in their axoplasm may predispose them to formation of intraneuronal inclusions in various degenerative diseases. we performed a prospective study of preoperative magnetic resonance imaging (mri) in consecutive patients with intractable partial epilepsy who underwent a stereotactic resection of an extrahippocampal temporal lobe foreign-tissue lesion, "lesionectomy," between june and january . interpretation of the mri studies was performed by an investigator blinded to the presurgical evaluation, surgical outcome, and pathology. hippocampal formation (hf) atrophy was assessed using mri-based volumetry (n = ) and visual grading of the h f (n = ). mri-detected hf atrophy has been shown to be a reliable marker of moderate to severe mesial temporal sclerosis (mts) (cascino gd, et al, ann neurol ; : - evidence from experimental animals indicates that endogenously produced platelet-derived growth factor (pdgf) is an important regulator of glial proliferation and differentiation. because of the striking degree of glial proliferation in chronic epilepsy, we sought to determine whether cultured glia from human epilepsy tissue would be responsive to pdgf. the effects of pdgf on dna synthesis, proliferation, and relative distribution of a b (+) glia were studied in a cell culture derived from temporal lobe white matter of adult epilepsy lobectomy tissue. by immunocytochemistry, glial fibrillary acidic protein (gfap) was detectable in % of cells in untreated or -day pdgf-treated ( ng/ml) cultures, which confirmed their astrocytic nature. in contrast, a b ( +) cells increased from to % in untreated cultures to % after pdgf treatment, which suggested that type astrocytes (a b [ + , gfap[ +]) had been elicited. dna synthesis of cells resembling oligodendrocyte-type astrocyte ( - a) progenitors occurred within hours after program and abstracts, american neurological association pdgf treatment as evidenced by nuclear incorporation of brdu in bipolar a b ( +) cells. these studies demonstrate that expansion of adult human gfap( +) astrocyte populations is sensitive to regulation by pdgf. further, these data imply the existence of pdgf-responsive - a progenitor cells in astrocyte-rich cultures derived from human epilepsy tissue. ( we have recorded vagal and esophageal-evoked potentials after electrical (e) and balloon (b) stimulation in epileptic patients who had vagal stimulators for the control of intractable epilepsy and the results were compared with esophagealevoked potentials in healthy controls and diabetic patients. the vagal and esophageal-evoked potentials showed similar configurations with major positive and negative potentials. the amplitudes of the responses habituated rapidly over trials at per second up to per seconds. latencies were shorter from the upper esophagus ( cm above lower esophageal sphinctereles]) cf. lower esophagus ( cm above les) yielding conduction velocities of to meters per second but conduction was significantly slower in the diabetics. the vagal-evoked potentials have validated the use of esophageal-evoked potentials as a practical method of assessment of the integrity and speed of conduction in vagal afferent pathways in man. ronald e. kramer and neil l. rosenberg, englewood. co seizure disorders were analyzed in patients in whom toluene was the sole or major drug of abuse. toluene abuse is increasing; therefore, physicians should gain experience with its neuropathological and ciinical sequelae. a retrospective chart review found patients meeting criteria. the average patient age was years; abuse onset averaged . years; abuse averaged . years; and patients were male. ten were daily, were weekly, and were intermittent users. seizures occurred in . one suffered a single generalized tonic-clonic seizure without recurrence and without treatment. his we characterized the clinical dose-response curves for relief of parkinsonism and production of dyskinesias as a function of plasma levodopa and - -methyldopa levels in patients with parkinson's disease (pd) and fluctuating responses to oral levodopa/carbidopa. dose response to graded intravenous levodopa was measured after overnight drug withdrawal on occasions, first after chronic, intermittent oral levodopa/ carbidopa and second after to days of continuous intravenous levodopa. continuous intravenous levodopa shifted the dyskinesia dose-response curve to the right, and reduced maximum dyskinesia activity, but did not significantly alter dose response for relief of parkinsonism. improvement in dyskinesia was apparent by the second day of continuous levodopa, during which ratios of plasma dopa/ - -methyldopa remained constant. our results support the hypothesis that relief of parkinsonism and production of dyskinesias occur by separate mechanisms. continuous dopamine-mimetic therapy should be sought as a therapeutic goal for advanced pd. dopa-responsive dystonia (drd) is a distinct subset of idiopathic dystonia with diurnal fl uctuation and a dramatically beneficial response to l-dopa. it has hitherto been considered an autosomal-dominant disease with reduced penetration (mckusick no. ) . we studied an arabic family of members with d r d spanning generations. we examined members and of their spouses. l-dopa was withheld for hours from patients in treatment. five family members had generalized dystonia with diurnal auctuation ( i male, in an arabic family females). dystonia started between the age of and years with gait difficulty and involvement of the legs. mri, eeg, evoked potentials, and screening for wilson's disease were negative. an excellent response to l-dopa was noted in all patients with continued long-term clinical stability for as long as years. the patients were the products of consanguineous marriages, and their siblings were normal. the patients were descendants of the same great-great-grandparents. this pedigree suggests an autosomal-recessive type of inheritance. we believe this is the first report of d r d with an autosomal-recessive type of inheritance. a. achiron, m . gornish, h . goldberg, i . ziv, r. djaldetti, y. zoldan, h. smka, and e. mekzmed, petah tiqva, israel freezing gait is an incapacitating symptom that occurs often in advanced parkinson's disease and also in other neurological disorders, eg., multiinfarct state, multisystem atrophies, and normotensive hydrocephalus. we evaluated, videotaped, and rated patients ( men, age k , - yr) who developed pure progressive freezing gait during . . , . - years. severity was mild in with sudden motor blocks mainly when confronted with obstacles; moderate in with gait arrests upon any attempt to initiate walking and changing direction, requiring a walking stick or partial external assistance; and severe in with total inability to start walking, requiring a walker, massive assistance, or a wheelchair. in all, freezing was associated with postural instability. they could mimic normal gait when seated or lying prone and could overcome arrests by the "walking over lines" maneuver. neurological examination was otherwise normal with no signs of dementia, parkinsonism, or pseudobulbar palsy. ischemic risk factors including ischemic heart disease, hypertension, and diabetes occurred in and previous strokes in . brain c t and mri were normal or showed mild cortical atrophy in and putative lacunae in only patients. none responded to levodopa or dopamine agonists. progressive pure freezing gait should be recognized as a separate nonparkinsonian neurological entity. it may be due to degenerative or ischemic non-nigral brainstem lesions. we describe patients with causalgia and dystonia, triggered by peripheral injuries in patients and occurring spontaneously in patients. the injury was often trivial. the mean age at presentation was . years. the legs were affected in patients, and the arm was affected in the remaining patients. all had burning pain, allodynia, and hyperpathia, along with vasomotor, sudomotor, and trophic changes. all developed typical dystonic muscle spasms in the affected part. the spasms typically were sustained, producing a fixed dystonic posture, in contrast to the mobile spasms characteristic of idiopathic torsion dystonia. dystonia always followed the causalgia and was painful. there was spread of the causalgia and of the dystonia from its initial site both in the affected limb and to other extremities, the latter in a hemiplegic, transverse, and triplegic distribution. all forms of conventional treatment failed to relieve either the pain or the dystonia. we suggest that functional changes in the corticobasal ganglia-thalamic system are responsible for this painful dystonic syndrome. program and abstracts, american neurological association holiday for parkinson's disease: a controlled clinical trial r. kurlan, c . m . tanner, c. g. goetz, j . sutton, p. carvey, c. deeley, l. cui, c. itvine, and m . mcdemzott, rochester, ny, chicago, il, and san jose, c a the efficacy and mechanisms of levodopa (ld) drug holiday for parkinson's disease (pd) remain controversial. we performed a double-blind, randomized study with advanced pd patients ( men, women; aged - yr) with entry criteria of inadequate response to ld plus dose-limiting ld-induced side effects (dyskinesias, hallucinations, and confusion). subjects were assigned to: ( ) % placebo for ld (complete drug holiday) or ( ) % ld and % placebo for ld ( % drug reduction) for days. after subsequent open-label ld dose optimization, subjects were followed to end point (defined as the time when entry criteria were again satisfied or a maximum of year). median survival time to end point was not significantly different for the complete drug holiday ( days) and % drug reduction ( days) groups ( p = ) . aspiration pneumonia occurred in complete drug holiday patients and no significant morbidity occurred with drug reduction. after a -mg dose of ld, clinical and pharmacological responses were no different before and after drug holiday ( p = . ) or reduction ( p = ). subject to the limitations of our small sample size, we conclude that complete drug holiday is associated with greater morbidity and confers no major advantage over % drug reduction. we found no evidence of significant alterations of pharmacokinetic or pharmacodynamic properties of ld after drug holiday or reduction. ( (pc) of the substantia nigra on t -weighted images. the narrowing of the pc signal has been attributed either to atrophy of the pc or to increased deposition of iron in this region. we have studied details of iron distribution in the midbrain of formalin-fixed human brains by scanning pixe analysis. three p d brains, juvenile pd brain, and control (amyotrophic lateral sclerosis) brains were studied. in the controls, the iron content of the pars reticulata (pr) was almost equal to that of the red nucleus (rn), but that of the pc was less than % of the pr. in parkinsonian brains, the iron content in the pc was significantly higher than in the controls. the iron content ratios of pc/pr and pc/rn in parkinsonian brains were significantly higher than in the controls. these findings suggest that iron deposition increases in the pc of parkinsonian brains. the difference in the pattern of iron content corresponds to the intensity profile pattern noted on mri. mri findings in parkinsonian patients may reflect a change in the iron distribution pattern. (jankovic and brin, nejm, ) . such resistance within exposures is not likely due to toxin antibody formation. of cd patients evaluated per protocol receiving or more botox tx under multichannel emg monitoring, ( . %) showed no benefit after the first and second tx, despite mild neck weakness on static muscle testing and, in some instances, emg signs of denervation. the responders ( men, women) had younger age onset cd (mean yr vs yr), but similar duration (mean yr vs yr) compared to the male and female nonresponders (in contrast to jankovic and schwartz, arch neurol, ) . both groups had similar degrees of severity and tx dose (mean iu, range . - ). although disparate group size prohibits statistical analysis, some interesting comparisons include: nonresponders were more apt to have extranuchal dystonic sites ( % vs %), antecollis ( % vs %), dark eyes ( % vs %), women with elevated antinuclear antibody titer ( % vs %), history of intracranial operation ( % vs o%), significant for age focal mri abnormality ( of vs of ). history of cervical operation ( patients) did not limit responsiveness. rates of prior remission, perinatal stress, antecedent trauma, left-handedness, and family history of movement disorder were similar for both groups. antecollis presents problems for optimizing tx to affected muscles, but central mechanisms may play a role in why some patients with focal dystonia do not improve with botox tx from the outset. enrico fazzini, new york, n y with parkinson's disease does deprenyl have a symptomatic effect on patients with untreated and l-dopa-treated parkinson's disease (pd)? once deprenyl is started, how long is it before another medication is needed to control symptoms of continued disease progression? there has been controversy over whether deprenyl has effects on delaying disease progression (nejm ; : ) and/or in alleviating the symptoms of pd. one hundred seventy-five patients already taking l-dopa (group ) and patients who had never taken l-dopa (group ) were treated with deprenyl mg/day. unified pd rating scale (updrs) scores were measured before and after deprenyl. patients were followed until pd symptoms progressed to the point of requiring additional medication. one hundred eighteen of ( %) patients in group (reduced updrs mean activities of daily living [adl) to , motor [mtr] to ) and / ( %) patients in group (reduced updrs mean adl to , mtr to ) reported symptomatic benefit. an average of months' duration was found in both groups before further medication adjustments were needed. deprenyl provides symptomatic benefit for an average of months in the majority of patients with p d regardless of whether or not they are being treated with l-dopa. yasuo iwasaki, masao kinoshita, toshiya shojima, and ken ikeda, tokyo, japan, and cleveland, oh in parkinsonian patients we measured fasting plasma amino acids in parkinson's disease patients and controls matched for age and sex. all patients were receiving l-dopa and they were free of any medications other than l-dopa. normal controls were free of any medication. there were no differences in diets between patients and controls. fasting blood specimens were collected in heparinized tubes and immediately were centrifuged at , g for minutes. analysis of plasma amino acids was performed by automated ion-exchange chromatography with lithium-based buffer and an amino-acid analyzer. parkinsonian patients had significant elevations of aspartate, glutamate, and glycine. the other amino acids were not significantly different from those in controls. n o correlation between severity or activity and degree of abnormality in plasma level of amino acids in patients was established. we conclude that excitatory amino-acid metabolism is altered in patients with parkinson's disease. bonnie e. levin, rachel tomer, and william weiner, miami, fl disease there is evidence linking obsessive-compulsive symptoms (ocs) to basal ganglia dysfunction. we investigated the presence and severity of ocs in a sample of patients with an unequivocal diagnosis of idiopathic parkinson's disease (pd) using the leyton obsessional inventory. ocs was found in the majority of the patients, with ( %) scoring above the normative cutoff for the symptom score and ( %) scoring above the normative cutoff for the trait score. when severity of oc symptoms was correlated with a battery of neuropsychological measures, significant relationships were observed between ocs and a preponderance of tests associated with right-hemisphere functions. these findings were observed especially on those tests with a strong frontal lobe component (block design: r = -. ; embedded figures: r = -. ; set shifting: r = -. ; and perseverative responses: r = . ; p < . for all measures). in all cases, the more severe oc symptoms, the poorer the performance. a similar trend was observed between the leyton trait scores and the cognitive measures. these findings suggest that ocs is present in a subgroup of pd patients, which may reflect greater compromise of right-hemisphere basal ganglia-frontal lobe pathways. intraclass correlations (iccs) were calculated for the total motor score and for each individual sign. results indicated excellent agreement (icc > . ) for the total motor score, resting tremor, gait, arising from a chair, and speeded, repetitive movements; good agreement (icc > . ) for rigidity, action tremor, posture, postural stability, and bradykinesia; and poor agreement (icc < . ) for speech and facial mobility. a factor analysis was then performed on updrs motor scores for pd patients from a community-dwelling cohort. three factors were extracted by principal components analysis with subsequent varimax rotation, accounting for . % of the total variance: factor -balance and stability (posture, postural stability, gait, arising from a chair, and bradykinesia); factor -rigidity and motor speed (rigidity, speech, facial mobility, rapid alternating movements, leg agility, hand movements, and finger tapping); factor -tremor (resting and action). these results indicate that the updrs motor examination is reliable between raters and measures the cardinal signs of pd. an open pilot study was performed to evaluate the efficacy of botulinum a toxin (botox) injections for disabling hand tremors. a previous report on the use of botox for hand tremors suggested that it was helpful, but relied on subjective clinical rating scales. the extent of normal clinical fluctuations or a placebo response could not be determined. to investigate these issues more objectively, patients with parkinson's disease and with essential tremor with refractory hand tremors underwent electromyographically guided intramuscular injections of botox into wrist flexors and extensors. patients without great medication-related tremor fluctuations were selected. results before and after botox were determined by comparing ( ) patient perceptions of functional improvement, ( ) clinical assessments using the unified pd rating scale for tremor and the webster rating scales, and ( ) physiological measurements using accelerometric analysis of hand tremors of tremor frequency, amplitude, and waveform characteristics. all patients reported some improvement, ranging from mild to marked with a mean of . on a to ( = marked) global rating scale. however, only / patients showed a significant improvement in the clinical rating scales, confirmed by > % reduction in tremor amplitudes. these findings show that most patients reported improvement not confirmed by the clinical or physiological measures. efficacy of botox injections for tremors is implied, but controlled trials are needed before this procedure can be generally recommended. christopher g. goetz and glenn t . stebbins, chicago, i l we tested whether hallucinations, motor disability, and cognitive decline were risk factors for nursing home placement in advanced parkinson's disease (pd) and whether these effects were independent or synergistic. between and , we identified patients admitted to long-term nursing homes. using case control methodology, we matched each for age, pd duration, and sex with control pd patients remaining at home. parkinsonism was assessed by the motor and activities of daily living subscales of the unified p d rating scale (updrs); hallucinations and dementia were determined by scores on the thought disorder and intellectual impairment items of the updrs. tests of synergy were based on a mantel-hentel model. hallucinations were a significant risk factor with odds ratio = . , x = . , p < , . motor impairment alone and cognitive impairment alone were not significant risk factors for nursing home placement (x for motor severity = , , p > . , and x for cognitive impairment = . , p > . ). furthermore, combined odds ratios for hallucinationslmotor severity and hallucinations/cognitive impairment showed no synergy of effect (x < . for both,p > . ). of the variables studied, hallucinatory behavior is the most prominent and independent risk factor for nursing home placement in these patients; the data suggest that aggressive control of hallucinations may be warranted to prevent nursing home admission. temperature-sensitive paramyotonia congenita phenotype* louis j . ptacek, philip mcmanis, hzrbert kwiecinski, alfred george, robert barchi, launce gouw. and mark leppert, salt lake city, u t , rochester, mn, warsaw, poland, and philadelphia, pa the periodic paralyses are a group of autosomal-dominant muscle diseases sharing a common feature of episodic paralysis. in one form, paramyotonia congenita (pc), the paralysis is temperature-sensitive, usually occurring with muscle cooling. electrophysiological studies of muscle from patients with pc have revealed temperature-dependent alterations in sodium channel (nach) function. this observation led to the identification of distinct mutations in an s segment of a skeletal muscle nach in unrelated pc families. we describe the use of the single-strand conformation polymorphism (sscp) technique to define a third allele specific to pc patients in an additional family. this aberrant pattern, though distinct from the first , occurs in the same exon of this nach gene. sequencing is currently underway to define the molecular alteration causing this aberrant pattern. two additional families with the pc phenotype have been sampled and do not demonstrate these sscp variants. we are currently searching for new mutations in these families to define further the molecular heterogeneity of this temperature-sensitive pc phenotype. parag mehta and roger w. kukz, brooklyn, n y abnormal accumulation of calcium (ca) in myofibers is thought to play a role in pathogenic myonecrosis. attempts at reducing intracellular ca content with ca channel blockers in duchenne muscular dystrophy (dmd) have been clinically unsuccessful. dantrolene, however, which acts at the sarcoplasmic reticulum to inhibit ca release from intracellular stores, has produced dramatic reductions in serum creatine kinase (ck) in dystrophic mice and more recently in dmd. we investigated the effect of low-dose dantrolene in a group of patients with limb girdle dystrophy (lgd), dmd, and other myopathic disorders. all subjects received dantrolene in incrementing doses from to mg daily over a to -week period. mean baseline ck was compared to ck with dantrolene treatment. dramatic reductions in serum ck levels averaging % were seen at to -mg doses in lgd patients ( ). dmd patients ( ) and patients with other myopathies ( ) showed a similar but less dramatic reduction in ck. three of the weakest patients complained of increased fatigue while taking mg, which suggests that higher-dose dantrolene may confound longer-term trials assessing clinical muscle strength and function. dantrolene in dosages well below conventional antispastic doses has a dramatic effect on serum ck and possibly myofiber necrosis in lgd, other dystrophies, and other muscle disorders. p . antigen-specific therapy in myasthenia gravis: myasthenia gravis (mg) is mediated by anti-acetylcholine receptor (achr) antibodies, believed to be t-cell dependent, and antigen-specific therapy would be preferable to current nonspecific immunosuppression. exposing mouse t-cell clones to mhc class i molecules complexed with relevant antigen on planar membranes induced proliferative unresponsiveness (quill and schwartz, ) , and soluble mhc class i molecules complexed with myelin basic protein (mbp) peptide resulted in unresponsiveness of specific tlymphocyte clones in vitro (sharma et al, ) . we have used our well-defined dr -restricted t-cell clone (ong et a [, ) isolated from an mg patient and specific for p - of the achr alpha subunit. overnight incubation of these t cells with a soluble p - : dr complex substantially inhibited the subsequent response to challenge with soluble antigen and presenting cells. in contrast, antigen response after preincubation with dr complexed to an irrelevant peptide (mbp - ), soluble dr alone, or an experimental approach studied in vitro p - alone (at equimolar concentrations) did not differ appreciably from that in untreated cells. the p - :dr complex had no effect on other non-achrspecific cell lines/clones. these results suggest that the use of soluble mhc-peptide complexes may be an approach to selective immunotherapy in mg patients. p . high-dose intravenous immunoglobulin in the shawke a. soueidan and marinos c. dalakas, bethesda, md inclusion body myositis (ibm) is a severe disabling inflammatory myopathy with characteristic clinical and histological features. it is commonly suspected when a patient with presumed polymyositis does not respond to available immunotherapies. the need for an effective treatment in patients with ibm prompted the present pilot study using high-dose intravenous immunoglobulin (hd-ivig), an apparently effective immunomodulating agent in several autoimmune neuromuscular disorders. we treated patients with muscle biopsy-proven ibm with up to monthly infusions of gml kg ivig. after the first infusion, of the patients showed definite functional improvement consisting of independent ambulation, fewer falls, and increased ability to lift weights. the muscle strength of the proximal and less atrophic muscle groups improved by one grade mrc scale (from to ), whereas the distal and atrophic muscles remained unchanged. the improvement, sustained up to months, was greater in patients with the most severe endomysial inflammation. we conclude that hd-ivig may be the first promising agent that can improve the strength of certain muscle groups in patients with ibm. because ivig is prohibitively expensive, the present encouraging results warrant a large-scale controlled therapeutic study. hays, and n . lutov, new york, n y , and milan, italy anti-myelin-associated glycoprotein (mag) antibodies from patients with neuropathy cross-react with the glycolipid -sulfated glucuronyl paragloboside (sgpg). among patients tested by enzyme-linked immunosorbent assay and western blot, had highly elevated antibody titers ( , ) to both mag and sgpg, had highly elevated titers to mag alone, and had highly elevated titers to only sgpg. immunostaining of normal nerve myelin by the antibodies correlated better with anti-mag than anti-sgpg activity. twenty-one of the patients, including patients in all groups, had predominantly sensory or sensorimotor neuropathy, and biopsy specimens revealed deposits of igm and complement on affected myelin sheaths. three patients presented with motor syndromes, all with antibodies specific for sgpg; had a predominantly motor demyelinating neuropathy, had upper and lower motor neuron signs and peripheral neuropathy, and had amyotrophic lateral sclerosis confirmed post mortem. all had deposits of complement on peripheral nerve myelin sheaths. these studies suggest the following: ( ) that anti-mag or sgpg antibodies may differ in their fine specificities and biological activities, ( ) that anti-sgpg antibodies also may occur in motor neuron diseases, complicating the clinical presentation, and ( ) that both mag and sgpg should be used as antigens in testing for autoantibody activity in peripheral neuropathy. david b. williams, john steele, ulla-katrina craig, sandra bryant, peter o'brien, and leonard kurland, newcastle, new south wales, australia, mangilao, guam, and rochester, m n continuing surveillance of neurodegenerative diseases in the mariana islands reveals changes in frequency and clinical characteristics since the s that resemble those in other known western pacific foci (kii peninsula, japan, and irian jaya, new guinea). recent surveys of patients years and older were conducted on rota, tinian, and yigo, guam. possible cases of dementia, parkinsonism, and amyotrophic lateral sclerosis (als) were identified by local trained personnel using a questionnaire, world health organization neurology test, and cognitive screening. those who failed the screening were examined by a neurologist. in the small populations of rota and tinian, there were no definite cases of als compared to i to cases present in previous surveys. the high prevalence of parkinsonism-dementia complex (pdc) was unchanged and dementia was increased compared to earlier surveys. in yigo, als and pdc continue to be prevalent; however, the als patients are predominantly long-term survivors (> -year disease duration). in areas of previous high prevalence of als/pdc, dementia (as pdc) was associated with extrapyramidal signs, whereas in areas of previously low prevalence of als/pdc, dementia alone, possibly of alzheimer type, predominated. these observations help to confirm previous reports of changing clinical patterns, but suggest that the geographic distribution of the (presumed) environmental etiological agent for als/pdc remains stable after almost years. p. v . fragokz, . frongillo, m. michisanti, g. antonini. derangements of the cardiac conducting system are the most common features of heart involvement in myotonic dystrophy (md). in view of chis patients with various grades of md ( males and females, mean age yr) underwent -lead ecg and holter monitoring. in patients ( %), almost all with a severe grade of md, or more conduction defects were found: first-degree atrioventricular block (i-avb) in cases, second-degree avb in case, right bundle branch block in cases, left anterior hemiblock in cases, left bundle branch block in cases, and trifascicular block in case (pacemaker implanted). an -year-old boy had a chronic atrial fibrillation with slow ventricular rate; he died suddenly while awaiting electrophysiological study. thirty-seven patients were followed over a mean period of months (range - mo). a -year-old woman experienced a myocardial infarction and was excluded from subsequent considerations. conduction defects de novo appeared in patients: i-avb in and i-avb plus -avb (mobitz i and i type) in . nine patients, all with i-avb at initial evaluation, showed deterioration of their defects' conduction: a bifascicular block was observed in cases and a trifascicular block in cases (pacemaker implanted). conduction defects may run a malignant course in md, mainly in patients with more severe grades of the neuromuscular disease; thus, a close cardiological evaluation is mandatory for a proper therapeutic approach in single cases. hiroshi mitsumoto, surest kumar, kevy h. levin, robert w. shields, jr, michelle secic, asa j . wilbourn, and rajendra g . desai, cleveland, oh, and santa ana, ca twenty patients with amyotrophic lateral sclerosis (als) entered a pretreatment study with monthly quantitative isometric muscle strength tests ( muscles in each extremity) and quantitative tufts scales including vital capacity, bulbar diadochokinetic rate, timed water drinking, timed rising from a chair, and timed walking meters. after to months of pretreatment observation, the patients received mg/kg intravenous immunoglobulin (ivig) (gamimune-n, miles) every month for up to months. during the study period, patients died and patients withdrew from the study. the slope of each variable's changes over time before and after the ivig treatment were compared statistically. none of the quantitative scales showed significant change with ivig. however, the slope of the upper extremity muscle strength revealed improvement with ivig treatment ( p = . and . , right and left, respectively). when all extremities were combined, the slope was also significantly improved with ivig ( p = . ). lower extremity muscle strength alone showed similar trends but no statistical significance. electrophysiological and immunological data were also analyzed. our results warrant a double-blind, controlled study with ivig for the treatment of als. leber's hereditary optic neuropathy (lhon) is a mitochondrial disorder with predominantly optic nerve abnormality. it can be associated with dystonia, ataxia, encephalopathy, cardiac abnormalities, and other less well-characterized neurological syndromes. we describe members of a family with lhon with a slowly progressive motor polyneuropathy. a -year-old man and his -year-old sister have had mild motor impairment since early childhood. a gait disorder and distal muscle weakness became evident at puberty. the girl, but not the man, also has blindness, distal numbness, type i diabetes mellitus, and short stature. physical examination showed in both: bilateral foot drop, limb hyperreflexia but absent ankle reflexes, distal sensory loss, and a slight brownish scaly skin discoloration over the forearms. only the girl had clonus and optic nerve atrophy. the man had peripapillary telangiectasias. the jaw jerk was normal in both. motor nerve conductions in both showed absent tibia and peroneal responses, whereas other motor and sensory nerve conductions were normal. emg revealed denervation, more so distally. muscle biopsy findings showed recent denervation and previous denervation followed by reinnervation. n o raggedred fibers were observed with the modified trichrome and sdh stains. brain mri was normal in both. cerebrospinal fluid in the girl was normal. blood samples from both patients and maternally related family members revealed a mitochondrial dna point mutation at position (d. c. wallace). in this family, only male had lhon; females had lhon and others, including the patients' mother, were asymptomatic carriers. this association of chronic motor neuropathy and hyperreflexia with lhon appears to be a distinct syndrome. the pathogenic mechanism by which the mitochondrial dna defect causes the neuropathy (and other neurological deficits) requires analysis. duchennelbecker muscular dystrophy henry j . kaminski, mazen al-hakim, r. john leigh, bashar katirji, and robert l. ruff; cleveland, oh fast-twitch extremity muscle fibers are preferentially affected in duchenne/becker muscular dystrophy (dbmd). since saccades are thought to be mediated by fast-twitch fibers, saccadic velocities would be expected to be decreased among these patients. to investigate involvement of extraocular muscle (eom) by dbmd, we studied with infrared oculography patients who were wheelchair-bound and able to perform only minimal activities of daily living. saccades were slightly slowed but were within % confidence limits of normal. all patients showed square wave jerk movements (swj). in patients, the frequency of the swj exceeded that of normal subjects, which suggested central nervous system dysfunction. clinical neuroophrhalmological examination of other dbmd patients was normal. this investigation is the first study of ocular motility in dbmd and demonstrates that eom function is relatively preserved even in far advanced patients. eom is composed of a heterogenous mix of fiber types that differ in anatomical and physiological characteristics from extremity muscle. study of eom in dbmd may prove to be useful in understanding why some muscles are resistant to dbmd and in characterizing properties that limit muscle degeneration. (supported by nih grants ey , ey , the department of veterans affairs, and the evenor armington fund.) since patients with myotonic dystrophy (mtd) exhibit a marked resistance to insulin effect on glucose uptake and an impaired handling of the insulin-sensitive amino acids, it is possible that muscle wasting in mtd may reflect a derangement of insulin action on muscle protein metabolism. increased muscle protein breakdown in mtd would be expected if the normal inhibitory effect of insulin on protein catabolism is impaired. the forearm perfusion technique combined with measurements of -methylhistidine ( -mh) arteriovenous (a-v) differences by high-performance liquid chromatography provides a unique method to investigate skeletal muscle myofibrillar protein degradation in vivo. we studied -mh (a-v) and efflux from the forearm muscles in men moderately affected with mtd and normal men. efflux values (q) were calculated as the product of -mh (a-v) times forearm plasma flow measured by the indicator dilution technique. forearm -mh release (estimated as {a-v} or q) of mtd patients did not differ significantly from normal controls. we conclude that myofibrillar degradation is not increased in mtd even when measured in a muscle compartment selectively affected by wasting. the possibility of an impaired anabolic action of insulin in mtd has yet to be determined. to study the relationship between the ragged red fibers (rrf) and age, we have reviewed muscle biopsy specimens prospectively. patients with well-established mitochondrial myopathy syndrome and with myopathies known to produce secondary rrf were excluded. the number of ragged red fibers (rrf) was counted under x (lpf) magnification. rrf were identified by the modified trichrome and sdh stain. for the final analysis, the sdh staining was used. the frequency of rrf was analyzed in relation to patients' ages. the frequency of cases with more than rrf increased with aging: % in the first decade, % in the fourth decade, and % in the eighth decade. the frequency of cases with more than rrf also increased with aging: % in the first three decades, % in the fourth decade, and % in the eighth decade. of patients with well-established mitochondrial myopathy syndrome, had more than rrf under lpf. the number of rrf in muscle increases with aging, indicating that mitochondrial activity in muscle is affected by aging. this finding may complicate the diagnostic criteria of mitochondrial myopathy in older individuals. ten rrf under lpf seems to be a reasonable cutoff point for the diagnosis of mitochondrial myopathy. schwartz-jampel, a rare autosomal-recessive syndrome characterized by short stature, myotonia, skeletal abnormalities, and peculiar facies, was reported by aberfeld in . the same sibship was earlier reported by schwartz and jampel in with emphasis on blepharophimosis. as of this writing about cases have been reported in the literature. most of the features of this syndrome are believed to be secondary to primary muscle disease. several peripheral electrophysiological studies showing features of myotonia have been reported. we describe patients with schwartz-jampel syndrome showing evidence of central conduction disturbance documented by somatosensory-evoked potentials (seps). median nerve seps showed normal latencies to erb's point and n- in all. interpeak latencies between n and n were prolonged in with complete block in . emg showed typical myotonic discharges in all. motor nerve conduction velocities, visual and brainstem auditory-evoked potentials, ct, and mri were normal in all. seps in the parents were normal. we believe this is the first report documenting evidence of central nervous system (cns) involvement in schwartz-jampel syndrome. schwartz-jampel syndrome and myotonic dystrophy may have similar cns ''lesion'' as sep abnormalities also have been shown in myotonic dystrophy. epidemiological studies have associated consumption of certain batches of l-tryptophan (lt) with development of the eosinophilia-myalgia syndrome (ems). , '-ethyledenebisltryptophan) (ebt or peak e), a derivative of lt, is a trace contaminant associated with implicated batches of lt. three female lewis rats received ebt, mg per gm daily, by intraperitoneal injection. four control rats received unimplicated lt. n o peripheral eosinophilia, rash, or weakness were observed in either group. one rat from each group died during the experiment (control-bowel infarct; ebt-death under anesthetic). after days, forelimb and hindlimb muscles of the remaining animals were frozen and fixed for program and abstracts, american neurological association ultrastructural and histological studies. two ebt rats had a myopathy involving soleus with a perimysial infiltrate containing lymphocytes, macrophages and sparse eosinophils, and necrotic fibers; the other showed few necrotic fibers in gastrocnemius. occasional eosinophils were seen in fascia in both animals given ebt but not in controls. fiber-type specific quantitative analysis of the microvasculature showed no decrease in the capillary index. ultrastructural examination revealed an increase in the size of microvessels in ebt animals. no denervation or reinnervation were demonstrated. the perimysial inflammation replicates an important feature of human ems and supports the epidemiological evidence that ebt is the causative agent of the disease. britta ostermeyer-shoaib, bernard m. patten, and tetsuo ashizawa, houston, t x five women (patients - ) developed motor neuron disease (mnd) years (range - yr) after receiving silicone gel-filled breast implants. at explant in patients, had both and had the left implant ruptured with silicone spilled into tissue. one woman (patient ) developed amyotrophic lateral sclerosis (als) years after numerous injections of free silicone into her face. biceps muscle biopsy specimens in all showed neurogenic atrophy. patient developed als with bulbar involvement and died years later of respiratory failure. she had anti-gm antibodies and autopsy findings confirmed the diagnosis of typical als. patient developed als, but also fatigue, myalgia, arthralgia, and skin rash. she had anti-gm antibodies, antisilicone antibodies, positive antinuclear antibodies (ana), and decreased serum igg, iga, and c , but increased igm and creatine phosphokinase (cpk) and chronic inflammation was revealed in muscle biopsy specimens. patient developed als, but also had hair loss, skin rash, fatigue, headache, sjogren's syndrome, and positive ana. patient developed als, but also had myalgia and arthralgia. patient developed lower mnd, but also fevers, arthralgia, and joint stiffness. she had anti-gm antibodies, positive ana, antimyelin antibodies, and decreased serum igg and iga with chronic inflammation shown in nerve biopsy findings. patient developed a steroidresponsive and steroid-dependent als with bulbar involvement. she had a monoclonal gammopathy in the cerebrospinal fluid and increased cpk. we suggest that silicone acts as an adjuvant that damages motor neurons via an indirect autoimmune mechanism. implants and silicone injections into the face p . silicone adjuvant breast disease: more forty-five women developed mixed sensory-motor neuropathy ( ), motor neuron disease ( ), multiple sclerosis ( ), multiple sclerosis-like syndrome ( ), or myasthenia gravis ( ) years (range mo- yr) after receiving silicone-gel breast implants ( ), saline-filled silicone-covered breast implants ( ), or direct injections of silicone into the breast ( ). most patients had, in addition, severe fatigability, myalgia, arthralgia, morning stiffness, skin rash, lymphadenopathy, sjogren's syndrome, and short-term memory problems. laboratory results revealed in most of the women decreased or increased serum immunoglobulins, autoantibodies, a serum monoclonal gammopathy, or oligoclonal bands in cerebrospinal fluid. at explantation in , had both and had implant neurological cases ruptured. biopsy of the fibrous implant capsule in most patients showed foreign-body giant cells containing refractile material consistent with silicone whether or not the elastomer shell was ruptured, indicating silicone bleed. the major finding on surd nerve biopsy was loss of myelinated fibers, on biceps muscle biopsy was neurogenic atrophy, and on pectoralis muscle biopsy was myositis with vasculitis and free silicone in some. we suggest that silicone may provoke damage to nerve and muscle, probably indirectly promoting autoimmunity. james f. howard, jr, m . kathleen donovan. and m. susan tucker, chapel hill, nc urinary symptoms of urgency and incontinence have been reported only rarely in patients with myasthenia gravis (mg) and then most often in association with myasthenic crisis. we report the case of a -year-old woman who in december had the onset of chest pain and was found to have a lymphocytic thymoma. in june she developed urinary incontinence, was found to have an open bladder neck. and underwent a suspension procedure for stress incontinence in january . eight months later she developed exertional fatigue and a diagnosis of m g was made. in july there was a recurrence of urinary incontinence. these symptoms clustered toward the end of the day and at trough mestinon dose. neuro-urophysiological studies demonstrated her previous open bladder neck, the inability to sustain a pelvic floor contraction, and increased bladder wall contraction. singlefiber electromyography (sfemg) recordings from the anal sphincter demonstrated a mean consecutive difference (mcd) of ysec, and % of fiber pairs had impulse blocking while recordings in the extensor digitorium communis muscle were normal. following a course of plasma exchange, there was significant clinical improvement with a reduction in the frequency of urinary incontinence, and improvement in anal sphincter sfemg studies (mcd, ysec with no blocking). this case demonstrates that in those myasthenic patients with predisposing bladder outlet dysfunction, urinary incontinence may be a manifestation of worsening mg. diana m. escolar, mohamed eldaly, and jaime rich, boston, m a debate still exists as to the role of antibody versus celmediated factors in the pathogenesis of guillain-barre syndrome (gbs). we describe a patient with increased proportion of circulating t cells and a t-cell lymphoma who developed gbs and responded to intravenous immunoglobulin (ivig). a -year-old man with t-cell lymphoma drveloped gbs by clinical, nerve conduction, and cerebrospinal fluid criteria. he had an elevated proportion of t cells and markedly reduced b cells with a normal cd /cd ratio. he responded rapidly to ivig, with return of nearly normal motor function in week. three weeks later, he relapsed and his vital capacity dropped. ivig was again administered and within hours he nearly recovered. a third relapse, days later, again responded to ivig. he has remained asymptomatic with ivig maintenance. the role of t-cell lymphocytes in initiating experimental autoimmune neuritis has been shown by adoptive transfer experiments. this patient with t-cell neoplasia may represent an analogous model in hu-guillain-barre syndrome mans supporting the role of t-cell (cell-mediated) autoimmunity in the pathogenesis of gbs. ivig therapy may act primarily by inhibiting the t-cell-mediated attack on myelin. p . sympathetic skin response: age effect it is frequently stated that the sympathetic skin response (ssr) can be elicited in all normal subjects, but the age of the investigated population usually is not considered to be a significant factor. we have examined the ssr in the upper and lower limbs of normal subjects, aged to years ( of them males). the ssr was elicitable in the lower limbs in all subjects under the age of years and in the upper limbs in all subjects younger than years. in contrast, it could be elicited in the lower limbs in only % and in the upper limbs in % of octogenarians. the amplitude of the response, though highly variable, showed a remarkable decline with age, both in the upper ( p < . , r = . ) and in the lower ( p < . , r = . ) limbs. these results indicate that age affects both the elicitability and the amplitude of the ssr. this has to be taken into consideration when evaluating the autonomic function in the elderly. we reviewed records of patients appearing to have motor neuron disease (mnd) to whom we recommended immunosuppression over years ( of m n d patients). atypical findings engendered hope rhat they might have treatable neuropathy. electrophysiological studies were mainly consistent with mnd, but also showed conduction block or other evidence of relatively mild peripheral nerve disease in . sensory symptoms were present in ; or more reduced or absent deep tendon reflexes in ; elevated cerebrospinal fluid protein in ; and nonspecific abnormalities on sural nerve biopsies in of . anti-gm levels were measured in (including who improved), but none was significantly elevated. immunosuppression included cyclophosphamide ( patients); prednisone ( ); plasma exchange ( ); intravenous gammaglobulin ( ); cyclosporine ( ); and total lymphoid irradiation ( ). seven treated patients died, worsened, remained stable for years, and improved. two patients declined treatment. one died and the other did not worsen in years. we conclude that immunosuppression by our methods is, at best, rarely effective in atypical mnd. we studied serum antiglycolipid antibodies by enzymelinked immunosorbent assay in patients with typical miller fisher syndrome (mfs), patients with atypical mfs who were lacking in some of the cardinal signs, patients with guillain-barrc syndrome (gbs) with ophthalmoplegia, patients with gbs without ophthalmoplegia, patients with multiple sclerosis (ms), and patients with other immunological disorders (oid) including systemic lupus erythematosus, polymyositis, and mixed connective tissue disorder. all patients with typical mfs had increased activity of igg antibody against ganglioside g q l b in the early phase, and it reduced with time. such anti-gqlb igg activity also was detected in of the patients with atypical mfs and in of the patients with gbs with ophthalmoplegia. in atypical mfs, the only patient without increased anti-gq b igg activity demonstrated normal eye movement with ptosis, whereas eye movement was impaired in the other patients. no patients with gbs without ophthalmoplegia, ms, or oid had increased anti-gqlb igg activity. these findings suggest the close association between increased anti-gql b igg activity and impaired eye movement in mfs and gbs. serum anti-gqlb igg activity possibly plays a role in impaired eye movement in mfs. our goal is to develop an assay that can be used to monitor a relevant immune effect of interferon p (ifnp) in multiple sclerosis (ms) patients during the course of ifnp immuno-' therapy, since recombinant ifnp is being tested in multicenter clinical trials. this report extends our prior studies of the inhibitory effect of ifnp on t-cell activation. peripheral blood mononuclear cells (pbls) from healthy donors and clinically stable ms patients were studied. pbl cultures were stimulated with cona, mab to cd , or with the phorbol ester pma in the presence of the calcium ionophore ionomycin. parallel cultures were studied in the presence of ifnp, uiml. t-cell activation was monitored by determining the percent cells positive for il- receptor (il- r) using facs analysis, or with a sensitive enzyme-linked immunosorbent assay for ifny. ifnp markedly inhibited il- r expression induced by cona, by mab to cd , or by pma and ionomycin, which activate t cells via different pathways. the results suggest that ifnp inhibits t-cell activation by actions independent of membrane receptors. we observed significant inhibition of cona-induced t-cell il- r expression in both ms patients ( . % inhibition, p < . ) and controls ( . % inhibition, p < . ). there was no significant difference in percent inhibition between ms and controls, but there was more variance among the ms patients. variability of biological effects of ifnp on t cells may relate to differential therapeutic responses to exogenously administered ifnp in ms patients. preliminary experiments suggested that ifnp inhibited ifn gamma secretion by pbl stimulated with cona. ifnp inhibits a number of events associated with t-cell activation, in both normal and ms t cells. response to ifnp appears more variable in the ms cases. immunological monitoring of t-cell activation in patients receiving ifnp may assist in understanding the observed therapeutic responses and planning clinical protocols. myelin destruction is associated with many central nervous system disorders, such as multiple sclerosis, head trauma, and ischemic injury. inflammatory cells, monocytes/macrophages, and polymorphonuclear leukocytes (pmn) may me-program and abstracts, american neurological association diate myelin injury, and lipid peroxidation may be an important mechanism. inhibiting myelin oxidation could have substantial benefit, so we evaluated the ability of a -minosteroid, u a, to inhibit myelin oxidation by monocytes and pmn. fresh rat brain myelin was harvested by multiple sucrose gradient, ultracentrifugation steps, and the final product was confirmed to be pure myelin by sds-page electrophoresis. human monocytes or pmn were obtained from healthy, unmedicated volunteers by gradient separation techniques. monocytes ( . x lo cells/ml) and pmn ( . x lo cells/ml), myelin ( pg protein/ml), and lipopolysaccharide ( pg/ml) were incubated for hours with or without wm u a in -ml wells. myelin oxidation was evaluated by a thiobarbituric acid reactive substance assay for production of malondialdehyde (nmol/ ml). myelin oxidation by monocytes was . +- . (mean standard error of mean) without u a and was reduced to . ? . by pm u a ( p < . ). pmn-mediated myelin oxidation was . _t . without drug and . ? . with drug ( p < . ). these results demonstrate that u a markedly inhibits monocyte-and pmn-mediated myelin oxidation and suggest that the aminosteroids may help disorders associated with inflammatory cell-induced myelin injury. microglia cells participate in the pathological reactions of the cns to multiple insults including trauma, inflammation, and neuronal degeneration. functional roles for these cells could include mediating tissue in jury, promoting repair, or modulating immune responses. with regard to the latter, we have observed that the majority of adult human-derived microglia express major histocompatibility complex (mhc) class molecules under basal culture conditions, in contrast to astrocytes derived from the same surgical biopsy specimens. all morphological subtypes of the microglia (ameboid, bipolar, and ramified) expressed mhc class i molecules, indicating a discordance between morphology and mhc antigen expression as markers of microglia activation. the microglia actively ingest myelin constituents, as assessed using fluorescein-labeled myelin basic protein and laser confocal microscopy. autologous t cells (e') freshly isolated from the systemic blood and cocultured with candida antigen underwent active proliferation in the presence of to % microglia, indicating the functional capacity of the microglia to serve as antigen-presenting cells. y-interferon augmented both mhc class expression and functional antigen-presenting capacity. these results indicate the potential of the adult human microglia to promote immune reactivity within the cns. protein (mbp) neutralize anti-mbp purified from multiple sclerosis cerebrospinal fluid active phases of multiple sclerosis (ms) are associated with increased titers of intrathecally produced antimyelin basic protein (anti-mbp). anti-mbp can be purified by antigenspecific affinity chromatography from csf igg of patients with acute relapses of ms. eighteen synthetic peptides of human myelin basic protein (h-mbp) containing between and amino-acid residues and covering the entire length of the molecule were synthesized by the fmoc method. purified anti-mbp was reacted with increasing amounts of h-mbp as well as each of the peptides in an initial liquid phase assay, and subsequently titers of f anti-mbp in all resulting mixtures were measured by a solid-phase radioimmunoassay . purified anti-mbp was neutralized by h-mbp and of the synthetic peptides containing overall residues corresponding to to of h-mbp. the remaining synthetic peptides covering both the amino and carboxyl terminals of h-mbp did not significantly react with purified anti-mbp from these patients. in conclusion, anti-mbp purified from csf of ms patients has affinity for epitopes located between residues and of h-mbp. in a double-blind study involving patients, we recently demonstrated that -aminopyridine ( -ap) is superior to placebo in the treatment of multiple sclerosis (ms) (ann neurol, in press). the related agent , -diaminopyridine (dap) also appears to be effective. to enable a preliminary comparison, patients, who in our previous study had not benefitted from -ap, were now treated ( wk) with dap (up to . mg/kg/day) for weeks in an open-label fashion. instruments for assessment and registration of side effects were the same as in the previous trial. the optimal dose of dap was . mg/day compared to . mg/day for -ap. significant changes in the edss ( . point or more) were not found, whereas significant improvements in neurophysiological parameters were found (no difference between -ap and dap, allp > . ). subjective side effects during -ap ( patients) mainly suggested cns-function disturbance (dizziness and gait disturbance) and during dap ( patients) mainly suggested peripheral nervous system-function disturbance (paresthesias). systemic tolerability clearly was diminished for dap compared to -ap, with patients withdrawing because of severe gastric complaints and developing liver function abnormalities. these data suggest that -ap is more valuable than dap in the treatment of ms. cy clophosphamide/methylprednisolone therapy in multiple sclerosis multiple sclerosis (ms) is a presumed autoimmune disease in which various forms of immunotherapy have been attempted. mri studies show the disease to be more chronically active than is clinically evident, thus a single treatment is unlikely to provide lasting benefit. recently, the northeast cooperative treatment group found that pulse cyclophosphamide ( mg/m every other month for years) slows progressive ms. we initiated a pilot study to determine the effect of a more intensive and prolonged pulse therapy regimen in both progressive and earlier stages of the disease. pulse therapy was given after induction with either iv cyclophosphamide/corticotropin ( mg/m x over days) or iv methylprednisolone ( gm x over days). patients received a single iv dose of cyclophosphamide ( - , mg/m ) adjusted to produce leukopenia plus gram of iv methylprednisolone monthly for a year, every weeks for the next year, and every months in the third year. another group received pulse methylprednisolone without cyclophosphamide. as of this writing, patients have been treated, of which have completed years. interim analysis shows that patients treated with pulse methylprednisolone were more likely to become treatment failures than those treated with pulse cyclophosphamide/methylprednisolone ( % vs %) independent of induction therapy. withdrawal due to toxicity, however, was higher in the pulse cyclophospharnide group. current regimens involve methylprednisolone induction alone followed by pulse cyclophosphamide/methylprednisolone, analogous to lupus nephritis pulse therapy. this regimen can be given solely on an outpatient basis, does not cause alopecia, and is more amenable for use in earlier stages of the disease. to determine the incidence of pathologically confirmed malignancy in multiple sclerosis (ms) patients in funded clinical trials of cyclophosphamide (ctx) and of azathioprine (aza), data were collected longitudinally using telephone interviews, written questionnaires, physical examinations, and medical records for ctx and aza patients from a community in-hospital and out-patient ms clinic in fargo, nd. in the ctx study (goodkin et al, arch neurol ; : - ) , clinically definite (cd), chronic progressive ms patients were enrolled. twenty-four were controls and received a mean induction dose of . grams. fourteen of the induced patients then received boosters every other month for months resulting in a mean total dose of . grams. no malignancies were detected. in the aza study (goodkin et al, neurology ; : - ) , c d relapsing ms patients participated. twenty-five were controls and received mgtkg of aza daily by mouth adjusted to maintain a white blood count of greater than , o/cmm for years (mean dose . mg/kg). two of aza patients developed resectable skin cancers: basal cell (bcc) at months and i squarnous cell (scc) at months. the incidence of developing a bcc or scc was not significantly increased after initiating therapies as compared to the untreated ms controls (aza: fisher exact testp value = . ). no other malignancy has been detected during to months of clinical follow-up. allergic encephalomyelitis paula dore-dufly, ruth washington, and robert h. swanborg, detroit, m i postcapillary endothelium at sites of inflammation undergoes many changes referred to as activation. activated endothelial cells (ec) exhibit increased surface expression of immunorelevant proteins (icam- ; ncam, elam, and mhc class i and class i antigens [ags)). the sequence of events that characterizes ec activation may be important in susceptibility, induction, and perpetuation of experimental allergic encephalomyelitis (eae). in this study we examine expression of ec activation antigens in central nervous system (cns) microvessels in response to interferon gamma (ifn-y). cns microvessels from sjl and bio.s mice were incubated for hours in ifn-y ( u/ml), fixed, permeabilized, and then stained with an antibody that recognizes class i, class i mhc antigens, icam- , and factor viii. relative fluorescence intensity was determined using a laser cytometer. results indicate that microvessels from all strains tested expressed no detectable icam- and class i ags. little class i antigen and transferrin receptors were expressed. upon stimulation with ifn-y, sjl microvessels exhibited increased surface expression of all ec activation ags. b o.s microvessels exhibited icam- and class i mhc but mhc class i ags were not upregulated. results indicate that there are strain differences in the ec response to ifn-y. resistance of b o.s mouse ec to activation by ifn may be a factor in decreased susceptibility or induction of eae, or both. protein-t-cell line-mediated experimental to investigate a possible pathogenic role of interferongamma (ifn-y) in experimental allergic encephalomyelitis (eae), an immunocytochemical study was undertaken to localize this cytokine in the spinal cord of lewis rats in which eae was produced by adoptive transfer of myelin basic protein-specific t cells. one pm-thick cryosections of spinal cord were labeled with monoclonal antibodies (mab) db- and db- recognizing different epitopes of rat ifn-y. in the spinal cord of naive rats, mab db-i, but not db- , stained processes of astrocytes, suggesting that astrocytes contain a protein with an epitope cross-reacting with ifn-y. in rats with at-eae, numerous ifn-y-positive cells stained with both mab db- -and db- -positive cells were present from days to after cell transfer and had disappeared on day . at day they entered the spinal cords predominantly through subpial vessels. ifn-y-positive cells could be identified as w / + leukocytes as well as ed -positive macrophages. as in naive rats, astrocytes in at-eae were labeled only with mab db- , but not db- . we never observed labeling of motor neurons with these mab. the transient presence of ifn-y in the rat spinal cord at the onset of at-eae suggests a pathogenic role of this cytokine in acute immune-mediated demyelination of the cns probably as a local stimulus for expression of mhc class i antigens and adhesion molecules, as well as for the release of tnf-a and toxic oxygen radicals from macrophages and microglia. immune responses to stress or heat shock proteins are implicated in the pathogenesis of several autoimmune diseases, including multiple sclerosis (ms). we examined the hypothesis that antigens in myelin cross-reacted with stress protein antigens. two techniques were used: immunocytochemistry and western blotting. frozen histological sections were prepared from normal human central and peripheral nervous system tissues. sections were incubated with murine monoclonal antibodies to different mycobacterial stress proteins. antibody binding was determined using avidin-biotin complexed antimurine antibody linked to alkaline phosphatase. program and abstracts, american neurological association a monoclonal antibody to the stress protein sp from m . leprae strongly stained both central and peripheral nervous system myelin. no myelin staining was noted with antibodies to sp or sp . proteins from purified central and peripheral nervous system myelin were separated by sds-page. western blots were prepared using a monoclonal antibody to sp and a polyvalent rabbit antibody to myelin basic protein (mbp) as primary antibodies. antibody binding was determined using antimurine or antirabbit igg antibody coupled to alkaline phosphatase. strong staining of central but not peripheral mbp by the anti-sp antibody was observed. the rabbit anti-mbp antibody stained both central and peripheral nervous system mbp. the presence of antigenic epitopes shared by a stress protein and the potential autoantigen, mbp, supports the hypothesis that immune responses to stress proteins may be involved in the pathogenesis of presumed autoimmune diseases such as ms. ( ). of patients with borderline or positive csf lyme titer, received parenteral ceftriaxone. all had later relapses consistent with ms. one patient received a month of oral doxycycline. the fifth patient had a negative western blot and was not treated. we conclude that an incidental borderline or positive lyme serology in an ms patient is unlikely to indicate neurological lyme disease. borderline serologies should be documented to rise on later testing; positive serologies should be confirmed by retest in a different laboratory or by western blot. csf abnormalities suggestive of neurological lyme disease (pleocytosis, protein elevation, intrathecal lyme antibodies) are distinct from those suggestive of ms (ogb, elevated igg index, mbp). in such patients antibiotic treatment may be appropriate, but will not alter disease course. when designing and analyzing therapeutic trials for multiple sclerosis (ms), investigators commonly compare the proportion of patients in the experimental and control groups who worsen one or more steps on the disability status scale (dss) or expanded dss during the study (typically years' duration). however, the intervals between the scores in the dss may not be equal. it may be easier to change by one or more steps in the lower end of the scale (e.g., dss = - ) than in the midportion of the scale (e.g., dss = - ). to evaluate this possibility, we compared the proportion of patients who worsened by one or more steps in the years after entering our program with dss = or with dss = . fifty-one percent ( ) natural history data may be useful for designing therapeutic trials for multiple sclerosis (ms). since , we have collected such data in a standard format on patients in the ucla multiple sclerosis research and treatment program. t o describe the course in our group, we have performed survival analysis (kaplan-meier) of patients with or more assessments who entered the clinic with disability status scale (dss) scores of to (n = ). an increase of one or more steps in the dss score persisting for more than months defines worsening. median times to worsening for a dds at entry of to were approximately years (range . - . ); but were . years for dss and . years for dss . for those starting at dss (n = ), only % worsened by year, % by years, and % by years. the percent worsening when starting at dss (n = ) were %, %, and %, respectively. these variable rates of worsening (i.e., time spent at each starting level) influence therapeutic trial design. including patients with dss or will increase the sample size and study duration. for testing nontoxic agents, we recommend enrolling patients with dss to . for more toxic treatments, we suggest dss to . (partially supported by usphs grant ns , the conrad n. hilton foundation, and various donors.) pi . cholinergic antagonists and p-adrenergic agonists inhibit experimental allergic encephalomyelitis in an additive manner mark a. jensen, avertano noronha, and bawy g. w. amason, chicago, il lymphoid organs receive a sympathetic (sns) and possibly a parasympathetic innervation. lymphocytes express padrenergic and cholinergic receptors and thus are sensitive to regulation by these neurotransmitters. the severity of experimental allergic encephalomyelitis (eae) is increased in sns-ablated animals. local parasympathectomy decreases plaque-forming responses in submandibular nodes. p,-adrenergic receptors are upregulated on cds t cells in progressive multiple sclerosis, as are m,-muscarinic acetylcholine receptors on cd t cells. we examined the effect of isoproterenol, a p-adrenergic agonist, and scopolamine, a cholinergic antagonist, on the course of eae in lewis rats. eae was induced by injection of . ml of incomplete freund's ad juvant containing guinea pig spinal cord ( % wlv) and m. tubercdosis ( mgiml) in one hind footpad. scopolamine ( . mglkg, twice daily) and/or isoproterenol(o. mglkg, twice daily) or saline were injected subcutaneously starting on the day of immunization. scopolamine or isoproterenol alone reduced severity ( p < . , t test) and duration ( p < . , t test) of disease compared to controls. the combination of scopolamine and isoproterenol further reduced disease severity compared to either agent alone ( p < . , x test), suggesting an additive protective effect of cholinergic antagonists and p-adrenergic agonists in eae. antigen-presenting cells a . conrad, v. sanders, p. schmid, and w. w . tourtellotte, los angeles, c a tissue is cryopreserved by the method of tourtellotte; this procedure minimizes or eliminates ice artifacts and preserves surface protein markers. the dissected plaques are lightly fixed in % paraformaldehyde and then suspended in % sucrose. blocks are mounted in oct, cryosectioned at p,m, and picked up on gelatinized slides. the activity of plaques is determined by the presence or absence of myelin debris (antimyelin basic protein stain or lux fast blue) or presence or absence of neutral lipids indicating myelin digestion as seen by oil red (oro) staining and the presence or absence of a class i major histocompatibility complex antigen (evidence for an antigen-presenting cell) on macrophages or microglia as seen by immunocytochemically staining for hla-dr (hb atcc). the following is our classification of the activity of multiple sclerosis (ms) plaques. type i, the most active, is defined as an area of hypercellularity, positive for hla-dr with no o r staining or staining for myelin debris. type , or active, is defined as an area of hla-dr-positive cells that stain mildly with o r at the plaque edge but positive for myelin debris; evidence for demyelinating activity < hours (prineas; raine). there is an inner area of plump cells that are positive for hla-dr and oro. type , or modestly active, is defined as a "shelf" of plump hla-dr-positive cells at the edge loaded with program and abstracts, american neurological association oro-stained neutral lipid but a paucity of or no myelin debris. a region of hypocellularity is observed at the center of plaque. type iv, least active or inactive, is defined as scattered hla-dr-positive cells at plaque edge with little or no o r staining and no evidence of myelin debris. the frequency of plaque types was determined from a random sample of ms tissue blocks from patients who died of ms. ten percent of the plaques were type i; %: were type ; % were type . the majority of plaques ( %) were inactive (type iv). accordingly, it is necessary to classify the demyelinating activity of ms plaques for protocols designed to investigate etiopathogenesis. do these results suggest that whatever causes ms can be eradicated in half of the demyelinating areas by the time of death? p . localization of g d l b ganglioside antigen in the human peripheral nervous system susumu kusunoki, atsuro chiba, tadashi tai, and lchiro kanazawa, tokyo, japan serum antibodies against ganglioside gm and/or g d l b frequently are detected in autoimmune neuropathies such as rnultifocal motor neuropathy, igm paraproteinemic neuropathy, and guillain-barre syndrome. some of them bind to gm or g d l b monospecifically but the others cross-react with both of the antigens. to investigate respective localizations of gm and g d l b antigens in the human peripheral nervous system (pns), immunohistochemical study of dorsal root ganglia (drg), dorsal roots, ventral roots, and sympathetic ganglia (sg), which were obtained from human autopsy specimens, was performed by using mouse monoclonal antibodies, each monospecific to gm and gdlb. ggr , monospecific to gd b, immunostained nerve cell somas and axons of drg, sg, and dorsal and ventral roots. ggrl also recognized some myelin, including paranodal areas. however, gmb , monospecific to gm , did not bind to either neuron or myelin. thus, serum anti-gdlb antibody can bind to neurons and some myelin in the human pns. further study is necessary to identify the localization of gm antigen, because previous biochemical studies have shown that gm is also present in the human pns. the purpose of this study was to compare t and t lymphocytes in migraine patients versus controls, and a review of the literature was done. fifty-six migraine patients, aged to , were tested, as were controls. the t :t ratio in migraine patients was : , compared to : for controls. suppressors (t ) were reduced from in controls to in migraine patients. helpers (t ) decreased from , in controls to in migraine patients, and total ?' lymphocytes decreased from , to , . previous studies have revealed similar differences in t lymphocytes, with higher t : t ratios being found in both migraine and tension-type headache patients. in food-induced migraine, an increase in circulating immune complexes was noted, with increased t levels. differences in serotonin binding to mononuclear cells have been noted in migraine patients. a decreased sensitivity of the lymphocyte beta-adrenergic receptor in migraine patients was suggested by one study. after lymphocyte incubation with il- , the natural cytotoxic response is augmented in cluster patients. the percentage of lymphocytes expressing receptors for il- was decreased in cluster patients in a fur-review of the literature ther study. this il- receptor defect was independent of whether the clusters were present. there is a loss of highaffinity binding sites for serotonin on lymphocytes in both episodic tension and chronic tension headaches. we used positron emission tomography (pet) to measure local cerebral blood flow in volunteer subjects while they performed tasks of memory-guided saccades and a visual fixation control. tasks were performed continuously for seconds during emission scans, after bolus injection of h lso. eye movements were verified with electrooculography. areas of significant increase in regional blood flow between tasks were matched to three-dimensional reconstructions of brain magnetic resonance images of each subject. compared to the visual fixation control, saccade tasks evoked bilateral activation in the posterior superior parietal lobule with extension into the inferior parietal lobule. activation was also seen bilaterally in an area of frontal cortex immediately rostra to the precentral gyrus extending from the superior frontal gyrus to the inferior frontal sulcus. the increased blood flow in the posterior parietal cortex most likely corresponded to enhancement of visual attention required during saccades, while that in the frontal lobe, which included the frontal eye fields, indicated activation for saccade motor output. pamela blake, alexander s. mark, martin kolsky, and jorge kattah, washington, dc fifty patients with third cranial nerve (cn) palsy underwent precontrast and postcontrast mri to assess the utility of this study in this clinical context. mri demonstrated an appropriate lesion in cases. six patients had brainstem lesions ( infarcts, mass lesion, cryptic vascular malformation, hemorrhagic shearing injury, with compound q toxicity). lesions of the cisternal segment of the nerve were present in patients ( aneurysms, lymphomas, ophthalmoplegic migraine, viral meningitis, coccidiodomycosis, nerve avulsion), with enhancement of this segment in patients. fourteen patients had cavernous sinus lesions ( lymphomas, nasopharyngeal carcinoma, tolosa-hunt syndrome, cavernous carotid aneurysms, pituitary apoplexy, aspergillosis). eighteen patients, all with history of diabetes or vascular disease, had normal mri results, suggesting microvascular infarction of c n . in patients with cn i palsy, mri can detect the presence of brainstem or cavernous sinus lesions and often can suggest their cause. mri with contrast enhancement can demonstrate involvement of the cisternal segment of cn i in patients with inflammatory or infiltrative processes that previously could not be radiographically demonstrated. our study suggests microvascular infarction does not cause nerve enhancement on contrast-enhanced mri. we describe patients with acute hyperglycemic, hyperosmolal, nonketotic stupor who had ocular flutter or opsoclonus clinically. these are the fourth and fifth adult patients reported with the acute onset of stupor and opsoclonus; all patients had nonketotic hyperglycemia and hyperosmolality (rapid eye movement sleep also causes stupor and saccadic eye movements). three of the patients had myoclonic jerks in addition to opsoclonus. in the , opsoclonus began when glucose and osmolality acutely increased, and completely resolved when glucose and osmolality became normal, showing that opsoclonus is a specific and reversible effect of the metabolic disorder and implying that either acute hyperglycemia or hyperosmolality directly causes opsoclonus. since acute hyperosmolality caused by nacl or sucrose can cause a similar syndrome in experimental animals (trans am neurol assoc ; : - ) and infants, hyperosmolality is probably more important. opsoclonus is thought to be due to abnormal activity of saccadic "burst" cells in the pons. acute hyperosmolality may cause spontaneous saccades by disinhibiting burst cells from normal "pause" cell inhibition or by directly activating burst cells. the combination of acute deterioration in mental status and either ocular flutter or opsoclonus should suggest acute hyperosmolality, in particular, nonketotic hyperglycemia. neural cell adhesion molecule (n-cam) and the related cell adhesion molecule l play significant roles in axon outgrowth and mediation of cell-cell contact in development, and after peripheral nervous system injury. to understand the role of these molecules after injury in the adult cns, we studied alterations in n-cam and l in the rat brain's response to entorhinal cortex (erc) lesion. post lesion, reactive synaptogenesis and axonal sprouting follow a well-defined temporal course in restoring the synaptic density of the dederented outer two-thirds of the hippocampal dentate gyrus molecular layer (ml) to near prelesion levels. we found striking regionand lamina-specific staining of n-cam and l in the normal hippocampus and marked alterations in these molecules after injury. embryonic n-cam, present in high amounts during development but expressed at very low levels in the adult hippocampus, was massively re-expressed in the denervated zone; the embryonic form was still heavily expressed days later, when synapse number returned to >so% of prelesion levels. l staining, normally evenly distributed through the ml of the dentate, was completely lost in the outer ml, which is denervated by the erc lesion. this staining had not returned by days after lesion. neural cell adhesion molecules play a role in specificity of neural connectivity both in development and after injury. in reactive synaptogenesis and axonal sprouting after injury, both ontogenetic (the reexpression of embryonic epitopes) as well as uniquely adult sequences of repair are utilized. following hemispherectom y" a. pascual-leone, h . t. chugani, l. g. cohen, j . p . brasil-neto, e. m . wassermann, j . and m. hallett, betbesh, md, and los angeles, ca we studied subjects, aged months to years, who underwent hemispherectomy months to years earlier for intractable epilepsy. all had a spastic hemiparesis contralateral to the resected hemisphere, which was present presurgically. we used focal transcranial magnetic stimulation to map the areas of the preserved hemisphere targeting the abductor pollicis brevis (apb), the biceps, and the deltoid ipsilaterally and contralaterally. in subjects who had hemispherectomy after age , the same area targeted ipsilateral and contralateral muscles. in the remaining subjects, who were more functional, areas targeted ipsilateral muscles. one area coincided with the contralateral representation, but stimulation induced motor-evoked potentials (meps) of lower amplitude and longer latency in the ipsilateral muscles. the other area, to cm anterolaterally, targeted exclusively ipsilateral muscles and stimulation induced meps of normal amplitude and latency. this separate ipsilateral representation was more distinct in subjects studied a long time after the hemispherectomy and in those who were younger at the time of the operation. these results show evidence of motor reorganization after hemispherectomy. better motor function is associated with topographically differentiated ipsilat-era and contralateral representations, which may depend on age at the time of hemispherectomy and the time since then. cynthia l. comella, glenn t . stebbins, nancy brown-toms, and christopher g. goetz, chicago, il in a single-blind, crossover study, we evaluated the effect of an intensive outpatient physical rehabilitation program (re-hab) on the severity of parkinson's disease (pd). the re-hab program consisted of -hour sessions per week for weeks. sixteen patients completed phases, a rehab phase and a control phase, separated by months. the order of participation in each phase was randomized. all patients were evaluated using the unified pd rating scale with subscales for mentation (ment), activities of daily living (adl), and motor function (mot) by an investigator blinded to the rehab phase of the patient. all patients were evaluated immediately before and after each phase. pd medications were not changed during any phase. following the re-hab phase, there was significant improvement in adl score (pre-rehab , post-rehab , p = . wilcoxon) and in mot score (pre-rehab , post-rehab , p = , wilcoxon), but no change in ment score. after the con-trol phase, there was no significant change in any outcome measure. this is the first controlled, crossover study of an intensive rehab program in pd. it demonstrates that re-hab improves objective motor function and adl scores. sensitive and quantitative measurements of leg weakness, one of the most common deficits in multiple sclerosis (ms) patients, can be made using specialized extremity testing equipment. to determine whether such determinations could be used in clinical trials, ms patients with leg weakness that had been stable for at least months were evaluated every days over a -month period. each testing session was carried out at the same time of day and medication dosages and schedules were kept constant (only patient was taking baclofen and his dosing remained constant). quadriceps and hamstrings strengths were measured in isometric contraction in a mechanical testing apparatus (kincom). variability for each series of determinations was expressed as the standard deviation of the mean as a percent of the mean. the overall variability then was expressed as the mean of the individual variabilities. the mean variability for the strength determinations over months was . k . , and only one series of determinations out of had greater than % variability. these results suggest that quantitative strength determinations might be useful in clinical trials, and early experience in trials of aminopyridines will be discussed. polymyositis (pm) is an inflammatory myopathy of unknown cause, but the accumulating data strongly suggest an autoim-mune pathogenesis. the histological picture is of muscle fiber necrosis and inflammation, whereas in postviral fatigue syndrome (pfs), a disorder characterized by severe fatigue with myalgia and psychiatric symptoms, the histological picture of muscle is essentially normal. enteroviruses have been implicated on epidemiological and serological studies in both. we have used the polymerase chain reaction (pcr) and an enteroviral-specific probe and found persistent enteroviral genomic material in both pm and pfs muscle biopsy specimens. furthermore, we used a radiolabeled full-length cdna probe derived from coxsackie b in an in situ technique to look for viral d n a in pcr-positive cases. coxsackie genome was clearly identifiable in the muscle biopsy specimens of patients with pm but negative in pcr enteroviral-positive cases of pfs. the virus excites an inflammatory reaction only in pm. a murine animal model for pfs developed in our laboratory showed positive muscle pcr using enterovirus probes and a conspicuous increase in interleukin within the brain. these results provide major clues in the search for the etiology of these two puzzling disorders. human t-lymphotropic virus type i (htlv-i) is a cause of adult t-cell leukemia and tropical spastic paraparesis. in a specific population of iranian jews originating from the city of mashad, there is a high incidence of htlv-i infection ( . %) and associated t-cell leukemia. we evaluated the incidence of possible correlation between htlv-i infection and spastic paraparesis in israeli mashadi-born jews. we have examined mashadi-born immigrants in a mashadi community center ( men, women, mean age t_ . yr) and non-mashadi iranian-born jews. blood samples were tested for htlv-i antibodies by particle agglutination test. the polymerase chain reaction (pcr) was used to amplify htlv-i sequences of d n a from peripheral blood mononuclear cells. twelve mashadi-born immigrants ( %) were seropositive for htlv-i. in of those serologically positive for htlv-i ( %), neurological examination revealed spastic paraparesis of varying severity. none of the non-mashadi iranian jews were seropositive for htlv-i or had clinical signs of spastic paraparesis. these results support other studies of htlv-i-associated myelopathy. the high incidence of htlv-i-associated spastic paraparesis in the mashadi community might be related to their unique history of a high rate of intermarriage among members of this ethnically segregated group. further epidemiological studies are underway to evaluate the incidence of htlv-i in mashadi families as well as in mashadi-originating jews born in israel, to identify whether infection might be genetically transmitted. lymphotropic virus t y p e i-associated acute t-cell leukemia/lymphoma william j . harrington, jr, william a. sheremata, susan snodgrass, and mark raven, miami, fl human t-cell lymphotropic virus type i (htlv-i)-associated acute t-cell leukernia/lymphoma (atl) is thought to produce important c n s disease infrequently. we wish to correct this impression by presenting neurological findings in patients seen between and the present. all had positive western blots to htlv with polymerase chain reaction confirmation of htlv-i infection. only had a concomitant human immunodeficiency virus infection. all were black, aged to years, were men and women. all but americans came from the caribbean nations of haiti ( , dominican republic (l), jamaica ( ), and trinidad ( ). sexual transmission was the risk factor for htlv-i for all except for intravenous drug user. all patients were systemically ill. three had preceding neurological abnormality ( , months, and yr) and had major neurological disease concomitantly. two of these had tumor masses demonstrated in brain and in the spinal canal. one had a minor facial sensory abnormality; only had no deficits. we conclude that cns disease is commonly associated with atl, and that in the us atl occurs principally in caribbean natives. a. nath, v . hartloper, and m . furer, winni$eg, manitoba, canada microglia and astrocyte cultures were established from human fetal brain. microglia were infected with human immunodeficiency virus (hiv) strains, hiv,, or hiv,,,, resulting in a rising titer of p antigen in the supernatants. multinucleated giant-cell formation, vacuolar changes, and rising levels of lactate dehydrogenase in the supernatants were seen, indicating a cytopathic infection of microglia. astrocytes were infected with free virus or cocultivated with an hiv-infected lymphocyte cell line (hut- ). after a productive phase (rising titers of p antigen and detection of hiv antigens by immunocytochemistry), the cells went into a latent phase where hiv could be detected only by dna polymerase chain reaction. a -fold increase in astrocytes staining for hiv antigens was seen after cocultivation with hut- cells. lymphocytes adhered to astrocytes by hours of cocultivation. no adhesion was seen to microglia. fusion of plasma membranes was seen on electron microscopy. infected astrocytes did not show cytopathic or morphological changes. cell-to-cell contact may be important in viral transmission to astrocytes. hszao-huei chen, steven b. stein, wing kong, and raymond p. roos, chicago, i l one of our goals is tq delineate molecular determinants for disease phenotypes produced by theiler's virus (tv), a mouse picornavirus. the identification of these genes and gene products may clarify viral pathogenesis and also lead to the identification of genes that are important in normal cns function and nonviral cns disease. members of the gdvii subgroup of tv cause an acute, fatal neuronal infection, whereas members of the to subgroup are less neurovirulent and produce a demyelinating persistent infection. our studies of infectious tv cdna clones have demonstrated that the gdvii b(vp )- c segment is critical for neurovirulence. several other areas of the genome, including the ' untranslated region (s'utr), also affect tmev-induced disease. the 'utr of poliovirus, another picornavirus, has a critical role in paralysis; this effect on neurovirulence is believed to result from an altered translational efficiency related to bind-region ing of neural cell proteins. tv 'utr has an unusual predicted secondary structure, even for picornaviruses. our studies demonstrate that the tv 'utr affects translational efficiency and has a distinctive protein-binding pattern. investigations of the tv 'utr may clarify features of translational regulation of cns genes in general. p . coronaviruses infect primate brain from g a y f. cabirac, ronald s. murray, galen cai, kristen hoel, and kenneth soike, englewood, co, and covington, la recently, we described finding coronavirus (cv) rna and antigen in active demyelinating plaques of multiple sclerosis (ms) brain tissue (murray et al, ann neurol, in press). molecular analysis showed the cv rna to be more closely related to murine cvs than to human cvs. we then demonstrated that, following intracerebral inoculation, the murine cv jhm and the putative ms isolate cv-sd could infect and cause demyelination in primate brain (murray et al, virology, in press). we now have data showing that murine cv can infect primate brain following intranasal or intravenous routes of inoculation. standard virology, histopathology, and the molecular analysis of viral cytotropism will be presented. we conclude that cvs related to murine cvs can infect primate cns from peripheral routes and warrant consideration as potential human pathogens. probes (gag, pol, or enw). eleven were white and were black. a history of transfusion was obtained in , and sexual risk of transmission was present in but not in others. fulminant disease occurred in transfused men months to years later but such disease was only seen in woman (in month). in contrast, of women with multiple sexual partners had rapid progressive disease. the male-to-female ratio was : for transfusion association and : for those at sexual risk but : for unknown risk, transfusion is an important risk for tsp/ham and the diagnosis must be considered in all gait problems, regardless of the "diagnosis."transfusion association should decrease with regular testing of blood donors, but this will not affect the risk of sexual transmission. spastic paraparedhtlv-i-associated myelopathy (tsp/ ham). it is unclear why htlv-i infection causes atl in some individuals and tsplham in others. differences in the genome of viral isolates or immunological and host factors have been hypothesized to play a role in disease expression. at present there are no animal models of tsplham and no suitable animal models of htlv-i infection that can address these issues. we transplanted severe combined immunodeficient (scid) mice with peripheral blood mononuclear cells (pbm) from tsplham patients in an attempt to produce htlv-i disease. two weeks after transplantation of pbm from tsplham patients, we detected anti-htlv-i igg in serum samples of of scid mice by enzyme immunoassay using sonicated whole virus. five weeks after transplantation, we detected anti-htlv-i igg to p , p , gp , or gp in serum samples of of scid mice by immunoblot of disrupted virus. these findings suggest that scid mice may be valuable in the study of molecular and pathological determinants of htlv-i-induced disease. theiler's virus produces an encephalomyelitis in susceptible mice. during the course of the disease, specific regions in the cns become infected. compared to the immunocompetent mouse, the nude mouse provides a useful model where viral dissemination can be studied in the absence of functional t lymphocytes and antibodies. we investigated the distribution and spread of the da strain of theiler's virus in the cns of nude mice. by immunohistochemistry, the hippocampus, arnygdaloid nuclei, entorhinal cortex, cingulate cortex, thalamus (anteroventral nuclei), midbrain, and spinal cord all contained viral antigens by weeks after infection. in addition, the olfactory nuclei, mamillary body, hypothalamus, basal ganglia, and nucleus raphe dorsalis often were involved. in the brain, the limbic system was the site commonly infected by theiler's virus. the time course of virus dissemination varied depending on the site of initial virus infection, though the final distribution of virus was the same. olfactory bulb injection, which is a direct inoculation into the olfactory pathway, resulted in more rapid spread than did cortex injection. we demonstrated the constant presence of viral antigen in the limbic system and a different kinetics of viral dissemination between the two different routes of intracerebral inoculations. these results suggest that limbic structures and their connections are important to the dissemination of theiler's virus. -associated myelopathy in a northwest native indian d. foti, d. werke, g. dekaban, g. p. a . rice, andj. oger, vancouver, bc, and london, ontario, canada a -year-old indian of the oweekeno tribe was admitted for investigation of a myelopathy. initially symptomatic with midthoracic radicular pain, she developed progressive spastic paraparesis over year with mild sensory symptoms and urinary retention. mri of the cord and brain were normal. csf showed elevated protein ( mgll), lymphocytes, and weak oligoclonal banding with evidence of intrathecal igg synthesis. antibodies to human t-lymphotropic virus type i (htlv-i) were positive by enzyme-linked immunosorbent assay and western blot on both serum and csf. presence of htlv-i was demonstrated by polymerase chain reaction of blood lymphocytes. htlv-i-associated myelopathy, or tropical spastic paraparesis, is endemic in southern japan, the caribbean basin, and several tropical islands but has not been reported in natives of northwest canada. this patient's only risk factors for htlv-i infection were blood transfusions years previously. ongoing familial and epidemiological studies as well as virus sequencing should indicate if this case represents an indigenous or an imported infection. caused by herpes simplex virus type lawy blankensbz) and herbert . newton, columbus, oh myeloradiculitis occasionally occurs secondary to herpes simplex virus type (hsv ) infection, but rarely has been reported after herpes simplex virus type (hsv ) infection without encephalitis. we describe a -year-old man who developed cervical myelopathy and radiculitis, never developed symptoms of encephalitis, and had positive hsvl spinal fluid cultures. h e initially developed extremity weakness and incoordination, numbness, paresthesias, and neck pain. evaluation was negative except for mri results, which showed a high-signal lesion centrally within the cervical cord. the weakness, sensory loss, and radicular pain progressed over several months. subsequent mri showed extension of the high-signal abnormality and mild enlargement of the cervical cord. symptoms stabilized briefly with dexamethasone but soon worsened, and were accompanied by paroxysmal kinesiogenic dystonic episodes of his arms and right leg. repeat evaluation was unrevealing except for the spinal fluid, which grew out hsv . the patient was treated with dilantin and a i-month course of intravenous acyclovir, with slow improvement of neurological status and resolution of the dystonic episodes. this case illustrates that hsvl can cause a myelopathy with a subacute and protracted course, requiring serial was more frequent in the middle-aged group ( p < . , p = . ). history of hypertension, previous strokes, diabetes mellitus, and antithrombotic treatment was similar, as were sex ratio, qualifying event type (transient ischemic attack or nondisabling stroke), and angiographic features; stenosis severity in either side and presence of ulceration were all similar. in elderly patients, ecad is associated with symptomatic cardiac disease (scad or af), whereas in middleaged patients it is associated with precursors of generalized atherosclerosis (smoking and hyperlipidemia). to identify the anatomic factors correlating with dementia in patients with lacunar infarctions, we examined digitized ct data on elderly patients (mean age = . yr; education = yr) who presented with acute lacunar infarction. dementia was diagnosed in patients ( . %) based on neuropsychological tests given months after stroke onset. the following ct variables were assessed: infarct location and number, total infarct volume, brain parenchymal and csf areas at levels, and width of the frontal horn, third ventricle (tvw), and lateral ventricle plus their ratio to the intracranial width. atrophy and leukoaraiosis were rated semiquantitatively using a standard scoring method. in the group overall, mean infarct volume was . cc and mean infarct number was . . in univariate analyses, dementia was significantly related to infarct volume, number, tvw, bilaterality, and infarct predominance on the left side, but not to leukoaraiosis or atrophy. in a regression model adjusting for demographic factors, the ct variables correlating independently with dementia status were infarct number (p = . , p = . ) and the presence of left cerebral infarcts (p = . , p = . ). we conclude that the most important ct variables related to dementia in lacunar stroke are lesion multiplicity and the presence of lesions on the left side. brain ischemia results in potassium (k+)-induced voltageregulated presynaptic calcium (ca") accumulation, which may contribute directly to neuronal in jury presynaptically, and also promote excessive release of excitatory neurotransmitters leading to cell damage postsynaptically. k+-induced depolarization of brain synaptosomes may be used as an in vitro model to study the therapeutic potential of pharmacological agents to alter ischemia-induced presynaptic ca + accumulation. we preincubated gerbil cerebral cortical synaptosomes in r (janssen pharmaceutical) at concentrations of to lo-' m, subsequently depolarized the synaptosomes with k + , at concentrations of to mm, and measured intrasynaptosomal ca ' ([ca +]) with the fluorescent indicator fura . r had no effect on ecaz'i in nondepolarized synaptosomes, but significantly (<. , student t ) depressed depolarization-induced {ca +] at to lo-' m in a dose-dependent fashion. the greater the degree of depolarization employed, the greater degree of depression in [ca +] was seen at each dose of r . since r had no effect on [ca +] when utilizing ca +-free incubation media, it was demonstrated that r prevents depolaritation-induced [ca ' ] increase by blocking voltage-regulated influx. because r appears to block voltage-regulated presynaptic ca ' accumulation, it should be further evaluated as a potential therapeutic agent after cerebral ischemia. sneddon's syndrome (ss) is a focal and diffuse arthropathy affecting mainly the vascular wall of the skin and cerebral arteries. etiology is not determined. we studied patients with ss ( females, males), aged to years. clinical, radiological, and immunological studies were done. all patients developed cerebrovascular disorders: ischemic stroke in %, transient ischemic attack (tia) in %, and ischemic stroke and tia in %. cerebral scan showed small and medium (less than cm) ischemic lesions in %. these lesions were superficial in the cerebral cortex ( %); deeper in the centrum semiovalis, internal capsule, and basal ganglia ( %); and both superficial and deeper ( %). ultrasound and angiogram studies revealed obstruction of intracranial arteries in %, and of extracranial arteries in %. partial or complete improvement of cerebrovascular symptoms was observed in %. immunological studies showed increased content of b-cell lymphocytes ( p < . ), increased levels of igm ( p < o.oool), and circulating immunocomplexes ( p < . ). anticardiolipin antibodies were increased ( %) and lupus anticoagulant detected ( %). cerebrovascular disorders in ss that lead to small ischemic cortical lesions have a good prognosis. pathogenesis of this syndrome may be related to antiphospholipid antibodies. the cheiro-oral syndrome is characterized by pure sensory deficit limited to the hand and mouth. this syndrome has been described in diverse lesions of the parietal operculum and brainstem, but occurs most commonly due to lesions of the contralateral thalamus, and suggests a humuncular representation of sensation in the ventral posterior lateral (vpl) and ventral posterior medial (vpm) nuclei. we describe a -year-old hypertensive woman who presented with sudden onset of numbness of the left side of her body. examination revealed a left hemisensory deficit to all modalities that spared the hand and peri-oral regions. cat scan and mri demonstrated an acute infarction of the posterolateral right thalamus, with a rim of preservation adjacent to the internal capsule. pure hemisensory loss with sparing of the hand and mouth ("inverse cheiro-oral syndrome") has not been reported previously, and complements previously published studies of the cheiro-oral syndrome in demonstrating somatotopic sensory representation in the thalamus. to examine the relationship between depression and dementia after stroke, we administered the -item hamilton depression rating scale (hdrs) and neuropsychological tests to elderly patients months after ischemic stroke. using dsm- -r criteria, we found dementia in ( . %). hdrs score was . -t . overall, and higher in demented compared to nondemented patients ( . . vs . t . , p = . ). the frequency of depression (total hdrs score > ) was also higher with dementia ( . % vs . %, p = . ). however, demented patients did not differ from nondemented patients on ratings of depressed mood. instead, hdrs items for psychomotor retardation, reduced work activities, and impaired insight best distinguished the groups. in multiple regression analysis, stroke severity (p = . , p = . ) was the most important correlate of hdrs score; dementia status was not correlated independently. mean scores on mini-mental state examination and neuropsychological tests assessing memory, orientation, verbal, spatial, attentional, and abstract reasoning skills did not differ by depression status. although weakly related to intellectual impairment, hdrs score in our stroke sample was most importantly associated with stroke severity. higher scores on hdrs in demented stroke patients may be explained by physical and cognitive symptoms that are expected with dementia. these findings do not support a causal link between depression and dementia, and argue against the importance of "depressive pseudodementia" as an explanation for intellectual decline after stroke. to investigate the pathophysiological mechanism of the white matter lesions in progressive subcortical vascular encephalopathy (psve) of binswanger type, we measured regional water partition coefficient (pc) (reflecting water content) and effective p h (pht) (weighted average of intra-and extracellular ph) with dynamic positron emission tomographic technique using - co,, o,, and c- co,. si-multaneously, regional cerebral blood flow (rcbf) and regional cerebral metabolic rate of oxygen (rcmro,) were evaluated. eight subjects ( normal, psve, multiple infarction) were examined. in the white matter lesions in psve, corresponding to high-intensity areas in t -weighted images of mr, the pc increased and pht was unchanged or decreased, whereas both rcbf and rcmroz declined. the ratio of white matter pc to gray matter pc was . in psve and . in normals. in the frontal gray matter, the pc decreased in psve, whereas rcbf and rcmroz also decreased. these results suggest that tissue water content increases in the white matter lesions in psve reflecting the edematous status of the damaged regions. elevated pht with high pc may reflect the increase of extracellular water of the tissue. measurement of pc and pht provides useful information about the pathogenesis of psve. stroke has been the second most common cause of death in korea but its risk factors (rfs) have not been studied intensively, so the rfs or causes were investigated prospectively in , consecutive stroke patients who were admitted to the chungnam national university hospital, taejon, korea, between and . they included cases of cerebral ischemia (ci) ( . %), cases of intracerebral hemorrhage (ich) ( . %), and cases of subarachnoid hemorrhage (sah) ( . %). control data were obtained from healthy spouses of the patients. multivariate analyses showed that hypertension (ht) was the strongest rf for all stroke types and was followed by old age, diabetes mellitus (dm), smoking, high-density lipoprotein cholesterol, and fibrinogen. the rfs for atherothrombotic ci included old age, ht, dm, smoking, fibrinogen, and cholesterol. for lacunar infarcts, ht, dm, old age, fibrinogen, alcohol abuse, smoking, and female sex were the significant rfs. ht was the cause of ich in ( . %) and alcohol abuse ( , . %) and vascular anomalies ( , . %) followed. most alcoholassociated ichs occurred characteristically in the posterior fossa. frequencies of hospital admission of ich patients correlated positively with diurnal variation of temperature ( r = . , p < . ). aneurysmal rupture was the cause of sah in patients ( . %). three major sites of aneurysms identified on cerebral angiograms were the anterior communicating artery ( , . %), the middle cerebral artery ( , . %), and the posterior communicating artery ( , . %). thirty-nine patients ( . %) had no identifiable cause of sah. in korea curvilinear subinsular lesions have been noted on ct but the underlying pathology is unknown. we reviewed the cranial mr scans ( . tesla ge machine) of serial patients over the age of who had no cause for mr hyperintensities (hi) other than age or vascular risk factors. seven ( %) had linear subinsular h i (sihi). four of ( %) patients with sihi and of ( %) without sihi had marked periventricular h i compatible with subcortical arteriosclerotic encephalopathy (pvhi) ( p < . ). patients with sihi were older ( . yr) than patients without sihi ( . yr) ( p < . ). four of ( %) patients with sihi had hypertension program and abstracts, american neurological association or vascular risk factors. a further patient with diabetes, hypertension, and the opercular syndrome (bilateral facial, pharyngeal, and lingual weakness) had subinsular lesions on ct. the brain arteries were injected postmortem with a lead/ gelatin suspension, and mr of the whole brain and x-ray films of the brain slices were taken. bilateral sihi were seen on mr and corresponded with linear cavitary infarction pathologically, which on microangiograms was found to lie in the border-zone between cortical and basal penetrating arteries. we conclude that sihi are associated with older age and pvhi, and can be due to infarction in a deep watershed territory and can be associated with clinical deficits. hemodilution-treatment results in consecutive cases james l. frey, phoenix, az because precipitous neurological deterioration occurred during blood pressure reduction in a seminal case of lacunar infarction, subsequent patients with partial or evolving lacunar deficits were treated with hemodilution and blood pressure nonintervention to test the hypothesis that lacunar strokes represent perfusion failure. isovolemic hemodilution was performed using hetastarch with target hematocrit of to . results of pretreatment ct brain scans, carotid ultrasound, and echocardiograms were normal. nine patients recovered normal neurological function, and regained complete functional independence in close temporal correlation with hemodilution. mri brain scans demonstrated appropriate single white matter lesions in cases. no specific risk factor combination could be identified. n o patient has had recurrent stroke in follow-up from to months. response to hemodilution suggests a hemodynamic pathophysiology. successful treatment requires ( } blood pressure nonintervention and ( ) hemodilution prior to severe clinical deterioration. the hemodynamic classification for the carotid-cavernous sinus fistula (ccf) is important for the implication of prognosis and therapy, but satisfactory objective criteria for such differentiation is still lacking. retrospectively, we studied the application of extracranial duplex sonography in cases of ccf with emphasis on the hemodynamic parameters of resistivity index and flow volume. a correlation was made with the angiographic findings in an attempt to evolve an objective hemodynamic classification by this noninvasive method. the alterations in membrane metabolism and structure could be the primary etiological event in alzheimer's disease (ad) that results in the clinical and neuropathological findings. to investigate in vivo brain membrane phospholipid and highenergy phosphate metabolism in probable ad patients and control subjects, the building blocks (pme) and breakdown products (pde) of membranes and the high-energy phosphates pcr and atp were measured noninvasively by in vivo brain p mrs in probable ad patients ( males; females) and controls ( males; females). all subjects were assessed by mini-mental, mattis, and blessed scales. we found that, at clinical onset, ad females had elevated pme ( p = . ), decreased pcr ( p = . ), and decreased atp ( p = . ). similar changes were not seen in ad males at clinical onset, but the severely demented ad males had increased atp ( p = . ). correlation analysis for the ad patients revealed that increasing dementia was associated with decreasing pme ( p = . ; r = . ), increasing pde ( p = . ; r = . ), increasing pcr ( p = . ; r = . ), and increasing atp ( p = . ; y = . ). similar metaboliccognitive correlations were not seen in the controls. these results demonstrate alterations in membrane and energy metabolism at the earliest clinical stages of ad. increasing dementia correlates with markers of membrane degeneration and decreased utilization of high-energy phosphates. both of these findings suggest the dementia in ad is secondary to membrane changes resulting in synapse loss. alzheimer's disease: postmortem mri and histological correlates fen-lei f. chang, j. e. purisi, c. r. jack+ jr, and r. c. petersen, rochester, mn hippocampal atrophy, defined by mri-derived volumetric measurement, has been useful in differentiating alzheimer's disease (ad) patients from normals. since several studies have demonstrated anatomical and functional gradients along the rostral-caudal (r-c) axis of the hippocampus, it is tempting to speculate on the existence of a differential distribution of morphometric changes along this axis. the hippocampi from patients with clinically and pathologically confirmed ad were studied by postmortem mri and by reconstruction of serial histological sections. there was good correspondence between these two methods. the r-c length of the hippocampus in ad was preserved compared to normal. this length was longer on the left, both in normals and ad. the adassociated atrophy was due primarily to the reduction of the coronal cross-sectional area of the hippocampus. with increasing hippocampal atrophy, volume reduction was more prominent in the rostral area (pes hippocampus). this nonuniform reduction in volume may be associated with different connectivity patterns between rostral and caudal hippocampus. the purpose of this study was to determine the neuropathological validity of nincds-adrda criteria (nac) for probable and possible ad. mckhann et al ( ) provided clinical criteria for the categories probable ad and possible ad. the validity of these categories has not yet been reported. a retrospective, blinded evaluation of the complete neurological history, examination, neuroimaging, laboratory, and psychometric data was done for subjects from the state of florida brain bank. pathological classification, which was blind to clinical diagnoses, was in categories: pure ad, ad + , and other dementias. ninety-three percent of probable ad (n = ), whereas only % of possible ad (n = ) patients, had ad or a d + ( p = . ). pure ad was found in % of probable ad and % of possible ad patients ( p = . ). pathological evidence of coexisting parkinson's disease was present in % of all ad brains. these results suggest differential predictive power of nac for probable and possible ad, as suggested by the labels. nac are, therefore, usefui for research and clinical purposes. our prior study of falls in the elderly had shown significantly more white matter low attenuation (wmla) on ct scan among fallers than nonfallers, but no association between wmla and cognitive impairment among nondemented subjects. as these subjects were followed over time, it appeared that fallers were becoming demented at a more rapid rate than nonfallers. as a result, we analyzed the relationship between wmla and rate of change on the blessed test of information, memory, and concentration (bimc) in a combined cohort of subjects from the falls study and from a longitudinal study of dementia and normal aging. we selected of these subjects whose initial bimc score was less than (i.e., not already severely impaired) and who had at least yearly bimc evaluations. ct scans were scored on an -point ordinal scale for hemispheric wmla. linear regression was used to summarize the rate of change for each subjects' test scores. the rate of change on bimc was . points per year with standard error (se) of . among subjects who eventually became demented; nondemented subjects declined at . points per year with se of . . multiple regression analysis was performed with initial bimc score and wmla as the independent variables and rate of change of bimc as the dependent variable. wmla accounted for % of the variance (partial r = . , t = . , p < . ). these data suggest that elderly subjects with wmla may be at increased risk for rapid cognitive decline. such as g proteins and adenylate cyclase. the activities of adenylate cyclase, and of the g protein-associated enzyme activity, low-km glutamyl transpeptidase (gtpase), were assayed in membranes prepared from the postmortem brains of alzheimer-diseased and age-matched control subjects. both basal and fluoroaluminate-stimulated adenylate cyclase activities were significantly reduced in ad frontal cortex compared to control subjects ( p < . ; two-tailed student's t test). in addition, a significant, though smaller, reduction in basal gtpase activity also was detected in ad frontal cortex ( p < . ). in contrast, no significant change in the activity of either enzyme was detected in the hippocampus. the stimulation of gtpase activity by muscarinic and gababreceptor agonists was not altered significantly by the presence of alzheimer's disease. however, the degree of stimulation was much lower in human tissue compared to that observed using fresh rat brain, suggesting that the ability of receptors to activate g proteins declines post mortem. these results suggest that alzheimer's disease causes alterations in some key components involved in signal transduction. the association of lobar hemorrhage (lh) with cerebral amyloid angiopathy (caa) and that of caa with alzheimer's disease (ad) are well known. to determine how frequently lh and caa occur in ad, we reviewed patients with cerebral or cerebellar hemorrhage and caa. five patients were treated surgically, none was demented, died, and came to autopsy. eight patients died of lh and came to autopsy. of the autopsied patients, had ad, both clinically and neuropathologically. they comprised . % of cases of autopsy-confirmed ad in our laboratory. none of the other patients were known to be demented. five had senile plaques, with or without neurofibrillary tangles, in the hippocampus, and occasional senile plaques in the cortex, but none met the consortium for establishing a registry for alzheimer's disease neuropathological criteria for ad. ad patients were , , and years old and the ages of the nondemented patients ranged from to (mean = . yr). seven were younger than years of age. despite the frequent occurrence of caa in ad, we found that lh was uncommon. in addition, most of our patients with lh and caa were not demented and tended to be younger than ad patients with lh. these results indicate that the hf is involved primarily in acquisition or leaning processes and less so in retrieval of previously learned information. these findings relate to memory and structural brain changes found in normal aging. alzheimer's disease y . stern, l. stricks, g. alexander, . prohovnik, and there is an inverse relationship between parietotemporal cerebral blood flow and years of education in alzheimer's disease (ad) patients matched for clinical severity, which suggests delayed clinical manifestation of ad in patients with higher education (stern et al, soc neurosci abs ). we classified the lifetime primary occupations of ad patients using the dictionary of occupational titles of the us department of labor and derived factor scores describing intellectual, interpersonal, and physical job demands. after controlling for age, education, age at onset, illness duration, and dementia severity (mental status and activities of daily living), relative perfusion in the parietotemporal region (assessed using -xenon inhalation) showed significant correlations with job complexity (pl: r = -. , p < . ) and interpersonal (p : r = -. , p < . ) factor scores. in a stepwise multiple regression, job complexity and interpersonal skills increased explained parietotemporal flow variance by . % ( f = . , p < . ) over that explained by demo-graphic and severity indices; physical demands then accounted for another . % of the variance ( f = . , p < . ). we conclude that occupational demands, similar to but independent of education, may provide a reserve that delays the clinical expression of ad. richard mayeux and ming-xin tang, new york, n y risk factors for alzheimer's disease (ad) were collected from patients with ad and healthy elderly controls in an urban community population consisting of ethnic groups: black, hispanic, and white. advanced age (> yr) (or = . ; % ci . - . ) and head injury with loss of consciousness (or = . ; . - . ) were associated with ad, controlling for all known putative risk factors. factors such as low education (< yr) (or = . ; . - . ) and family history of ad (or = . ; . - . ) were not found to be significantly related to ad. head injury occurred in . % of the patients and .?% of controls. most ( %) head injuries in the patients with ad occurred after age , prior to disease onset. in controls with head injury, had experienced a head injury before age . the duration of unconsciousness was consistently longer in patients with ad than in the controls. the overall effect in each ethnic group was similar (or,, . ; . - . ). these results confirm and strengthen the previously described putative relationship between head injury and ad. we also conclude that both the severity and the timing of the head injury as well as the frequency of head injury in the population at risk may be important factors in understanding the causal relationship between head injury and ad. the purpose of this study was to determine how native language affects the cutoff scores in screening tests for dementia. there is a paucity of data o n this issue at present. screening tests used in the study were: folstein mini-mental state (mms); clockdrawing (clock); preparing a letter for mailing (mail); -item grocery list (list); and hamilton depression scale (ham). the subjects included ( demented) native english speakers (eng) and ( demented) native spanish speakers (spa) with memory complaints. diagnosis of dementia was determined by neurological, neuropsychological, and psychiatric evaluation. age and gender were unrelated to mms. in spa only, education was positively related to mms. ham scores were higher in de- and . (spa); c d and list did not add discriminative power to mms for eng but did so for list in spa. mms discriminates between demented and nondemented far better in english than in spanish speakers. only mail adds discriminative power to mms. a. heyman, g. fillenbaum, s. mirra, and participating cerad neuropathologists, durham, nc, and atlanta, ga the clinical diagnosis of alzheimer's disease (ad) has become more accurate in recent years due to the application of specific clinical criteria, wider use of neuroimaging procedures, and greater expertise among physicians. we report the frequency of clinical misdiagnosis of ad among patients who at autopsy were found to meet the rigorous clinical diagnostic criteria imposed by the consortium to establish a registry for alzheimer's disease (cerad) study. these patients included men and women (mean ages and yr, respectively) who were among the group of patients who died in cerad medical centers in the us between and . the clinical diagnosis of ad was neuropathologically confirmed in ( . %) of the cases. of these cases, varying degrees of concomitant cerebrovascular disease were present in % and coexisting parkinson's disease changes were found in %. in of the patients without neuropathological evidence of ad, the diagnoses were: lobar atrophy, diffuse lewy body disease, nonspecific neurodegenerative changes, and mesocorticolimbic dementia, respectively. the fifth patient showed no morphological abnormalities. on the basis of these results, it would appear that application of strict diagnostic criteria, as well as the use of brain scans and detailed clinical and neuropsychological tests by experienced clinicians, cannot yet distinguish some types of primary degenerative dementias from alzheimer's disease. we designed a scale that measures an underexplored facet of functional decline in alzheimer's disease (ad): the patient's dependence on others for supervising or performing activities. two hundred twenty-three informants for patients with mild ad (clinical dementia rating [cdr] = for ; cdr = for ) were interviewed and dependence was staged from to . interrater reliability was assessed by separate interviews of informants; agreement was % for dependence stage. dependence stage differed significantly at the cdr levels (chi square = . , p < . ) and correlated significantly with modified mini-mental state (mmms) ( r = -. , p < . ) and blessed dementia rating scale-part (bdrs) ( y = . , p < . ). seventy-eight percent of patients in a health-related facility were at stage or higher vs % of patients living at home. in a multiple regression model, both the bdrs and dependence scale accounted for unique portions of the variance in mmms, suggesting that they assess unique aspects of functional ability. dependence increased significantly in patients retested at year. we conclude that the dependence scale is reliable and relates to both disease severity and progression. formal assessment of dependence should prove useful for studies of the natural history of ad as well as for clinical trials. cortical-basal ganglionic degeneration (cbgd) is a disorder characterized by an asymmetrical akinetic-rigid syndrome and cortical signs such as apraxia, alien limb phenomena, and cortical sensory loss. dementia has been present in many cases, but always as a late manifestation. we report cases pathologically consistent with cbgd, presenting as primary degenerative dementia, fulfilling nincds-adrda criteria for probable alzheimer's disease (ad). the first patient presented with changes in memory and personality, language dysfunction, decreased verbal output, and shuffling gait. follow-up examinations over years showed progressive dementia, wide-based gait, and frequent falls. the second patient presented with complaints of memory loss. neuropsychological examinations showed progressive deficits in memory, attention, calculations, and visuospatial functioning. no movement disorder developed over years of follow-up. at autopsy, both patients had typical changes of cbgd and lacked pathological features of ad. definitive diagnosis of cbgd rests on both clinical and pathological criteria. cbgd should be considered in the differential diagnosis of patients with dementia resembling that found in ad, especially if extrapyramidal signs are present. a quick, easily administered and scored test for praxis is desirable in evaluation of neurological patients. during months in , each patient seen in the outpatient setting by the principal investigator (e. k.) received of praxis screening batteries. thirty-six patients were tested with a short battery. eleven had normal cognition based on neurological history, examination, and a short test of mental status. twenty-five had cognitive decline (cd). handedness, male/ female ratio, education, and mean age were similar in both groups. mean time of completion of the test was seconds in normals and * seconds in patients with cd. total scores (maximum ) were . * . in the normals and . in the cognitively declined patients. twenty-five other patients, with cd and with normal cognition, were tested with a longer battery containing oral/ facial, upper and lower limb, axial, sequential, and imitation subtests (maximum score ). normals completed the battery in i , and cognitively declined patients completed the battery in ? seconds. of the various subtests, tests of sequential praxis were performed most poorly by patients with cd: . * . in normals vs . * . in patients with cd. oral/facial praxis was least affected by cd: olivopontocerebellar atrophy (opca) is generally understood to be a nondementing neurodegenerative disorder affecting the cerebellum, lower brainstem, and spinal cord. one of us (s. k.) recently reported that postmortem cerebral cortex from patients with dominantly inherited opca shows a widespread reduction of cholinergic markers similar to that observed in alzheimer's disease (ad). we were interested to determine the status of other neurotransmitter systems in opca postmortem cerebral cortex. samples of frontal, parietal, temporal, and occipital cortex were dissected from confirmed cases of opca and age-matched controls. after processing, neuropeptide levels were measured by radioimmunoassay. concentrations of somatostatin were significantly reduced by to % in of the cortical areas of opca brain that were examined. the area that was spared was the inferior temporal gyrus, a region in which somatostatin levels are markedly reduced in ad. levels of neuropeptide y were normal in all areas, while concentrations of cholecystokinin, vasoactive intestinal polypeptide, and substance p were significantly increased in of the areas. these data show widespread neuropeptide changes in the cerebral cortex of opca postmortem brain. in contrast to cholinergic markers, the pattern of neuropeptide changes is different from what is observed in ad. it has been postulated that demise of the corticomotoneuron is the initial event in amyotrophic lateral sclerosis (als) and that the anterior horn cell dies as the result of antegrade glutamatergic excitotoxicity (muscle nerve ; : ). excitability of the corticomotoneuronal system can be tested by measuring threshold-to-cortical magnetic stimulation and the motor-evoked potential (mep)/compound muscle action potential (cmap) ratio, which estimates the number of corticornotoneurons stimulated. cortical threshold and mep/ cmap ratio were measured in patients early in the course of als. the mean time interval from onset of first symptoms was . months. mean threshold and mepicmap ratio measured . f . % and . rfr . %, respectively. in ( . %) patients, threshold was paradoxically low (< %, mean . +. . %) and in ( . %) patients there was no response. there was a significant ( r z = . ) inverse power relationship between cortical threshold and mep/cmap ratio given by . x mep/cmap-'j. six months later, / ( . %) patients still had low thresholds but the mean mep/ cmap ratio had dropped to . ? . % and in . % there was no response. we conclude that early in als the corticomotoneuronal pathways are abnormally excitable. this may explain early cramping and fasciculation, which characteristically diminishes as als progresses. one of the distinct clinical features in patients with amyotrophic lateral sclerosis (als) is loss of elasticity of skin. however, little is known concerning the biochemical nature of skin elastin in als. in our study, cross-links unique to elastin, desmosine and isodesmosine, were measured and compared in skin tissue (left upper arm) from patients with als and from age-matched controls. the contents of desmosine and isodesmosine were decreased significantly ( p < . and p < . , respectively) in patients with als (mean * sd, . ? . and . * . nmol/mg dry weight; range . - . and . - . nmol/mg dry weight, respectively) as compared with those of controls (mean sd, . * . and . . ;range . - . and . - . , respectively), and were negatively and significantly associated with duration of illness in patients with with amyotrophic lateral sclerosis als ( r = - . , p < . , and r = - . , p < . , respectively). the ratio of desmosine and isodesmosine was constant ( : ) in all samples analyzed. the decline in skin desmosine and isodesmosine is more rapid in als than in normal aging. thus, cross-linking of skin elastin is affected in als. (supported in part by n i h grants de , de , de , ar , ar , and nasa grant nag- - .) pl . natural history of amyotrophic ( ) collection of large numbers of twin pairs in disease of low prevalence is difficult. to circumvent this, we devised a new approach termed the "death discordant twin pair" method. eleven thousand deaths from motor neuron disease (mnd) were extracted from the office of population censuses and surveys during to . birth indexes from onward were searched for possible twins. for each twin so identified ( pairs), the national health service central registry located the relevant family practitioner committee and thence the co-twin's general practitioner. the search produced: ( ) living co-twins; ( ) embarked; ( ) dying as adults or infants; ( ) not mnd; and ( ) validity of the accuracy, sensitivity, and specificity of the world federation of neurology (wfn) subcommittee on motor neuron disease working group criteria for the clinical diagnosis of amyotrophic lateral sclerosis (als) has been tested against neuropathological criteria in autopsied patients (neurology, in press). integration of clinical and electrodiagnostic data to meet wfn criteria for possible, probable, and definite als was studied in this samegroup. patients received . ifr . (mean * standard deviation) electromyograms (emgs) per patient and included . . emg levels (bulbar, cervical, thoracic, lumbar) per patient. proportionately fewer emgs were performed as the level of diagnostic certainty at presentation increased: suspected ( . %), possible ( . %), probable ( . %), definite ( . %). in only . % of all patients studied did the first emg alone change the level of diagnostic certainty of the diagnosis of als. only . % of patients presenting with suspected als alone or with possible or probable als were associated with a change in level of diagnostic certainty following or more emgs. however, although increasing the number of emgs performed per patient may be associated with an increasing chance of increasing the level of diagnostic certainty ( emgdpatient = . %; emgdpatient = . %), selection of the level of emg analysis was more crucial. the "el escorial" criteria emphasize the importance of emg evidence of lower motor neuron involvement in a limb with clinical upper motor neuron signs. our analysis of emg studies in autopsy-confirmed als patients suggests that complete evaluation of bulbar and thoracic levels for lower motor neuron changes and complete evaluation of motor unit recruitment patterns are important for the integration of emg data with clinical data in the application of the "el escorial" criteria for the diagnosis of possible, probable, and definite als. sibships on guam annette grefe, john steele, linda flares, and stephen waving, birmingham, al, and umatac and mangikao, guam reports in the s indicated that % of guamanian chamorro patients with amyotrophic lateral sclerosis (als) gave october a positive family history. subsequent investigators have inferred that purely genetic factors are not responsible for guamanian als or its clinical variant, parkinsonism-dementia complex (pdc). we report the first chamorro sibships selected in an ongoing study of familial aggregations. the basis for the initial selection was that the youngest patient in the sibship had als. age of onset was to years (mean yr). fourteen of persons in these sibships were affected. others in the sibship developed pdc, progressive supranuclear palsy, or pure dementia later in life (mean yr, range - yr). these cases developed to years (mean yr) after onset of disease in the first sibling. the age at onset of the first case and the intervals between earliest and latest cases in such sibships may help to determine minimal and maximal latency (i.e., interval between exposure to an exogenous agent and onset of symptoms). our observations suggest that exposure may have occurred early (before age ) with varying and often long latency (up to yr). we also find that variability of clinical expression may be correlated with the age at onset. concentrating on the study of familial cases on guam may enhance the identification of the etiologic agent(s) of this prevalent and tragic disorder. the spinocerebellar ataxias are an uncommon group of genetic disorders that have been well characterized in north america and europe. information concerning these conditions in africa and other parts is scant. to address this problem, a large-scale survey has been undertaken in the cape province of south africa. in this investigation, more than persons in affected families have been appraised and investigated and phenotypic features have been analyzed in detail. linkage studies have been undertaken in families with similar phenotypes in which the condition was transmitted as an autosomal-dominant trait. human lymphocyte antigen (hla) typing was carried out on members of the families and linkage analysis was undertaken using the liped program to analyze the data with a correction factor for age of onset. maximum lod scores were: family a: . ( = . ); family b: . ( = . ); family c: . ( = . ); family d: . ( = . ). these results indicate linkage to hla in out of families. these findings provide support for the concept of genetic heterogeneity in these phenotypically homogeneous families. pcr typing with the reportedly more closely linked d s locus is now being undertaken in these south african families. h.-p. hartung, g. f. hoffmann, and g. becker, wunburg, heidelberg, germany recently, l- -hydroxyglutaric acidemia has been described as a novel metabolic disorder in children. we report the occurrence of this disease in adults. one of brothers developed at the age of an abnormal gait and dysarthria; in the other , clumsiness and walking delay were noted at age . symptoms progressed and at the time of admission, when the patients were and years, neurological examination revealed a spastic ataxic gait, limb ataxia, dysmetria, dysarthria, dystonic posturing, and mental retardation. ct and mr imaging revealed subcortical white matter changes with loss of arcuate fibers, folial atrophy, and leakage in the cerebellar vermis, as well as atrophic changes in the cerebellar hemi-acidemia program and abstracts, american neurological association spheres. on biochemical screening, highly elevated concentrations of l- -hydroxyglutaric acid were found in csf, plasma, and urine. the pathological accumulation of l- hydroxyglutaric acid in these adults, along with the clinical picture characterized by cerebellar, extrapyramidal, and pyramidal symptoms and oligophrenia, and the neuroradiological findings of severe loss of myelinated arcuate fibers in subcortical white matter, conform with what previously has been described in the few neuropediatric cases. the biochemical abnormality underlying accumulation of this organic acid remains elusive. this study was undertaken to differentiate primarily affected areas from functionally suppressed areas due to remote effect in aphasic patients with focal brain degeneration, using an activation method with - water, in comparison with [sf] -fluoro- -deoxy-~-g~ucose (fdg) positron emission tomographic examination at rest. the subjects were patients with slowly progressive aphasia showing contrasted clinical symptoms (nonfluent type vs fluent type). regional cerebral metabolic rate of glucose (cmrglu) was measured with intravenous injection of mbq of f- fdg at rest. regional cerebral blood flow (cbf) was measured with intravenous bolus injection of . gbq of - water in different conditions: at rest, under repetition tasks, and under naming tasks. changes of cbf were evaluated between a resting condition and task-performing conditions. regional cmrglu was decreased focally in both broca's and wernicke's areas similarly in these cases in spite of the difference in clinical symptoms, whereas the patterns of regional cbf changes were different. the fluent patient showed prominent activation in the bilateral frontal areas on repetition tasks. the nonfluent patient showed, whereas the fluent patient did not show, focal activation in the left occipitoparietal area on a naming task. evaluation with an activation method can provide detailed information about the pathophysiological process and the location of primary lesion. defective complex i activity has been linked to huntington's disease (hd) and parkinson's disease (pd). intrastriatal injection of inhibitors of complex i reproduces the pathological features of hd, and the neurotoxin mpp+ kills dopaminergic neurons by inhibiting complex i. defects in complex i have been reported in hd and pd, but the distribution of this enzyme in the brain is unknown. to map complex i in brain quantitatively, we developed an assay using e h)dihydrorotenone to label the enzyme in tissue sections. this high-affinity binding is saturable and is displaceable by rote-in brain none and mpp+. using pm rotenone to define nonspecific binding, more than % of binding is specific. highest levels of binding are found in kidney, followed by myocardium. moderate levels of complex i are seen in striated muscle and some brain regions. within the brain, binding varies more than -fold and is heaviest in the cerebellar molecular layer and dentate gyrus. lower levels of binding are found in cortex and striatum and very low levels are located in substantia nigra. this assay may help to clarify the role of complex i in neurodegenerative disorders. ( in , patients with medically intractable parkinson's disease underwent autologous adrenal medullary-to-caudate transplants at the university of california-los angeles (ucla). these persons had been followed for several years before operation at -or -month intervals. at each visit, their disability had been rated on the quantified ucla scale and the hoehn and yahr stage of disease. these provided a longitudinal assessment of the progression of disease in each patient, which could be compared to the rate of progression in the cohort of cases followed at ucla for years. in addition, the unified parkinson's disease rating scale provided supplementary data for the immediate preoperative and subsequent postoperative evaluations. the hours "off" also were recorded for the preoperative and postoperative periods. after operation, the same evaluations were performed by the neurologist who previously had cared for the patients. the longitudinal postoperative data revealed that at to months after operation, all patients improved. after years, continue to be less disabled than their preoperative baselines. the progression of their disease, while still evident, is nonetheless proceeding at a slower rate than before transplant. the fourth patient had brief improvement shortly after operation, but then rapidly worsened to his previous level. his disease has continued to progress at a rapid pace, unchanged from progression before operation. individuals at risk for huntington's disease h . p. h . kremer, w. shtybel, b. snow, c. clark, j . theilmann, m . r. hayden, and w. in huntington's disease (hd), caudate hypometabolism as demonstrated by positron emission tomography (pet) is a well-established feature in symptomatic patients. in individuals at risk, however, conflicting findings are reported. since we have performed pet scans in asymptomatic persons at risk for hd (age - yr) . linkage analysis with independent dna probes or subsequent evolution to clinical hd (in patients) allowed a risk estimate for subjects. twenty were considered to be at increased risk (? %), at decreased risk (< %), and in individual no modification could be given. nine subjects were not tested. a pet scan was considered abnormal if either the caudate/thalamus ratio or the caudate/whole-brain ratio of rcmrglu was more than these criteria, scans in individuals were abnormal. none had received a decreased risk. comparison of the ratios of increased risk, decreased risk, unmodified risk, and control subjects failed to show statistically significant differences (analysis of variance). follow-up of persons with an abnormal scan showed conversion to symptomatic status within years after the first abnormal scan. this result suggests that an abnormal pet scan in a person at risk for h d heralds the onset of choreic movements. robitaille, m . el-awar, b. clark, l. scbut, m. ball, l. young, r. currier, and k. sbannak, toronto, ontario, and montreal, quebec, canada; pittsburgh, pa, minneapolis, mn, portkmd, or, and jackson, ms we measured the levels of dopamine in striatum of patients with end-stage dominantly inherited olivopontocerebellar atrophy (opca). on average, dopamine levels were reduced in putamen ( - , as compared with controls), caudate ( - %), and nucleus accumbens ( - %). however, individual patient values showed a wide variation (normal to - ), indicating that striatal dopamine loss is a common, but not constant feature of opca. seven patients had marked putamen dopamine loss (- to - ) but without corresponding severe substantia nigra cell damage; this suggests a "dying-back'' phenomenon in which nerve terminal loss precedes cell-body degeneration. in this regard, opca may offer the possibility of examining nigrostriatal dopamine neuronal degeneration at an early stage. although patients were found to have severe nigral cell loss with near total ( - to - %) striatal dopamine loss, none had depression in parkinson's disease (pd) has been correlated with low cerebrospinal fluid (csf) levels of -hydroxyindoleacetic acid ( -hiaa). l-dopa may precipitate or exacerbate depression in % of pd patients. to determine if l-dopa affects -hydroxytryptamine ( ht) metabolism, patients were studied. four had pd. of these, were taking l-dopa and both were depressed. the diagnoses in the remaining were progressive supranuclear palsy (psp), striatonigral degeneration (snd), normal pressure hydrocephalus, and pseudoseizures with depression. neuropsychological examinations and lps of all patients were done. three patients were started on l-dopa (the previously untreated pd patients and the psp patient) and retested days later. one pd patient started on l-dopa became depressed. mood in the others was unchanged. csf was analyzed for ht and -hiaa. ht could not be detected in the csf of patients who were not taking l-dopa, but was easily detectable in all of the patients who were taking l-dopa. -hiaa levels were low in the untreated pd patients, and also in the patients with psp, snd, and pseudoseizures with depression. -hiaa levels were even lower in the l-dopa-treated patients. the ratio of -hiaa: ht (an index of ht turnover) was lowest in the l-dopa-treated pd patients who were depressed. low csf -hiaa in untreated pd may reflect depletion of brain ht. l-dopa may induce depression by inhibiting ht turnover in ht-depleted brain. p . ventroposterolateral medial pallidotomy in the e. fazzani, m. dogali, a. ben;, d. eidelberg, j. gianutsos, t. kay, b. newman, s. loftus, d. samehon, and l. laitinen, new york, n y , and stockholm, sweden in patients with parkinson's disease (pd), as a consequence of low dopamine there exists an increase in inhibitory output from the globus pallidus. ten patients ( men and women) with pd received unilateral ( right, left) ventroposterolateral medial globus pallidotomies (vplmp). the average patient age was years (range - yr), and the average duration of disease was years (range - yr). patients fluctuated between "on" chorea and "off" parkinsonism. hoehn and yahr stage "on" was i in , in ; and "off" was i in , iv in , and v in patients. unified pd rating scale (updrs) score averages hours off medicines ( hom) were activities of daily living (adl): and motor (mtr): preoperatively (preop). capit score averages preop hom were pronation-supination (ps): seconds (s), finger tap (ft): s, board (b): s for the most affected contralateral side, and gait: s ( patients could not walk). re-examination was done to days after pallidotomy. updrs scores hom decreased an average of %. three patients had major bilateral improvement in bradykinesia. rest tremor, prominent in patients, also was diminished. capit scores hom decreased to ps: s, ft: s, b: s; the average gait of the patients who could walk preop improved to s. there were no side effects. vplmp leads to an immediate overall significant improvement in patients with pd. s. kish, y . there is a growing interest in the genetic aspects of parkinson's disease and other basal ganglia disorders. we have studied families whose ancestors immigrated to north america from contiguous regions of northern germany and southern denmark. the pedigrees contain , , and individuals spanning , , and generations with , , and affected members, respectively. autosomal-dominant inheritance is clearly present in families and probable in the third. typical levodopa-responsive parkinsonism with bradykinesia, rigidity, resting tremor, and impaired postural reflexes uniformly develops in affected individuals from all families. n o downgaze impairment, pyramidal signs, sensory disturbances, cerebellar dysfunction, or orthostatic blood pressure changes have been observed. dementia, however, has developed in a few elderly individuals, especially in family. laboratory studies are normal. mri shows moderately enlarged ventricles and cortical atrophy. -fd positron emission tomography demonstrated reduced striatal uptake in examined patient and normal uptake in l individual at risk. autopsy of only subject has been performed (in ). brain weight was , grams and there were no obvious gross abnormali- program and abstracts, american neurological association tuesday, october ties, but microscopic examination was limited. further research on these families is planned. electrophysiological study s. maurri, m . cincotta, a. ragazzoni, g. descisciolo, and f. barontini, florence, ltah many neurophysiological examinations were conducted of a -year-old woman with familial mirror movements. n o other neurological abnormalities were detected. examination included voluntary electromyographic (emg) activity from various muscles, f-wave as well as short-and long-latency reflex responses of the thenar muscles from electrical stimulation of the median nerve, mapping of motor-evoked potentials (meps) to transcranial magnetic stimulation, movement-related cortical potentials (mrcps), and somatosensory-evoked potentials (seps). emg documented mirror activity in the upper limbs, most marked in the muscles of both hands. onset latency of emg activity in response to an auditory stimulus was identical in active and mirror muscle. long-latency responses from median nerve stimulation were recorded on contralateral as well as ipsilateral thenar muscles. short-latency reflexes and f wave were strictly ipsilateral. unilateral scalp magnetic stimulation evoked bilateral responses at similar latencies in the thenar muscles; midline scalp stimulation activated no responses. scalp distribution of median nerve seps and of mrcps associated with self-paced thumb abduction were normal. our findings suggest that congenital inherited mirror movements in otherwise normal subjects can be generated by corticospinal fibers pro jecting to ipsilateral motoneurons of the spinal cord. we have previously identified dysphagia and constipation (both slow transit and defecatory dysfunction types) as common gastrointestinal (gi) problems in parkinson's disease (pd). since apomorphine has been shown to be capable of terminating off-periods when injected subcutaneously, we have evaluated the effects of apomorphine injection on objective parameters of dysphagia and bowel dysfunction in pd patients. nine subjects underwent the following battery of studies to characterize their pd features, swallowing, and bowel function: gi assessment survey, unified pd rating scale, videoesophagram, colon transit study, defecography, and anorectal manometry. specific abnormalities on the studies were noted and the most abnormal study was repeated after subcutaneous administration of mg apomorphine. all individuals were pretreated with domperidone mg four times daily for days prior to apomorphine administration. improvement in both esophageal motility and deglutition was noted in the individual in whom videoesophagram was repeated. for the other patients, defecography or anorectal manometry was performed. significant improvement in specific parameters was demonstrated after apomorphine administration, but individuals experienced syncope during radiographic procedures. we conclude that subcutaneous apomorphine administration holds promise as a potential therapeutic approach to dysphagia and, especially, bowel dysfunction in pd, but that further investigation and refinement are necessary. asymmetrical effect of unilateral thalamotomy or subthalamotomy on tremor in parkinson's disease nico diedericb, christopber g. goetz, glenn t . stebbins, harold l. klawans, k. nittner, a. kozrlosakis, p. sanker, and v . strum, cologne, germany, and chicago, il in the past, stereotactic operation was a regular treatment for unilateral tremor in parkinson's disease (pd). however, follow-up studies were usually short term and always unblinded. we examined pd patients in long-term follow-up (mean . yr after operation) who underwent unilateral thalamotomy for parkinsonian tremor. we used videotapes and the unified parkinson's disease rating scale to blindly compare tremor ipsilateral and contralateral to the side of operation. since the patients were specifically selected for stereotactic operation because of asymmetric tremor, we reasoned that a sign of long-term efficacy would be current postoperative reversal of tremor side predominance. upper extremity tremor was significantly better contralateral to the side of operation compared to the ipsilateral side ( z = . ; p < . ). for the lower extremities the difference was not statistically significant. in chronic follow-up, stereotactic operation improved the absolute magnitude of arm tremor or ameliorated its rate of progression. since asymmetric bradykinesia and dyskinesia were not prerequisites for the choice of surgical side, we cannot make any conclusion about longterm impact of operation on these features. subtle extrapyramidal signs resembles that of patients with parkinson's disease m . richards, k. marder, l. cote, y . stern, and r. mayeux, new york, n y to investigate the relationship between extrapyramidal signs (eps) and cognition, eps severity and neuropsychological function were assessed in normal elderly individuals and nondemented patients with idiopathic parkinson's disease (pd) from a community-dwelling cohort in new york city. multivariate analysis of variance (manova) indicated poorer neuropsychological performance ( p = . ) in pd patients on verbal memory, orientation, verbal fluency, visuomotor construction, and psychomotor speed, but not naming, abstract reasoning, or matching. controlling for eps severity abolished these differences. one hundred fourteen ( %) of the normal individuals had subtle eps (mostly postural abnormality, bradykinesia, or rigidity) but no identifiable neurological disorder. manova indicated poorer neuropsychological test performance ( j = , ) in these individuals than in normals without eps on verbal memory, orientation, abstract reasoning, naming, verbal fluency, matching, and psychomotor speed but not visuomotor construction. we conclude that: ( ) cognitive impairment in pd is specifically associated with eps, and ( ) a similar association occurs in individuals with subtle eps but no neurological disorder. whether this represents a preclinical stage of pd or ad is yet to be determined. disease in olmsted county, minnesota emre kokmen, fatma sibel ozekmekci, c. mary beard, and peter c. o'brien, rochester, m n , and istanbd, turkey there have been many studies of prevalence of huntington's disease (hd) in diverse populations around the world. to study the incidence, we took advantage of the availability of detailed health care records for the population of olmsted county, mn, from mayo clinic, its affiliated hospitals, olmsted medical group, county hospital, state hospital, records of solo practitioners, nursing homes, death certificates, and autopsy records. we reviewed all records with a diagnosis of hd, huntington's chorea, chorea major, and chorea otherwise unidentified, and sought evidence for progressive chorea, progressive cognitive and/or behavioral dysfunction, and family history compatible with autosomal-dominant inheritance with onset of symptoms in the period between january , , and december , , while the patient lived in the geographic boundaries of olmsted county. we found males and females who met these criteria. average annual incidence rate (age/sex adjusted to us white population) for hd for this -year period was . cases/ year/ , population. we also estimated prevalence by taking account of in-migration, out-migration, and deaths. the agelsex adjusted ( ) prevalence for - - was . , and for - - it was . / , . the small number of cases caused the instability of the prevalence rates, but our rates are similar to rates reported in other populations. alton e . btyant, , l. breeden hollis, john a. hamjian, john d. wooten, ill, and francis . walker, nc we described patients with unusual episodic movement disorders and normal diagnostic work-ups: a -year-old woman who had recurrent episodes of tonic jaw deviation and forced right-eye closure; a -year-old woman who developed unexplained pain and subsequent spells of tonic inversion of the left leg; a -year-old man who presented with a bizarre episodic right-arm tremor; and a -year-old woman who experienced intermittent abdominal undulations. examination of the affected body part provoked or enhanced symptoms in all patients. using suggestion and placebo activation in the form of a medicated patch, intravenous saline, or cervical massage, we first induced and then aborted typical episodes of their abnormal movements. postinduction discussions of the procedure led to a marked reduction in the frequency of attacks in patients. activation procedures are useful in diagnosing psychogenic disorders because they demonstrate that situational, not medical, factors govern the expression of the abnormal behavior. we speculate that patients who are refractory to simple suggestion may respond to induction because it offers the potential of validating their symptoms. as in the case of psychogenic respiratory distress or pseudoseizures, positive induction can assist in counseling and symptom control. had alzheimer's disease with parkinsonism (adp), had essential tremor (et), had cerebellar tremor in multiple sclerosis (ms), and had tardive dyskinesia (td). clozapine was used either to treat psychosis ( pd, adp, dys, td) or tremor ( pd, et, ms). two pd patients were retrospective analysis of patients counted twice, who was treated for psychosis and then tremor and who was treated on separate occasions for psychosis with different responses. all dys patients improved, with complete resolution of their dystonia on changing antipsychotic drugs. the patients with et ( mg) and ms ( mg) improved mildly but sedation and clumsiness caused drug discontinuation in the ms patient. one adp patient ( . mg) responded well and the other became sedated and confused ( mg). the p d responses for psychosis at a dose range of . to mg daily were good ( ), very good ( ), and excellent ( ), whereas were intolerant. pd tremor responses were good ( , very good ( ), excellent ( ), and poor ( ) at doses of . to mg daily. one patient died of unrelated causes shortly after initiation of the drug. adverse effects included sedation, weight gain, hypersalivation, fainting, clumsiness, transient granulocytopenia, and "spasms" necessitating discontinuation in patients ( pd, l td, and l ms). tourette's syndrome and attention-deficit disorder patients s. m. silverstein, p. g. coma, d. palumbo, l. west, and r. kurlan, rochester, n y impaired attention is a common comorbid behavioral feature of tourette's syndrome (ts) and a key clinical feature of attention-deficit hyperactivity disorder (adhd). however, the pattern of attentional impairments reported in adhd has not been observed in ts. we therefore compared ts patients ( male, female; mean age ? yr), adhd patients ( male, female; * yr), and normal controls ( male, female; ? yr) on specific neuropsychological (np) and computer-administered tasks of attentional ability. adhd, but not ts, subjects performed significantly worse than controls on the n p tasks (digit symbol, perceptual speed) and had a trend toward poorer performance on a computerized measure of attention. however, both the adhd and ts groups had significantly greater test performance variability on some, but not all, tasks and had more subjects with deviant scores. among ts patients, higher scores on an obsessive-compulsive disorder (ocd) inventory and a greater number of adhd symptoms correlated significantly with poorer performance on the attentional tasks. moreover, ts patients with observed tics during testing had greater attentional impairment than those without tics. these results suggest that: ( ) many adult ts patients do not have impaired attention; ( ) attentional impairment in ts differs from that observed in adhd; and ( ) attentional impairment in ts is associated with the full neurobehavioral spectrum of ts (i.e., tics, ocd, and adhd). frank r. sharp, cathleen miller, thomas rando, and steven greenberg, san francisco and palo alto, c a six patients are described with choreoathetoid movements and marked proprioceptive sensory loss. one patient had a traumatic injury to the right parietal cortex that produced severe proprioceptive sensory loss and choreoathetosis in the left arm. another patient had a left thalamic infarction that resulted in profound proprioceptive sensory loss and chorea on the right side of the body. two patients had cervical spinal cord disease, proprioceptive sensory loss, and diffuse choreoathetosis. another patient had dorsal root ganglionitis associ-a hypothesis program and abstracts, american neurological association ated with small-cell lung carcinoma that produced diffuse loss of all sensory modalities and chorea. the last patient had an ulnar sensory neuropathy and choreic movements of the fifth finger. lesions anywhere along the pathway that transmits limb proprioception may cause pseudochoreoathetosis. furthermore, choreoathetosis without sensory loss caused by focal lesions of striatum may occur because of disruption of cortical proprioceptive inputs to striatum-perhaps explaining why most focal lesions of striatum do not produce chorea. sporadic inclusion-body myositis (s-ibm) and autosomalrecessive hereditary inclusion-bod y myositis (h-ibm) are of unknown cause and pathogenesis. in both there are muscle fibers with rimmed vacuoles containing to -nm cytoplasmic tubulofilaments (ctfs) and denervation atrophy; in s-ibm, but not h-ibm, there is a varying degree of inflammation. vacuolated fibers contain ubiquitinated inclusions (askanas ) and congo-red positivity indicating amyloid (mendell ). because immunoreactive p-amyloid precursor protein (app) and p-amyloid protein (p-ap) are constituents of ubiquitinated senile plaques in alzheimer's disease (ad) brain, we studied immunolocalization of app and p-ap fibers in ibm muscle using antibodies against: ( ) non-p-ap fragments of app, viz. (a) c-terminus (residue - courtesy d. selkoe) and (b) n-terminus (residue - courtesy b. frangione and d. levartovsky); ( ) p-ap (sequence - , courtesy g. glenner, and sequence - courtesy d. selkoe); ( ) ub (chemicon). in of ibm patients, including one h-ibm, % of the vacuolated muscle fibers contained large or several small app and p-ap immunoreactive (ir) inclusions, which by double-labeling fluorescence were closely colocalized with each other and with ub-ir. none of control muscle biopsy specimens (including polymyositis) contained app-ir, p-ap-ir, or ub-ir inclusions characteristic of ibm. control experiments utilizing omitted, replaced, or absorbed primary antisera were negative. p-ap, a product of proteolytic cleavage of app, is receiving attention regarding the pathogenesis of ad. our study provides ( ) the first demonstration of app and p-ap accumulations in abnormal human muscle, and ( ) raises the possibility that in ibm muscle and ad brain rhey may form from similar cellular events. jeffrrey d. rothstein, lin jin, and ralph kuncl, baltimore, m d the pathogenesis of motor neuron death in amyotrophic lateral sclerosis (als) is unknown. accumulating evidence suggests that the disease is characterized neurochemically by a derangement in the control of neurotransmitter glutamate metabolism: csf levels of glutamate and aspartate are ele-of motor neuron degeneration vated and their high-affinity transporter is defective in brain and spinal cord. inefficient glutamate transport, and subsequent chronic increase in extracellular glutamate, could be responsible for selective motor neuron death. to test the hypothesis that chronic defects in glutamate uptake can produce motor neuron toxicity, we developed a tissue culture model employing organotypic rat spinal cord maintained under conditions of chronic glutamate uptake inhibition. slices ( pm) of lumbar spinal cord from -to -day-old rat pups were cultured on millicell membranes. chronic uptake inhibition was produced by culturing tissue in the presence of threohydroxyaspartate (tha) or pyrrolidine-dicarboxylic acid, both known to be specific inhibitors of glutamate transport. tha produced chronic elevation of glutamate in the medium and produced motor neuron toxicity after to days in culture using pm tha, and after days using pm tha, as determined by assay of tissue choline acetyltransferase (chat) activity and by histological analysis of -micron plastic sections. motor neuron toxicity was completely blocked by the non-n-methybaspartate (nmda) antagonists cnqx or nbqx, but not by the nmda antagonist mk- . this model demonstrates that the chronic loss of glutamate transport in als can produce motor neuron degeneration and that motor neurons appear to be susceptible to non-nmda-mediated glutamate toxicity. guillain last year, we described a distinct acute paralytic syndrome in children and young adults from northern china and differentiated it from guillain-barre syndrome (gbs) by epidemiological, clinical, and nerve conduction (nc) features. to distinguish chinese paralytic syndrome (cps) from gbs more clearly, we measured nc in cps patients (mean yr, range . - yr) and in gbs patients from johns hopkins (mean yr, range - yr). sensory nc was normal in all (n = ) but nerve of cps patients, whereas sensory nc was frequently abnormal in gbs patients: median nerve, %; ulnar nerve, %; and sural nerve, %. motor n c also differed between the groups. in all nerves, distal latency (dl) was significantly longer in gbs than in cps. for example, in the median nerve, mean dl was . ms (se ) in gbs and . ms ( . ) in cps ( p < . ). motor conduction velocity was significantly reduced in gbs median and ulnar nerves compared with cps nerves. f-wave latency was significantly longer in gbs median nerves than in cps nerves. these data support the distinction both clinically and electrodiagnostically between cps and north american gbs. the use of n c may be especially important in field epidemiological studies in separating the disorders. clinical manifestations and gene analysis of the first japanese kindred yoshihide sunada, teruo shimizu, lchiro kanazawa, and toru mannen, tokyo, japan familial amyloidotic polyneuropathy type iv (fap iv) has been clustered in the finnish population and only a few cases have been reported from the netherlands. denmark, and united states. we describe the first japanese family with fap iv. the family originates from nagano prefecture, a mountainous district in the middle part of japan, and has no relationship to the finnish population. this family has members in generations, and individuals are affected with slowly progressive cranial neuropathy and corneal lattice dystrophy. the genetic trait is autosomal-dominant. polarizing microscopy and immunohistochemistry show abundant amyloid deposits reactive to an anti-gelsolin monoclonal antibody. direct sequence analysis of a dna fragment spanning codon of the plasmagelsolin cdna from the propositus, and restriction analysis using a modified pcr from other family members demonstrate a single base substitution, g to a at the first base of codon , which is identical to the mutation of finnish fap iv. this suggests that the mutation causes the fap iv phenotype regardless of ethnic background. gene expression focal puncture injury has been used as a model to study degenerative and regenerative responses of skeletal muscle. previous studies have demonstrated the ultrastructural and metabolic effects of muscle injury. however, the early genomic response to focal injury is presently unknown. we asked whether the immediate early genes (iegs) or early response genes-~$ , c-jun, nur , and junb-are responsive to muscle injury. these iegs encode transcription factors and are expressed rapidly after cell-surface stimulation. we have previously shown that surgical denervation and neural stimulation of muscle induced differential patterns of ieg expression. in this study, we produced injury of mouse gastrocnemius muscle by injection of c . of normal saline. we used the contralateral (uninjected) muscle as a control and examined the milna levels of each of these iegs. we found that ~$ and junb levels were increased at and hours and returned to basal levels by hours. in contrast, mrna levels of nur and cjun remained unchanged. this pattern of ieg response is distinct from that seen after muscle stimulation or denervation. the selectivity of this pattern suggests that ieg expression may play a role in the response of muscle to injury. amyotrophic lateral sclerosis (als) is a degenerative disease that leads to the restricted loss of motor neurons (mn). the reason for the selective death of mn remains unknown. we hypothesize that mn-enriched or mn-specific genes are important for normal m n function and that their disturbance may play a role in the pathogenesis of als. we have produced clonal hybrid cells derived from embryonic and neonatal spinal cord m n for the study of m n gene properties. some of these hybrid mn clones express traits typical of mn, such as high levels of choline acetyltransferase enzyme activity and message, glycine receptor message, and neurofilament and neural cell adhesion molecule proteins. we are using molecular techniques to identify novel mn-enriched or mn-specific genes in these cells. with this strategy, we have identified several cdna clones preferentially expressed in mn hybrid cells but not in the parental neuroblastoma cells by differential hybridization of an embryonic mn hybrid cdna phage library. we are extending these observations by performing subtraction hybridization experiments. these results suggest that mn-enriched or mn-specific genes can be identified, and may lead to a greater understanding of the etiology of als. there is a syndrome of slowly progressive, mid-adult-onset fasciculating progressive muscular atrophy (pma) affecting upper more than lower limbs, without bulbar or corticospinal signs, more often in males, associated with igm monoclonal gammopathy, and no nerve conduction block. two such men, ages (a) years and (b) years, duration and and one-half years, csf protein and , had failed to achieve sustained improvement with: prednisone, cyclophosphamide, total-body irradiation, and multiple lymphoplasmaphereses in a; and interferon alpha a in b. intravenous immunoglobulin (ivig), . gm/kg/day, has provided dramatic benefit, sustained and increasing for > and > months to date. (there is a continuing base of depotestosterone, mg weekly, which initially alone provided very minimal improvement.) strength increase was evident at and days after the first course of daily ivig infusions. it further increased for to and one-half weeks after treatment, and then began to diminish. repeat -day treatment weeks after the first course resulted in summated improvement, now sustained and enhanced by an average of treatment per week. quantitated strength testing by a blinded observer has shown a -fold to >loo-fold gradually increasing muscle function in all limbs. patient a regained the ability to feed himself, get out of a chair, walk unaided, and go up steps; quantitated hip flexors increased -and -fold. patient b regained the ability to feed himself, take care of personal toilet needs, walk securely, and drive miles; quantitated hip flexors increased -fold, and biceps flexions increased from with no weight to > reps while holding -pound weights. bukhara jews: a new cluster with typical oculopharyngeal muscular dystrophy (opmd) is a rare, late-onset myopathy with autosomal-dominant inheritance. its ultrastructural hallmark is the finding in muscle fibers of intranuclear tubular filaments of . -nm outer diameter. most opmd cases were described among french canadians; in france, the homeland of their ancestors, the prevalence is / , (brunet et al, ) . in israel's central area live approximately , jews who have immigrated from the bukhara and samarkand regions in uzbekistan. they represent a homogeneous ethnic group with its own language and community life. among them we have identified opmd in families ( affected individuals). the inheritance, clinical, electrophysiological, and histological features of these pa-tients are similar to those described in other pdts of the world, with typical intranuclear inclusions seen on electron microscopy. the minimal estimated prevalence of opmd in this population is approximately : . this cluster of opmd among bukhara jews is the second largest in the world. because many bukharian families are large, they may be suitable for linkage genetic studies. human muscle during ontogenesis e . scarpini, g. conti, p. l. baron, and g. myoblast transfer has been proposed recently as a possible therapy for duchenne muscular dystrophy patients. because immune rejection can represent a major problem in myoblast implantation, immunological characteristics of human muscle should be investigated. previous studies showed that human muscle cells cultured in vitro can constitutively express human lymphocyte antigen (hla) class i, but not hla class . furthermore, human y-interferon induces the surface expression of hla class i on mononuclear myoblasts, but not on multinucleated myotubes. however, whether the cells produce and present the antigen by themselves or take this material from the environment, where it could be released by infiltrative cells, is not yet clear. in this study, we analyzed hla molecules at the protein level by immunocytochemistry with monoclonal antibodies against different hla-dr epitopes and hla-abc molecules on frozen serial sections of human muscle during development and at the adult stage. human muscle infiltration by macrophages and monocytesmacrophages also were studied with m and leum specific monoclonal antibodies at the same stages of development. our results show that during muscle development and maturation, hla-dr and hla-abc antibodies do not label muscle fibers but some m -and leum -positive cells within the muscle. these data can be useful to understand the role of infiltrating monocytes-macrophages in the muscle immune response. mounting evidence suggests that excitotoxicity, mediated via the glutamate receptor, is involved in the pathogenesis of amyotrophic lateral sclerosis (als), as well as in other neurological diseases. we therefore initiated an open label, phasen i trial of highdose dextromethorphan (dm), a noncompetitive, selective n-methybaspartate antagonist, in als. patients began with mg/kg/day, divided into doses, and incrementally escalated their medication to mg/kg/day or their maximum tolerable dose. thirteen patients, all extensive metabolizers of dm, were enrolled. total daily doses ranged from . to mg/kg. major side effects were lightheadedness ( ), slurred speech ( ), and fatigue ( ). no biochemical, hematological, or neuropsychiatric abnormalities occurred after up to months of maximal therapy, except for depression in patient. plasma kinetics of dextrorphan (dt) (the major metabolite of dm) were studied after an acute oral dose of . mg/kg dm. median elimination halflife was . hours. plasma dt concentration peaked at a median of hours, with a median cmax of . pm. median amyotrophic lateral sclerosis cerebrospinal fluid/plasma dt ratio was . . this study demonstrates the feasibility of long-term, high-dose dm therapy. we are now conducting a phase i study of highdose dm in als, designed to assess its efficacy. polyneuropathy: a chronic inflammatory demyelinating polyradiculoneuropathy variant? d. cros, k. h. chiappa, s. patel, and s. gominak, boston, ma, we describe patients ( men, woman) with a pure, adultonset sensory neuropathy. the course was chronic in all cases. three patients had a relapsing-remitting course over to years with several attacks every year; the onset was gradual and followed by a plateau in the fourth patient. all patients had positive and negative sensory symptoms, and had positive motor symptoms (fasciculations). in all patients, muscle power was normal at the time of peak deficit. all were areflexic and had large fiber sensory deficits, and patients had sensory ataxia. three patients had elevated csf protein, whereas the csf was normal in patient. mri demonstrated marked thickening of the lumbosacral spinal roots in patient. motor conduction studies were normal in all patients, and mild f-response abnormalities were noted in . neurophysiological investigations of the sensory pathways were abnormal in all. three patients had several studies over a -year period. sensory nerve action potentials were unobtainable in patients, and normal in the others. median and tibial somatosensory-evoked potentials showed conduction slowing consistent with demyelinating lesions affecting the peripheral sensory pathways, either globally or focally in the proximal segments. two patients appeared to respond to plasma exchange or intravenous immunoglobulin therapy, or both. glial fibrillary acidic protein cells in experimental motoneuron disease raul n . mandler, pam c. allgood, and james a. wallace, albuquerque, nm neuronal degeneration in human and animal motoneuron disease has been emphasized, but glial phenotype alterations have not been studied as extensively. we carried out a developmental and topographic study of astrocyte expression in the wobbler mouse model of motoneuron disease. wobbler mice and normal littermates were studied at , , , and weeks of postnatal development. anesthetized animals were perfused intracardially with paraformaldehyde. spinal cords were dissected and landmarks were identified carefully for systematic study. sections were stained with monoclonal antibodies against glial fibrillary acidic protein (gfap) neurofilament and neuron-specific enolase. cell quantitation was done with video-enhancing microscopy. in symptomatic animals, marked increases in gfap staining were found in rostral and caudal spinal cord areas. quantitation studies revealed a to -fold increase in gfap+ cells in the wobbler. we conclude that gfap+ cells are markedly increased in the wobbler mouse at cervical, thoracic, and lumbar areas. this cell may also be relevant in motoneuron disease pathogenesis. ( indirect evidence suggests that polio virus may persist in the human cns years after initial infection and may be a cause for the post-polio syndrome. to evaluate whether the polio virus genome can be detected in the cns of patients with previous polio infection, we identified patients who had died with autopsy findings and clinical history consistent with poliomyelitis. rna was extracted from paraffin-embedded sections of brain or spinal cord and subjected to reverse transcription followed by dna amplification by polymerase chain reaction (rt-pcr) using primers specific for heat shock protein (hsp ) and a conserved region of the polio viruses. hsp mrna could be detected in all specimens, indicating that amplifiable rna had been isolated. in no specimens could polio virus rna be detected. this study suggests that polio virus does not persist in the human cns in quantities detectable by the sensitive pcr method. with cmt type , seen at mayo clinic rochester between and , for the frequency of selective calf weakness in cmt type , the form of cmt most similar clinically to distal sma. anterior compartment weakness exceeded calf weakness in patients ( %); anterior and posterior involvement was equal in ( %). calfweakness exceeded anterior compartment weakness in patient ( %). selective calf weakness in distal sma thus helps distinguish this disorder from cmt type , and similarly from distal sma with weakness resembling cmt, in that we are unaware of the distributions in distal sma occurring in the same family. given the possibility of genetic heterogeneity, linkage studies of distal sma probably should include patient selection criteria such that the distribution of leg muscle weakness is homogeneous. p . conjugal amyotrophic lateral sclerosis: amyotrophic lateral sclerosis (als) is a sporadic neurodegenerative disorder of unknown cause. unusual cases may provide etiologic clues. we report a married couple, both of clue to etiology? whom developed als in year. the couple grew up in southeastern pennsylvania and attended the same schools. they married after high school and have healthy children. in september , a -year-old woman noted right-hand weakness and associated fasciculations that progressed to the entire right upper extremity. by january , the lower extremities were asymmetrically weak and fasciculating. she then developed left-arm weakness, d ysarthria, dysphagia, and emotional incontinence. she had hyperreflexia and bilateral extensor plantar responses. then, in may , her husband, aged , noted difficulty whistling, which progressed to frank dysarthria. later, he developed dysphagia, emotional incontinence, and weakness, wasting, and fasciculations in the upper extremities. hyperactive gag, jaw, and limb reflexes were present. in both, electrodiagnostic testing revealed widespread evidence of lower motor neuron degeneration. numerous laboratory tests were normal. although these cases may represent a chance association, the development of als in a young husband and wife suggests a possible environmental cause. the authors welcome suggestions about these cases from the neurological community. conduction block in demyelinating neuropathies usually is assessed from differences in the sizes of surface-recorded maximum m-potentials evoked by supramaximal stimulation at successively more proximal sites along the course of motor nerves. as the maximum m-potential is comprised of many bitriphasic surface-recorded motor unit action potentials (muaps), differences in the relative latencies between muaps may lead to phase cancellations, reducing the m-potential size and rendering any quantitative assessment of the extent of conduction block relative to phase cancellation difficult. cooling a muscle (not the nerve), however, by as much as °c increases the negative peak durations of muaps by as much as to times and moves the point at which maximum phase cancellation might occur to some theoretical point well proximal to the spinal roots. in cases of guillain-barre syndrome (gbs) studied to date, cooling produced little change in percent reductions in m-potential negative peak areas between successively more proximal sites of stimulation. this finding suggests that "true" conduction block rather than interpotential phase cancellation best explains reductions in m-potential size at successively more proximal sites of stimulation in gbs. associated with trimethoprim-sul famethoxazole rare cases of primarily motor polyneuropathy have been associated with the use of sulfonamides. the incidence of polyneuropathy has diminished substantially with the abandonment of earlier methylated compounds. we describe patients who developed allergic phenomena, including a skin rash and debilitating, painful sensory and autonomic polyneuropathy within days of receiving trimethoprimsulfamethoxazole. in patient, examination revealed resting tachycardia, marked blood pressure orthostasis and near-program and abstracts, american neurological association syncope, hyporeffexia, urinary incontinence, and reduced sensation distally in the lower extremities. his cerebrospinal fluid was acellular with a protein of mg/dl. the other patient showed a resting tachycardia, sluggish pupils, reduced distal vibration perception, and hyperpathia of hands and feet. conventional nerve conduction studies demonstrated normal motor results in both patients, absent or reduced sensory amplitudes in the first patient, and normal sensory results in the second. autonomic studies identified profound abnormalities in testing of sympathetic skin potentials, sinus arrhythmia, and valsalva's ratio. in both cases, nerve biopsy was not performed for fear of exacerbating the patient's hyperpathia. subsequent hemodynamic and electrophysiological testing showed improvement in autonomic function, paralleling the patients' clinical amelioration. although uncommon, a painful, sensory and autonomic, partially reversible polyneuropathy may develop after the use of trimethoprim-sulfamethoxazole. the remote effects of botulinum a toxin injections into vocalis muscles for treatment of focal laryngeal dystonia were investigated using single-fiber electromyography (sfemg). botulinum a toxin injections have been proven effective therapy for various dystonic disorders including focal laryngeal dystonia, blepharospasm, and torticollis. previous sfemg studies have demonstrated remote effects of the toxin in noninjected muscles after treatment for both blepharospasm and torticollis. these effects include an increase in fiber density, mean jitter (mcd), and percentage of fiber pairs with increased jitter. other researchers have postulated that the distant effects of this toxin may be related in part to the dose of botulinum toxin injected. to investigate this hypothesis we have studied patients treated for focal laryngeal dystonia because the amounts of toxin required are / th to / ooth of the doses used to treat other dystonias. using electromyographic (emg) guidance, bilateral injections of . or . mouse units of botulinum a toxin were injected into each vocalis muscle of patients. each patient had significant improvement in phonotory function within hours after injections and have been followed serially (usually within weeks and again at mo) after injections, with sfemg recordings of the left extensor digitorum communis and sternocleidomastoid muscles. five patients have had more than series of injections over the months since we began this study. sfemg studies have revealed no significant change in the fiber density, mean mcd, or percent of fiber pairs with normal jitter in either muscle. in conclusion, our studies support the hypothesis that the presence of remote effects of botulinum toxin may be related, in part, to the amount of toxin used. the c bl/ / a mouse exhibits the remarkable characteristic of prolonged survival of axons separated from their cell bodies (slow wallerian degeneration). previous work has demonstrated that the axon itself is responsible for the phenotype of prolonged survival. we investigated whether the lack of rapid axonal degeneration after axotomy in this substrain is due to an inability to break down cytoskeletal components, a process that is normally accomplished by activation of intrinsic calcium proteases. segments of desheathed sciatic nerves from normal and ola mice were incubated for hours under conditions that disrupt the axolemma (freeze/ thaw or in % triton x-loo), allowing external calcium free access to axoplasm. nerves were analyzed by western blot for neurofilament (nf) proteins and by electron microscopy. in high-calcium media ( mm caci,), nf immunoreactivity was lost and axoplasm was reduced to watery debris in both substrains, whereas in egta-buffered media, axoplasm was preserved. these results demonstrate that calcium-activated proteases are present and can be activated in ola nerves. the defect in these mice that allows for prolonged survival of transected axons is likely in the mechanism for calcium entry into the distal stump. the mechanism by which the analogue of adrenocorticotrophic hormone, acta - , prevents cisplatinum (cp) neurotoxicity is unknown. murine n e. neuroblastoma cells and neural crest-derived, squirrel fish erythrophore cells tuesday, have similar vesicular transport mechanisms to human neural cells. they were used to study the effects of cp and acth , on cellular transport. differentiated n e. cells were treated hour prior to observation with serum-free media (sfm, control); sfm/cp pg/ml; or sfm/cp pg/ml and ng/ml acth -,. organelle transport was studied ( neurites and - organelles per condition) using computer-enhanced video microscopy. mean fast anterograde ( . k . pmsec-' vs . * . pmsec-') and retrograde ( . . pmsec-' vs . +- . pmsec-') transport were decreased in cp-treated compared to control cells ( p < . ). in cp/acth ,-treated cells, mean anterograde ( . +_ . pmsec-') and retrograde ( . . pmsec-') velocities were greater than in cp cells ( p < . ). velocities in control and cp/acth , cells were not statistically different. erythrophore pigment granule transport was observed in a blinded study, using similar techniques. mean aggregation velocity was greater in control ( . k . msec-') and cp/acth , ( . f . msec-')-treated cells compared to cp ( . * . msec-') cells ( p < . ). incubation with cp for or hours affected velocities equally, but acute exposure was more easily reversed by control or acth,, containing media. there is striking inhibition by cp in cross-species models of organelle transport. this can be prevented by acth ,. erythrophores allow future study of individual transport components. neurotrophin to investigate signal transduction pathways involved in neurite growth, the cytoplasmic regions of p sngfr, the common neurotrophin receptor monomer, were searched for a motif analogous to the predicted secondary structure of the tetradecapeptide mastoparan. potential sequences were modeled using a semi-empirical molecular mechanical force field approach. the sequence rat ~ ~~~ - represents a highly conserved amphiphilic domain predicted to be involved in neurotrophin signal transduction via g-protein mechanisms. to test this prediction, peptides containing sequences homologous to p ngfr - were examined for effects on trophic factor-induced survival/differentiation responses of rat pc pheochromocytoma cells, chick embryo drg neurons, and chick embryo ciliary neurons. a peptide identical to ~ ~~~ - accelerated the neurite growth response to nerve growth factor (ngf) of pc cells and drg neurons in a time frame that paralleled uptake into cells, but mastoparan did not influence ngf-mediated neurite growth. millimolar mg+ + and benzalkonium chloride, known to block the actions of mastoparan, blocked the effect of the peptide on ngf-mediated neurite growth by pc cells. peptides mutated to alter cationic amino acid relationships or amphiphilicity were less effective than the peptide in accelerating ngf-mediated neurite growth. these observations complement and extend evidence suggesting a pivotal role of ~ ~~~ in ngf-mediated signal transduction. these studies complement and extend evidence suggesting a pivotal role of p sngfr in neurotrophin signal transduction and evidence that activation of intracellular signalling processes involving specific g-protein mechanisms are involved in neurotrophin-mediated neurite growth. crushing the hypoglossal nerve causes hypoglossal motor neurons to decrease expression of choline acetyltransferase (chat) and begin expressing p ngfr, the low-affinity ngf receptor. these changes are evident within days after the injury and continue for several weeks. inhibition of axonal transport by vincristine applied to uninjured nerves causes loss of chat expression without induction of ~ ~~" . we sought to determine if topical vincristine would alter p sngf' expression after nerve injury. hypoglossal nerves were surgically exposed unilaterally in anesthetized rats and crushed. one week later, rats were reanesthetized and the same nerves were re-exposed. vincristine or saline was applied at the crush sites by soaking a strip of cotronoid wrapped around the nerves. one week later, rats were anesthetized and perfused with aldehydes. frozen sections from the brainstems were stained by indirect immunoperoxidase to demonstrate chat and ~ ~~~' . saline-treated controls showed decreased chat and abundant ~ ~~" in hypoglossal motor neurons ipsilateral to the crush injury. vincristine-treated animals showed no chat and no p tngf'. we interpret these results as indicating that a signal originating from the injury site maintains ~ ~~" expression after nerve injury. catecholamines have been reported to be toxic to embryonic-derived rat neurons and glia via the formation of reactive oxygen species (rosenberg, ) . we tried to determine whether oligodendrocytes (ol) from adult -month-old rat brain are similarly susceptible. toxicity to ol was examined using light microscopy and galactocerebroside immunohistochemistry where the relative number of surviving ol and their extent of process formation were graded. five days of exposure to norepinephrine (ne) and epinephrine (epi) at and fm produced significant toxicity ( p < . , analysis of variance [anova)) to adult rat ol; this toxicity was evident by hours of exposure. treatment with catalase ( p,g/ml), a free-radical scavenger enzyme, completely prevented the toxicity of catecholamines. to ascertain whether astrocytes, which have free-radical scavenging capacity, could prevent the catecholamine-induced injury to ol, rat ol were seeded on neonatal rat astrocytes. under such conditions, the toxicity of n e and epi was reduced significantly ( p < . , anova). these findings suggest that impairment of this protective function of astrocytes may render ol and its myelin membrane susceptible to free-radical-mediated damage. lyme neuroborreliosis is an increasingly prevalent disorder, but the diagnosis generally has been indirect. thus, the pres-ence of other manifestations of the infection, consistent findings on neurological exam or lumbar puncture, or presence of csf antibody have been used rather than direct isolation or identification of the organism from the csf. we have previously developed polymerase chain reaction with hybridization (pcr/h) to identify borrelia burgdorferi in the blood and organs of infected mice, and found that the assay was equivalent or, in some cases, preferable to culture (ann neurol ; : ) . the assay used for primers oligos derived from a sequence of genomic b. burgdovfri d n a expressed on a plasmid by rosa and schwan. a two-stage nested pcr was performed on csf samples in which the d n a was isolated in a variety of ways. pcr products were subsequently hybridized with a digoxigenin-labeled internal probe by slotblot hybridization. the sensitivity of the assay was excellent, being mg), with higher single doses of taxol(> mg/m ), or with a preexisting neuropathy. we conclude that sensorimotor neuropathy and myopathy are dose-limiting neurotoxicities of combined cisplatin and taxol use, now that neutropenia can be controlled with neuropathy and myopathy g-csf. central nervous system lymphoma casilda balmacedz and lisa deangelis, new york, ny ally periventricular and may seed the csf by direct growth through the ependyma. we reviewed the csf profile of non-acquired immunodeficiency syndrome (aids) patients (pts) with pcnsl. all pts had lumbar puncture (lp) and had multiple samples from an ommaya reservoir. definite lm involvement was identified with a positive csf cytology, lymphomatous lm infiltration on a surgical specimen, or mri with gadolinium showing lm tumor. probable lm lymphoma was diagnosed in pts with suspicious or atypical csf cytology. there were women and men with a median age of (range - yr). at diagnosis, mean white blood cell count was /mm (range - , ); mean lumbar csf protein was mgldl (range - , ); and mean ventricular csf protein was mgldl (range - ). glucose was always normal. nineteen of pts sampled had oligoclonal bands, and / had elevated pz microglobulin. at diagnosis ( %) had an abnormal csf cytology: positive, suspicious, and atypical. one pt had pathological infiltration of the lm and had lm tumor on spine mri for a total of ( %) pts with definite or probable lm lymphoma. in pts with abnormal cytology, the abnormality was found in ( %) lps and / ( %) of the ommaya and ventricular specimens. in pts the lumbar cytology was the only abnormal specimen despite multiple ventricular samples, and in only the ventricular csf was abnormal. thirty-six of ( %) pts developed recurrent tumor afrer treatment. forty-two percent ( ) of all patients with relapse had lm recurrence. lm recurrence was accompanied by brain recurrence in pts, systemic in , ocular in , both systemic and ocular in , and isolated in . at diagnosis / patients received treatment directed against the lm. of these, ( %) had meningeal recurrence whereas of the ( %) patients who did not receive this treatment had lm recurrence. lm involvement by pcnsl is frequent, may be missed on a single csf sample, and requires specific therapy at diagnosis. sixty-three solid cancer patients with a single brain metastasis were prospectively randomized for neurosurgery and radiotherapy combined (arm ) or radiotherapy alone (arm ). they were stratified for lung or nonlung cancer and for active versus stable or absent extracranial disease. world health organization performance status was . age, sex, performance status, and location of brain metastasis were divided evenly over both groups. one-month mortality was % in arm and % in arm . median survival of months after combination therapy was significantly better compared to months after irradiation alone ( p < . ). it made no difference whether they had lung or nonlung cancer. the largest difference between both treatment arms was observed in patients with stable or absent extracranial disease ( vs mo, p < . ). when systemic disease activity was present, median survival was months irrespective of treatment arm. functional independent survival was to months shorter than overall survival and was significantly better for patients with stable extracranial disease after combined therapy. multivariate analysis showed that age was also an independent prognostic factor. patients older than years had a hazard ratio for dying of . (p. ). we will detail the type and pattern of neurological complications in t-cell non-hodgkin's lymphoma (nhl), and review how they differ from those associated with b-cell nhl, and the lymphomas in general. this study is the first step in a process to characterize these tumors to determine if special staging or cns prophylaxis are indicated in any of the subtypes of t-cell lymphoma. we recently have encountered women with breast cancer and an unusual sensorimotor neuropathy. the neuropathy was the major clinical problem. in women the initial symptom was severe itching, generalized and first localized to the involved breast and then generalized. all developed distal extremity numbness and burning that very slowly progressed proximally, and in became generalized. four complained of painful muscle cramps in the extremities ( ) and jaw ( ). all had mild extremity weakness, distal ( ) and proximal ( ) . three women developed symptoms up to months prior to cancer diagnosis, shortly after diagnosis, and years after diagnosis. four women had disease confined to the breast and regional lymph nodes, and had metastatic disease in remission. although annoying, symptoms were generally not disabling. three women stabilized or had slight improve-associated with breast cancer ment with cancer treatment, and continue to gradually progress while in cancer remission; required a cane to ambulate after years due to sensory ataxia. one who developed cancer relapse had concurrent neurological relapse. one woman treated with high-dose immunoglobulin did not improve. none had significant weight loss. laboratory abnormalities included elevated erythrocyte sedimentation rate ( - ) in , antinuclear antibody : in , csf with lymphocytic pleocytosis ( - white blood cellslmm) in / and elevated protein ( - mg/dl) in available. emgi ncv showed mild sensory-to-motor polyneuropathy in available. none had detectable antibodies against peripheral nerve or dorsal root ganglia. the etiology of sensorimotor neuropathy in these patients is unknown, but it may represent a distinct paraneoplastic syndrome that can herald the onset of, and parallel the course of breast cancer. our objective was to determine whether ceramide induces differentiation of anaplastic glioma cells. sphingomyelin hydrolysis resulting in ceramide production has been linked to differentiation of leukemia cells. t rat anaplastic glioma cells, seeded at x lo cells per well, were grown in serum-a glioma cell line program and abstracts, american neurological association free media. on day , cells were photographed, scored for processes longer than one cell body, and counted. c ceramide changed plump cells to flattened cells with many long processes: ceramide treatment increased the percentage of cells with processes from % (sd) to * % (n = , p < . ). control cells grew to . x lo cells/well . x lo cells; ceramide-treated cells grew to . x lo ? . x los (n = , p < . ). although one ceramide analog reproduced the c ceramide-associated changes, the optical isomer of this analog did not, demonstrating stereospecificity. cerarnide did not decrease cell viability by trypan blue. ceramide inhibits proliferation and induces process formation in a glioma cell line, causing it to assume a more differentiated phenotype. cerarnide or its analogs represent possible future therapeutic agents that would inhibit the growth and affect differentiation of anaplastic gliomas. [bashir, mod pathol ; ( ) : - )). this is similar to the pattern seen in ebv-infected human b cells and unlike the uniform latent infection seen in burkitt's lymphoma. we tested the hypothesis that long-term passaging of ebv-immortalized human b cells in immunodeficient mice leads to emergence of a uniform nonlytic pattern of ebv infection associated with appearance of the malignant profile. ebv-infected normal human b cells were serially passaged intracerebrally in severe combined immunodeficient cb mice ( x ' cells per mouse, mice per passage for a total of passages). frozen mouse brain sections from each passage were stained with vca antibody (ebv lytic cycle) and hybridized with biotinylated bamh -w sequence of ebv. all injected animals developed tumors as previously described (bashir, lab invest ; ( ): - ) . tumor cells continued to express vca and showed latent and lytic hybridization patterns with bamh,-w after passages despite exhibiting monoclonality (surface immunoglobulins) and random chromosomal changes. lytic infection of immortalized b cells with ebv is stable, resembling brain lymphomas in aids, and unlike the latent infection seen in burkitt's lymphoma. a previously healthy -year-old man developed diplopia and incapacitating, diffuse weakness over a period of weeks. examination showed a "one-and-a-half'' syndrome of horizontal gaze paresis, patchy severe weakness with atrophy and fasciculations, absent tendon reflexes in the legs and right biceps, and decreased vibration sense in the feet. csf contained a mild pleocytosis, elevated protein, and oligoclonal igg bands. electrophysiological testing indicated a generalized sensorimotor axonal neuropathy with diffuse denervation. small-cell lung carcinoma was diagnosed by bronchoscopy. prednisone produced mild subjective improvement. chemotherapy was begun but the patient developed fatal septicemia. serum was negative for anti-hu or anti-gm with paraneoplastic encephalomyeloneuritis antibodies. serum and csf contained high titers of igg antibodies reacting specifically with a protein antigen of approximately kd in immunoblots of human cerebral cortical neuronal nuclei or of human purkinje cells. this pattern of autoantibody reactivity was not present in sera from any of other patients with small-cell lung carcinoma, of whom had paraneoplastic encephalomyeloneuritis and anti-hu antibodies, nor was it present in many patients with other neurological disorders. the patient's serum has been used to probe a human cerebellum expression library and to isolate a cdna clone that is being characterized. acute encephalopathy is the problem in % of neurology consultations reported at mskcc. we studied patients ( prospectively and retrospectively) to determine clinical findings, causes, and outcome. fifty-five were women and were men, and the average age was years. all patients had cancer: lung ( %), gastrointestinal tract ( %), breast ( %), and others ( %), forty-two patients ( %) were delirious on admission and delirium developed an average of days later in %. encephalopathy occurred postoperatively in %. symptoms included confusion ( %), lethargy ( %), agitation ( %), hallucinations ( %), and seizures ( %). signs included deficits in attention ( %), memory ( %), language ( %), lateralizing signs ( %), and asterixis ( %). the average mini-mental status test (mms) score was ( = normal). a single cause for delirium was found in only % of patients with an average of etiologies per patient. metabolic abnormalities were found in % of patients, and were a primary cause in %; disseminated intravascular coagulation contributed to delirium in %. cns metastases were found in % and were a major cause of delirium in all. fifty percent of the patients had fever/ systemic infection, but sepsis was present in only %; only patient had cns infection. medication contributed to delirium in % but was a primary cause in only %. the -day mortality rate was % and delirium improved in % (average mms = ). patients with cancer have multiple, potentially treatable causes of delirium. delirium is associated with a high death rate, though patients generally improve. radiation therapy for brain tumors d. w. dodick, b. mokri, k. k. unni, g. m. miller, and e. g. shaw, rochester, m n osteosarcoma in a previously normal bone is a rare but recognized remote effect of radiation therapy. any bone in the field of radiation can be affected. involvement of cranial bones is exceedingly rare. we could identify only patients ( men and women) with postirradiation osteosarcoma of the calvarium seen at the mayo clinic over a -year period, from to . all had received radiation for brain tumor, osteosarcoma had appeared in the field of radiation in all, the interval from radiation therapy to the appearance of sarcoma ranged from to years, and diagnosis of sarcoma was confirmed histologically in all cases. the patients' age at the diagnosis of the brain tumor ranged from to years. the nature of the brain tumor was unverified in cases, was a low-grade ependymoma in the third case, and a pilocystic astrocytoma in the fourth case. one patient is still alive months after the diagnosis of the sarcoma. she received chemotherapy and subsequently underwent resection of the osteosarcoma. one patient died postoperatively after partial resection of the sarcoma. the other patients died months and months after the diagnosis of the osteosarcoma despite additional radiation therapy in the former and aggressive chemotherapy in the latter. element-la fusion gene as a potential marker of neural tumor differentiation lawrence recht, chiffon wu, and louis j. degennam, worcester, ma inducing cancers to differentiate into more benign differentiated tumors represents a novel oncological strategy. to establish a model that would permit assessment of this phenomenon at a molecular level, we created and have partially characterized a murine neuroblastoma line that has been stably transfected with a synthetic fusion gene containing the promoter element of the rodent synapsin i gene (synapsin i regulatory element isre)). in vivo, this promoter directs the neuron-specific expression of the synapsin i gene in normal adults. the gene also is expressed in varying amounts in neuronal tumors including neuroblastoma. in the synthetic fusion gene, the sre has been linked to the lacz gene that encodes bacterial p-galactosidase. a simple histochemical assay for p-galactosidase therefore provides a specific marker of the expression of the fusion gene. our preliminary experiments as of this writing have shown that it is possible to detect p-galactosidase activity in the transfected neuroblastoma cells both in vitro and in transplanted tumors. it appears possible therefore that this transfected neuroblastoma cell line can provide a useful model system with which to assess the effects of differentiation therapies. larger lesions (> cm ), and larger midline shifts (> mm). twenty-eight of ( %) patients with prior has had bt has compared to of ( %) patients without prior has. in patients, their bt h a was similar to their previous ha but was more frequent or severe. we conclude that has in bt patients are common but usually not severe. nausea, vomiting, an abnormal neurological examination, or a change in prior headaches warrant further investigation. cairncross and macdonald showed that procarbazine, lomustine, and vincristine (pcv) are effective for recurrent anaplastic oligodendrogliomas (ao) (ann neurol ; : - ) . pcv now has a major role in management of all forms of oligodendrogliomas ( ), but the biological basis for this response is unknown. to evaluate one subset of possibilities, we studied patients ( ao, ) with a ct method that permits measurement of blood-to-tissue transport (kj, tumor-to-blood transport (k ), and vascular volume (v,) (ann neurol ; : - ) . pcv was used to treat of the patients. k, (~ grr-' min-') values were highly variable for whole tumor, ranging from . to . (mean . k . ) with no difference between a and . k and v, were also highly variable. k, of tumor-free brain was . to . (mean . ? . ). in comparison to malignant astrocytomas, which have a mean k, in the range of . with some as high as . , a and appear to be much less permeable. this suggests that the efficacy of pcv may be due to factors other than capillary transport, such as tumor-cell sensitivity. frameless stereotactic localizer gene h. barnett, donald w. komos, and charles p . steiner, cleveland, oh extent of tumor resection has been shown to correlate with prognosis in malignant gliomas. although frame-based stereotactic techniques can provide information regarding tumor margin, they are often unwieldy and require expensive and elaborate computing systems. a frameless stereotactic neurosurgical localizing system was designed that overcomes these liabilities. this armless, frameless, stereotactic pointing device provides real-time three-dimensional localization information during operation. in addition to assisting in placement of a trephine craniotomy, it allows volumetric resection of the tumor with virtually complete excision of even large irregularly shaped tumors. mean error on localizing a point in space using this system has proven to be less than mm. a technical description of the system as well as surgical results are presented. to investigate the effect of age on response rate to chemotherapy and time to progression (ttp) and death ('itd) in patients with recurrent astrocytomas and malignant astrocytomas, we reviewed case records and scans of patients who received chemotherapy at the university of michigan with bischloroethylnitrosourea or procarbazine. three age groups were studied: ( ) < yr (n = ); ( ) - yr (n = ); ( ) > yr (n = ). tumors were grouped as grade r+ (recurrent grade plus grade , n = ) or grade (n = ). serial computed tomographic or magnetic resonance scans were analyzed in a blinded fashion and graded as progressive disease (pd), stable disease (sd), or partial response (pr, > % decrease in size). the pr rates for the age groups were %/ %/ % for grade r+ tumors ( p = . ) and %/ %/ % for grade tumors ( p = . ). median 'itp was weeks for grade r + and / weeks for grade . median ltd was / / weeks for grade r+ and / / weeks for grade . we conclude that age is an important prognostic factor with respect to likelihood of response to chemotherapy, duration of response, and survival irrespective of grade. cheryl p. harris and kurt a. jaeckle, salt lake city, ut intravascular malignant lymphomatosis (iml), a b-cell lymphoma confined to small venules and capillaries, often presents with neurological symptoms. this disease is uniformly fatal ( -month mean survival); no successful treatment has been identified. we observed marked reproducible neurological improvement after plasmapheresis in a -year-old woman with iml. presenting with a cauda equina syndrome, she progressed over year with neurological, hepatic, and hematological disease. persistent laboratory abnormalities included a high sedimentation rate ( mm/hr), coagulopathy, hemolytic anemia, and elevated liver enzymes. extensive evaluations for infectious, autoimmune, and neoplastic processes, including bone marrow examination, were inconclusive. because of neurological progression, empiric therapy with high-dose steroids followed by cyclophosphamide was initiated without response. plasmapheresis ( ml/kg in exchanges) effected resolution of encephalopathy and normalization of the coagulopathy and sedimentation rate. neurological progression recurred within weeks of pheresis; repetitive courses reproduced neurological response. finally, progressive dementia ensued, and a decision was made to cease pheresis; the patient died days later, months after presentation. autopsy disclosed diffuse intravascular cd- positive malignant lymphoma cells in small vessels of all organs. although the mechanism is unknown, the serendipitous discovery of response to plasmapheresis in this patient warrants further consideration. morphine is an effective analgesic in the rat after injection into a number of discrete brainstem regions, including the periaqueductal gray (pag), the locus coeruleus (lc), and the nucleus raphe magnus (nrm). early work with morphine gray and the nucleus raphe magnus established the existence of synergy between the brainstem and the spinal cord in rats. more recently, studies from our laboratory revealed synergy between two brainstem structures, the pag and the lc. in the current study, we explored the analgesic interactions between the pag and the nrm using indwelling cannulae. first, we established morphine dose-response curves and calculated the ed,, independently in the pag ( . pg) and the nrm ( . pg). we then simultaneously injected various morphine doses into both regions. injecting morphine at pg into either the pag or the nrm did not elevate tailflick latencies above baseline values. however, administered into both regions simultaneously, the -pg doses produced an % maximal response, corresponding to more than a threefold increase of baseline latencies. a fixed morphine dose of pg in the pag shifted the morphine dose-response curve fivefold in the nrm (ed,, . pg), whereas a fixed nrm dose of fg shifted morphine's dose-response in the pag approximately twofold. together, these results clearly show synergistic interactions for morphine between the pag and the nrm. the presence of synergistic interactions between brainstem nuclei as well as between the brainstem and the spinal cord underscores the complexity of opioid analgesic systems. p . the glutamate uptake inhibitor ~-trans- , -pyrrolidine dicarboxylate is neurotoxic in neonatal rat brain john d. e. barks and faye s. siloerstein, ann arbor, m i important evidence of the neurotoxicity of endogenous glutamate (glu) in mammalian brain was provided by the observation that dl-threo- -hydroxyaspartate, a high-affinity glutamate uptake (hagu) inhibitor, was neurotoxic in adult rodent striatum (j neurochem ; : ) ; however, the absence of neurotoxicity in neonatal brain was interpreted as evidence that immaturity of glutamatergic innervation limited the potential role of endogenous glu as a neurotoxin in the immature brain. yet, considerable data provide indirect support for the hypothesis that glu can be neurotoxic at this stage. to resolve this issue, we assessed the neurotoxicity of a novel, selective hagu inhibitor, ~-trans- , -pyrrolidine dicarboxylate (l-pdc) (j med chem ; : ), in postnatal day (pnd) rats (n = ). l-pdc (ph . ) was stereotaxically injected into right anterior striatum (str) ( nrnol, n = ) or through dorsal hippocampus into posterior str ( nmol, n = ; nmol, n = ). animals were killed days later, and neuropathology was assessed in cresyl violet-stained sections. after anterior injections, focal neuronal necrosis was evident in dorsal str; high-dose posterior injections caused prominent hippocampal lesions with pyramidal layer thinning and focal necrosis in dorsal thalamus, while nmol produced small foci of pyramidal cell loss. in both groups, focal cortical necrosis and callosal cysts were apparent adjacent to the injection track. l-pdc-induced brain injury provides direct support for the hypothesis that endogenous glu may be neurotoxic in the developing brain. (sax et al, ann neurol ; : a) . the signs and symptoms of of these patients lessened for to months. furthermore, a patient with a severe oral-lingual biting dyskinesia improved when taking doses up to milligrams per day for months. we noted no-significant adverse reactions, although patients had mild but labile elevations in sgop and sgpt. one patient receiving opioid analgesics for pain inadvertently failed to discontinue the naltrexone but noted no reduction in the pain-alleviating effects of the analgesic. although hyperkinesia, especially of midline functions, as well as quality of life improved for the hd patients, their cognitive deficits remained unaffected. these observations suggest that chronic naltrexone is a safe and effective agent to treat chorea, dysphagia, and oral dyskinesia in hd for periods longer than a year. furthermore, they indicate that naltrexone can be effective in ameliorating oral-lingual biting tardive dyskinesia. these findings support our previous hypothesis that endogenous opioids play a role in rhe modulation of the dopamine system in hyperkinetic stereotypic movement disorders. a. jon stoessl, elizabeth szczutkmuski, and hanna fydvszak, london, ontario, canada we previously have demonstrated (psychopharmacology ; : - ) that intraperitoneally (ip) administered cholecystokinin (cck)- s suppresses vacuous chewing mouth movements (vcms, a putative mode of tardive dyskinesia) in rats exposed to chronic neuroleptics. as cck is not thought to cross the blood-brain barrier in significant amounts, its site of action in this paradigm is unclear. other behavioral and neurochemical effects of ip cck are blocked by vagotomy. male sprague-dawley rats were administered fluphenazine decanoate (flu; mg/kg im) or its vehicle every weeks for approximately weeks. cck ( , , or ng intracerebroventricularly) had no effect on neuroleptic-induced vcms. another group of neuroleptic-treated rats was subjected to bilateral subdiaphragmatic vagotomy or a sham procedure. cck- s ( , , or pg/kg intraperitoneally) suppressed neuroleptic-induced vcms in shamoperated animals, which confirmed our previous results. in vagotomited animals, chronic flu failed to induce vcms and cck was without effect in vehicle-or neuroleptictreated animals. these data suggest that the effects of cck on flu-induced vcms may be mediated peripherally, and that vagal pathways may be important for generating this response. (supported by the ontario mental health foundation and the ontario ministry of health.) p . excitotoxic amino acids are not involved in dopaminergic neurotoxicity of m p t p eldad mehmed, jutta rosenthal, and avinoam reches, petah tiqva, tel aviv, and jerusalem, israel the dopaminergic (da) neurotoxicity of -methyl- phenyl- , , , -tetrahydropyridine (mptp) is mediated via its oxidation in cns to mpp + , which enters da neurons and poisons mitochondrial complex i. da neuronal damage induced by direct nigral mpp+ injection is prevented by pretreatment with n-methyl-d-aspartate receptor antagonists, which suggests that excitatory amino acids are involved in mptp toxicity. since local mpp + application may produce nonselective nigral damage, we examined whether excitotoxins have a role in toxicity of systemically administered mptp. c black mice were injected intraperitoneally, once, with mptp.hci( mg/kg) and decapitated days later. groups of animals underwent the following pretreatments: (i) decortication week prior to mftp; ( ) intracerebroventricular injections of the excitatory amino acid receptor antagonists -amino-phosphonoheptanoate and d-glutamyl-glycine; and ( ) intraperitoneal injections of the calcium channel antagonists nimodipine, diltiazem, and flunarizine minutes prior to mptp. mptp produced marked striatal da depletions. decortication, destroying glutamatergic corticostriatal projections, intracerebral amino acid receptor antagonists, and systemic calcium channel antagonists did not protect mice against mptp toxicity; mptp-induced striatal da decreases were similar to those given the neurotoxin alone. this study suggests that excitotoxins are not involved in the mechanism of mptp toxicity. scopolamine-induced cognitive deficits k . j . meador, m . e. allen, p. franke, e. e. moore, and d. w. loring, augusta, ga a unique neurophysiological role for thiamine in cholinergic systems has been suggested. total thiamine content in cholinergic nerve terminals is comparable to that of acetylcholine, and the phosphorylation state of thiamine changes with release of acetylcholine. thiamine binds to nicotinic receptors and may exhibit anticholinesterase activity. based on these observations, we investigated the effects of pharmacological doses of thiamine on the cognitive deficits induced by the anticholinergic scopolamine in healthy young adults using a randomized, double-blind, placebo-conrrolled, double crossover design. cognitive tests included the p eventrelated potential and free recall memory for a verbal paragraph. conditions included baseline (bl), thiamine gm by mouth and scopolamine . mg/kg intramuscularly (b + scop), and lactose by mouth and scopolamine (plac + scop). testing was performed hours post thiamine or placebo, and . hours post scopolamine. thiamine significantly reduced the adverse effects of scopolamine on p latency (f [i, = . , p . ) and percent recall memory ( f el, ) = . , p . ). means (+sd) and p latency (ms) were bl = ( ), b + scop = ( ), and plac neurol ; : - ) . we previously reported that cff improved in of ms patients ( %) given el- orally in divided daily doses ranging from . to . mg (stefoski et al, neurology ; : - . subsequent analysis revealed that in of the patients cff improvements and reversals followed in a phase-locked trend the rising and falling serum concentrations of el- , including patients whose changes remained below the % increase needed to qualify for the improved category. these results resemble the phase-locked effects of temperature on neurological function in ms. the cff changes, because they so closely reflect variations in serum concentration, suggest that el- tissue levels closely follow those in serum and that el- rapidly crosses the blood-brain barrier. efficacy of el- in ms is also predicted to have a close relationship to serum levels. p . development of a n internal standard detectable by proton and phosphorus- nmr and hplc w. e. klunk, k. panchalingam, r. j . mcclure, and j . w. pettegrnu, pittsburgh, pa comparison of quantitative results from different analytical techniques can prove difficult due to the peculiarities of the particular techniques and the lack of a common standard applicable to all of the techniques. recently, both in vivo and in vitro nuclear magnetic resonance (nmr) have been applied to the quantification of a large variety of metabolites. although nmr can be applied to the study of living tissue, the question arises of how this technique compares with more traditional techniques such as high-pressure liquid chromatography (hplc). although this question can be addressed partly by studying perchloric acid (pca) extracts, it is difficult to directly compare this in vitro nmr data with results from hplc. to address this question, we have developed an internal standard that can be quantified directly by in vitro phosphorus- nmr, proton nmr, and by -fluorenylmethyl chloroformate (fmoc) derivatization followed by separation by hplc. a variety of aminophosphonic acids were studied by 'p nmr, 'h nmr, and hplc. promising compounds were added to pca extracts of human brain. the optimal compound was found to be -aminopropylphosphonic acid (app, ho p-ch -ch,-ch -nh ). app is easily detectable by all techniques, falls well outside of the region of interest in phosphorus- nmr, and is well resolved by proton nmr at mhz. it is easily separable from the phosphomonoesters and phosphodiesters observable by hplc and from the amino acids that occur in brain in significant concentrations. app appears to be a useful internal standard in the study of phosphorus and amino acid metabolites by in vitro p nmr, 'h nmr, and hplc. theories of sentence comprehension hypothesize at least a grammatical component that establishes the relationship among words in a sentence, and a semantic component that determines the meanings of these words. we used positron emission tomography (pet) to quantify regional cerebral blood flow (rcbf) in neurologically intact subjects during their detection of a letter target, a grammatical target, or a semantic target in the same written sentences. a mixedmodel analysis of variance (anova) revealed significant main effects for region (f e , ) = . ; p < . ), condition (f , = . ;~ < . ), and a significant region times condition interaction ( f {go, = . ; p < . ), but there were no differences between individual subjects. subsequent anovas revealed increased rcbf in a unique set of brain regions during the subjects' response to a grammatical probe when compared to their response to a letter probe of the same sentences. a unique distribution of rcbf also distinguished response to the semantic probe from response to the grammatical probe and the letter probe. other brain regions apparently contributed to performance for several activation conditions. these findings support the hypothesized dissociation of specific linguistic components based on their unique cerebral topographical representation, and that a distributed network of brain regions subserves sentence comprehension. cerebral music processing-a comparison study of musically trained and naive individuals louis s. russo, jr, jachonville, fl we performed topographical mapping of brain electrical activity in right-handed symphony musicians and righthanded, musically naive individuals during various musical tasks; namely, listening to solo piano music, silent singing of familiar music, and silent reading of unfamiliar music. fast-fourier transform ( f r ) of electrocortical activity was carried out during task performance and the eyes-open resting state. data were analyzed using a computer-assisted model. increases in regional beta activity of greater than standard deviations from the resting state were considered significant of activation. during audition, the musicians showed activation in the right posterior parietotemporal region; the naive showed no change from the resting state. during silent singing, the musicians showed bitemporal activation, r > l; the naive showed activation in the right mid-and posteriortemporal regions alone. during silent sight reading, the musicians showed a major activation in both temporal regions, l > > r, the naive showed only a marginal change in the posterior temporal-occipital regions. these data suggest that music processing is primarily a right cerebral function in untrained individuals and a bilateral function in musicians. musicians, in contrast to the naive, show progressively more left brain activation as task complexity increases. the present study analyzes language profiles in patients who presented with primary progressive aphasia (ppa) without global dementia for at least years. language and cognitive impairment were evaluated using the western aphasia battery (wab) and the mattis dementia rating scale (drs). expressive language disability with reduced speech fluency and anomia, but preserved language comprehension and nonverbal cognition, were typical features in early stages. spontaneous speech was significantly more impaired in ppa than in anomic aphasia after left-hemisphere stroke and in language impairment in probable alzheimer's disease (ad) ( p = . ). the profile of aphasia suggests that ppa tends to affect anterior parts of the language-dominant cortex first. neuroimaging generally showed mild to moderate brain atrophy. in patients atrophy involved especially the left frontal progressive aphasia cortex. follow-up examinations that were done in patients or several years after the first assessment revealed continuous, most often rapid deterioration of language impairment. two patients died and years after the onset of ppa. neuropathological examination showed ad in patient and pick's disease in the other patient. beverly clarke, adrian upton, markad kamath, and helene griff;., hamilton, ontario, canada eight patients implanted with a cyberonics neurocybernetic prosthesis model to stimulate the vagus nerve were assessed for changes in cognitive performance. the patients had complex partial seizures for more than years, with more than per month. patients were years * . sd old. cognitive evaluation included response time to a randomized light signal appearing on a switch box (test a); test b, in which the signal appeared bilaterally; and test c, in which a response to the signal was required while the patient simultaneously ignored a second signal. data were collected and analyzed using an apple i e computer and switch pad. all patients were taking therapeutic levels of anticonvulsant medications and dosages were constant. testing occurred times during a day preoperatively (day l), weeks postoperatively with the stimulator on (day ), and months after turn-on (day ). patients were randomized into high-and low-frequency stimulation groups (hfg and lfg). hfg parameters were hz, so msec pulse width (pw), and lfg hz, msec pw. examiners were blinded as to group. student's t-test analyses of mean differences between groups and individual measurements showed a significant difference between hfg and lfg for test c ( p < . ). lfg showed a significant improvement for tests a, b, c between day and , and for test c between day and . no group effect was seen between day and in the lfg. individual measurements showed improvement for test b ( p < . ) for the hfg between day and , test b ( p < . s) between day and , and tests a and b ( p < . ) and ( p < . ) day vs . the lfg group improved between days and and and . between day and day , the lfg showed improvement only for test b ( p < . ). chronic stimulation of the vagus nerve improves cognitive function in epileptic patients and this improvement is more marked with low-frequency stimulation. a. guidotti, and j. d. rothstein, bologna, itah, washington, dc, and baltimore, m d we reported idiopathic recurring stupor (irs) in a patient with stuporous episodes without known causes and reversed by flumazenil, a specific benzodiazepine (bz) antagonist. ictal plasmdcerebrospinal fluid (csf) showed increased bz-like activity (ann neurol, in press). recently, an endogenous bzreceptor ligand (endozepine [ez]) has been purified from mammalian brain with properties similar to diazepam. it acts like diazepam to potentiate gamma-aminobutyric acidmediated postsynaptic inhibition. we hypothesized that irs might be due to an excess of this substance. irs was diagnosed in patients, and years old, who had recurring stupor or coma episodes lasting hours to days. ictal brain ct/mri, kidney, liver, heart, blood glucose, ammonia, and osmolality were normal. eeg showed fast -hz background activity while the patients were unreactive to stimuli, reversed by flumazenil. ictal serum or csf revealed an enormous increase of the ez in both patients, with levels as high as nm, compared to to nm in control serum/csf. interictal csf or serum in irs contained ez levels similar to control csf and serum. irs may be due to excess ez. the cause for increased ez is unknown. parkinson's disease: evidence from word learning murray grossman, jenger mickanin, barbara schaefr, kris onishi, matthew b. stern, steven gollomp, and howard hurtig, philadelphia, pa several reports have suggested that patients with parkinson's disease (pd) have intellectual impairments in several domains such as memory, but few studies have explored difficulties in language processing. we investigated the ability of nondemented pd patients with mild motor impairments to learn about the grammatical and semantic information represented in a new verb. the new verb was presented to patients in a sentence-picture matching context, and we probed their recall of the verb minutes later. a sentence judgment task assessed grammatical knowledge by asking patients to judge the new verb, known verbs, and pseudowords used appropriately or incorrectly in a sentence. we found that % of pd patients were significantly impaired in their grammatical appreciation of the new verb (f [i, = . ;p < . ). this was not related to their motor disorder or neuropsychological performance. a picture classification task used pictures illustrating specific aspects of the new word's meaning to evaluate semantic knowledge. pd patients were as accurate as controls at deciding whether a picture illustrated the meaning of the new verb (f ( , = .lo;p > . ). only pd patient ( %) had difficulty sorting pictures. selective difficulty recalling only grammatical aspects of a new word suggests that the word learning impairment in pd cannot be entirely explained by poor memory. instead, in agreement with other recent findings, pd patients may be impaired in some aspect of grammatical processing in language. we discuss the hypothesis that defects in the frontocaudate axis in pd underlie this impairment. neuropsychological performance on both verbal and nonverbal tasks is reported to differ between healthy men and women. some of these cognitive differences are postulated to reflect differences in interhemispheric and intrahemispheric cerebral organization. our preliminary study indicated that women with alzheimer's disease (ad) performed worse than men on a composite neuropsychological battery, even after effects of potentially confounding variables were considered (buckwalter et al, j clin exp neuropsychol ; : ) . to explore further the nature of gender-associated differences in ad, we analyzed data from a verbal and a nonverbal task (the boston naming test and drawings from the spatial quantitative battery supplement to the boston diagnostic aphasia examination) for men and women who met nincds-adrda criteria for "probable" ad. prior to ana-grip strength kg [range . - kg]). the electrophysiological examination showed improvement with reversal of conduction block in patients and was unchanged in . an apparent response to the placebo was seen in patients. improvement after ivig therapy was maintained for variable durations ( - wk) and reoccurred with subsequent infusions. an equally effective response was documented after infusion of a single ivig dose of gm/kg. we conclude that ivig therapy is effective in some patients with cidp, even after long duration of illness. the best responses were observed in patients with recent relapse. a single high-dose treatment may be equally effective. the object of this study was to examine whether borrelia burgdorjeri antigens could be detected in csf in the absence of detectable antibodies to b. burgdorjeri (the etiological agent of lyme disease). osp a is a -kd antigen that is specific for . duvgdorferi osp a was probed using western (immuno) blot and specific mouse monoclonal antibodies. polyclonal lyme antibodies were detected in csf using standard micro enzyme-linked immunosorbent assay. seven patients had osp a in csf without detectable lyme antibodies. there were men and women aged to years (mean yr). disease duration ranged from weeks to years. neurological syndromes included confusion with acute flulike illness, optic neuritis, hemiparesis with inflammatory brain lesion, encephalitis, headache with erythema migrans, bilateral facial nerve palsies, and encephalomyeloradiculitis. three patients had csf abnormalities. in patients csf parameters were otherwise completely normal. possible explanations for undetectable csf lyme antibodies included early infection ( patients), prior antibiotics ( patients), and prior steroids plus antibiotics ( patient). in patient there was no obvious explanation. we conclude that osp a, a specific antigen of b. burgdorferi, may be present in csf without a detectable humoral response. the diagnosis of neurological infection with b. bwgdorjeri should not require a positive csf serology. mollaret's meningitis: demonstration by polymerase chain reaction a -year-old man was seen in september for his fourth episode of aseptic meningitis over a -year period. the episodes conformed to criteria for mollaret's meningitis as published by bruyn, straathof, and raymakers, and subsequently by others; they lasted about week, and were characterized by fever, headache, meningismus, lymphocytic pleocytosis, elevated protein in cerebrospinal fluid (csf), and spontaneous resolution without residua. extensive prior evaluations had failed to uncover a cause. the patient was otherwise well and neither he nor his wife had any history of sexually transmitted diseases. suspicion of herpes simplex virus (hsv) arose due to a single transient, raised skin rash several weeks earlier that failed to yield virus on culture. the patient was treated with acyclovir, which resulted in rapid resolution of symptoms. though culture and immunological studies of csf and blood again were unrevealing, polymerase chain reaction (pcr) studies of csf confirmed the presence of hsv type . we suspect that herpes simplex virus is a more common cause of recurrent aseptic meningitis than current culture and immunological techniques would suggest. pcr offers increased diagnostic sensitivity for neurotropic viruses and should be considered in patients with recurrent meningitis of cryptic etiology. differentiation by inorganic lead: a role for protein kinase c j. lutewa, j. p. bressler, r. r. indurti, l. belloni-olivi, and g. w . goldstein, baltimore, m d microvascular endothelial function in developing brain is altered by inorganic lead. this may result from changes in protein kinase c (pkc) modulation. we examined the effects of inorganic lead on an in vitro model of neural endothelial differentiation. astroglial-induced endothelial differentiation into capillary-like structures was inhibited by lead acetate with % maximal inhibition occurring at . pm lead. inhibition was independent of effects on cell viability or growth. we examined the effects of lead on cellular pkc pools under conditions that inhibited capillary-like structure formation. membranous pkc increased in c astroglial and neural endothelial cells after exposure to lead acetate. exposing c cells to p,m lead for hours increased membranous pkc by % as determined by immunoblotting. membranous pkc increased in response to as little as nm lead and saturated at pm. phorbol esters were used to determine if pkc modulation was mechanistically related to lead's inhibition of capillary-like structure formation. -myristate -acetate ( nm) inhibited endothelial differentiation by * %, whereas -alpha-phorbol , didecanoate was without effect. these findings demonstrate that inorganic lead may induce cerebral microvessel dysfunction by interfering with pkc modulation in microvascular endothelial or perivascular astroglial cells. w. f. brown, b. v . watson, j . garland, g . c. ebers, and n . desai, london, ontario, canada gait difficulties in multiple sclerosis (ms) are commonly accompanied by fatigue and dyspnea. possible explanations for the latter include weakness andlor dyssynergia of the respiratory muscles, including possible abnormalities in central pathways regulating respiration. this study examined central and peripheral motor conduction to the diaphragm in ms patients whose gait was notably labored and accompanied by breathlessness. peripheral conduction was assessed by measuring the latency and size of the surface-recorded diaphragmatic maximum m-potential responses to supramaximal stimulation of the phrenic nerve in the neck, and central motor conduction by comparable measurements in response to magnetoelectrical stimulation over the vertex. peripheral motor conduction was normal. the most striking abnormalities were in central motor conduction. cortical stimulus-evoked diaphragmatic responses were absent on both sides in patients, and unilaterally in l patient, whereas in others the latency of the cortical stimulus-evoked response was increased and the size clearly reduced and entirely normal in only patients. these studies show that central conduction program and abstracts, american neurological association to the diaphragm is commonly abnormal and may play a role in the fatigue and dyspnea experienced by ms patients. six men ( - yr) developed myelopathy that progressed slowly over several months and was characterized by asymmetrical, incomplete spinal cord syndrome manifested at the sensory level at the trunk, mild spastic paraparesis, and urinary incontinence. the spinal cord lesions at appropriate levels were recognized by mri as enhancing lesions in of the men. coxiella burnetii infection was confirmed in the blood of all patients by immunofluorescence microscopic assay (ifa) and transmission electron microscopy (tem). in patients, we detected c. burnetti by tem and ifa using csf of the patients inoculated onto fresh peripheral blood lymphocytes. four patients who were treated with appropriate antibiotics responded with either partial resolution of symptoms or arrest of further neurological progression. in patients the lesion was shown on mri to have decreased in size. in summary, we report cases of transverse myelopathy associated with c. barnetti infection. this is the first report, to our knowledge, of coxiella-related chronic myelopathy. we present a series of patients with different labyrinthine lesions diagnosed by mri. twelve patients with sensorineural hearing loss were studied by gadolinium-enhanced mri, including -mm contiguous t -weighted images through the labyrinth. ten patients had enhancement of the cochlea or vestibule, or both. all patients with cochlear enhancement had severe neural sensory hearing loss. all patients with vestibular enhancement had severe vestibular symptoms. the patients' final diagnosis included viral labyrinthitis ( patients), syphilitic labyrinthitis ( patients), bacterial labyrinthitis ( patient), and vestibular neuromas ( patients). one patient had an acoustic neuroma extending in the basal turn of the cochlea. the enhancement in patients with vestibular neuromas was brighter and there was slight mass effect in comparison with the patients with inflammatory labyrinthine lesions. one patient had hemorrhage within the vestibule from an adjacent temporal bone hemangioma. one patient with ct-proven cochlear otosclerosis had pericochlear areas of enhancement on gadolinium mri. mri can diagnose a variety of labyrinthine lesions that correlate very well with the patient's clinical symptoms. gadolinium should be used routinely in patients with suspected labyrinthine disease. the diagnosis of meniere's disease and endolymphatic hydrops remains a diagnosis of exclusion. few radiographic findings have been correlated with the clinical symptoms of this entity. we describe patients with symptoms of hearing loss or vertigo, or both, who demonstrated enhancement of the endolymphatic sac on gadolinium-enhanced mri. no enhancement was noted in a series of controls with no symptoms of hearing loss and vertigo. enhancement in the brain correlates with inflammatory or neoplastic conditions. we thus can speculate that enhancement of the endolymphatic sac reflects an inflammatory process in this location that may interfere with the normal resorption of indulin and secondary hydrops. in addition to excluding an acoustic neuroma and a labyrinthine schwannoma (which clinically may be confused with meniere's disease), contrast-enhanced mri may provide objective evidence in favor of labyrinthine hydrops. it was intermittent ( %) but progressive. the ha was mild to moderate in severity; it was the worst symptom in only ( %) and the first symptom in ( %) patients. has were worse in the morning in ( %) and interfered with sleep in ( %) patients. unlike true tension-type has, bt has were worse with bending over in ( %), with valsalva's maneuver in ( %), and nausea or vomiting were present in ( %) patients. an abnormal neurological exam was found in ( %) patients with has and ( %) patients without has lyzing the effects of gender, we used a hierarchical regression procedure to control for possible effects of subject age, education, age at onset of dementia symptoms, dementia duration, and family history of dementia. significant gender effects were found for the verbal task ( p < . ) (mean boston naming test score of . for women and . for men), but not for the drawing task. we conclude that verbal abilities are more severely affected in women than in men with ad, a difference that may in part reflect premorbid gender-associated differences in cerebral hemispheric organization. hemispatial placement is known to affect line bisection in patients with neglect. whereas placing stimuli in neglected space increases bisection error, placing stimuli in nonneglected space attenuates error. the effects of hemispatial placement on line bisection were examined in patients with chronic neglect (over months after stroke). all patients had large (frontotemporoparietal), unilateral, right-hemisphere lesions. each patient bisected lines of different lengths ( , , , and cm) in hemispatial conditions ( cm left of midline, midline, and cm right of midline). like previous reports, when patients bisected lines in left hemispace, a consistent ( / trials) left-sided neglect was observed ( . cm). however, when lines were bisected in center space, misbisections occurred on either side of the midline; and, unlike previous studies, when lines were bisected in right hemispace, a consistent ( / trials) right-sided neglect was observed ( . cm). the magnitude and directional consistency of line bisection errors were significant. neither visual field defects nor limitations in reaching accounted for the results. recovery in chronic neglect may involve a realignment of limited attentional resources favoring the body's midline. consequently, performance in both hemispatial fields can be biased toward midline, resulting in neglect of opposite directions. despite agreement that depression is the most common neuropsychiatric symptom associated with multiple sclerosis (ms), many aspects of this emotional change are unclear. one of the more controversial issues concerns the relationship between severity of ms and depression. this relationship is used to evaluate whether depression is an integral or reactive symptom of ms. examination of this relationship is complicated by the presumed overlap between somatic features of depressive and neurological symptoms in ms. to clarify this situation, we examined the relationship between severity of ms and categories of depressive symptoms using the beck depression inventory (bdi). eighty-nine patients and normal controls were examined. for certain comparisons, patients were classified as mild (extended disability status scale of - ) or moderatelsevere ( ) ( ) ( ) ( ) ( ) ( ) . results indicated that total bdi scores and the depressive symptom categories (mood, self-reproach, vegetative, and somatic features) were elevated in patients with ms, but the extent of these elevations was not related to severity of disease. these results suggest that depression in ms is not a simple reaction to physical disability. furthermore, clinical examination of depressive symptoms is straightforward and not confounded by severity of ms. neurological involvement in wegener's granulomatosis was studied in consecutive patients diagnosed at the mayo clinic. one hundred and nine patients ( %) had neurological involvement. peripheral neuropathy was seen in ( . %), cranial neuropathy in , external ophthalmoplegia in , cerebrovascular events in , seizures in , and miscellaneous involvement in . the mean age and sex ratio did not differ in those with or without neurological involvement. among the patients with peripheral neuropathy, had multiple mononeuropathy, had distal symmetric polyneuropathy, and had unclassified peripheral neuropathy. multiple mononeuropathy was one of the major presenting symptoms in patients. kidney involvement was significantly higher in the patients with peripheral neuropathy compared to those without it (p < . ). among the cranial nerves, the second, sixth, and seventh nerves were affected most frequently. multiple cranial nerves were affected in patients. unusual neurological manifestations among the miscellaneous group included spastic paraparesis, temporal arteritis, homer's syndrome, and papilledema. this is the first comprehensive study on the frequency and distribution of neurological involvement in wegener's granulomatosis. chronic inflammatory demyelinating polyneuropathy: a double-blind placebo-controlled crossover study treatment with high-dose intravenous human immunoglobulin (ivig) has been reported to be beneficial in some patients with chronic inflammatory demyelinating polyneuropathy (cidp), yet most observations have been nonblinded. we examined the effect of ivig therapy in patients ( men, women) with cidp in a double-blind, placebo-controlled crossover study. disease was chronic progressive (n = ) or chronic relapsing (n = ) and of variable duration ( mo to yr). the diagnosis was confirmed by electrophysiological ( ) and nerve biopsy ( ) examinations. the trial consisted of two -day periods each. patients were randomly treated with ivig ( . mg/kg/day) or placebo on consecutive days and followed. function was assessed by a quantitative neurological disability score, functional grade, grip strength measurement, and electrophysiological examinations at the beginning and end of each treatment period. with ivig therapy, significant improvement was documented in / patients (improvement in neurological disability score mean key: cord- -w wxu i authors: kuriyama, akira; jackson, jeffrey l.; kamei, jun title: performance of the cuff leak test in adults in predicting post-extubation airway complications: a systematic review and meta-analysis date: - - journal: crit care doi: . /s - - - sha: doc_id: cord_uid: w wxu i background: clinical practice guidelines recommend performing a cuff leak test in mechanically ventilated adults who meet extubation criteria to screen those at high risk for post-extubation stridor. previous systematic reviews demonstrated excellent specificity of the cuff leak test but disagreed with respect to sensitivity. we conducted a systematic review and meta-analysis to assess the diagnostic accuracy of the cuff leak test for predicting post-extubation airway complications in intubated adult patients in critical care settings. methods: we searched medline, embase, scopus, isi web of science, the cochrane library for eligible studies from inception to march , , without language restrictions. we included studies that examined the diagnostic accuracy of cuff leak test if post-extubation airway obstruction after extubation or reintubation was explicitly reported as the reference standard. two authors in duplicate and independently assessed the risk of bias using the quality assessment for diagnostic accuracy studies- tool. we pooled sensitivities and specificities using generalized linear mixed model approach to bivariate random-effects meta-analysis. our primary outcomes were post-extubation airway obstruction and reintubation. results: we included studies involving extubations. three studies were at low risk for all quadas- risk of bias domains. the pooled sensitivity and specificity of cuff leak test for post-extubation airway obstruction were . ( % ci . – . ; i( ) = . %) and . ( % ci . – . ; i( ) = . %), respectively. the pooled sensitivity and specificity of the cuff leak test for reintubation were . ( % ci . – . ; i( ) = . %) and . ( % ci . – . ; i( ) = . %), respectively. subgroup analyses suggested that the type of cuff leak test and length of intubation might be the cause of statistical heterogeneity of sensitivity and specificity, respectively, for post-extubation airway obstruction. conclusions: the cuff leak test has excellent specificity but moderate sensitivity for post-extubation airway obstruction. the high specificity suggests that clinicians should consider intervening in patients with a positive test, but the low sensitivity suggests that patients still need to be closely monitored post-extubation. morbidity, duration of mechanical ventilation, and icu stay [ ] [ ] [ ] [ ] [ ] [ ] [ ] . in select cases, systemic corticosteroids before extubation can be used to prevent post-extubation airway complications [ ] . therefore, it is important to estimate the risk of laryngeal edema before extubation. since the endotracheal tube precludes direct visualization of the upper airway, the cuff leak test was proposed to predict the presence of laryngeal edema and post-extubation airway obstruction [ , ] . theoretically, when there is no laryngeal edema, there is an air leak around the tube after deflating the balloon cuff of the endotracheal tube [ , ] . in contrast, a failed cuff leak test suggests little or no air leak around the tube, suggesting potential airway obstruction from laryngeal edema [ , ] . the clinical practice guideline published by the american thoracic society and american college of chest physicians in recommends performing a cuff leak test in mechanically ventilated adults who meet extubation criteria to screen those at high risk for post-extubation stridor [ ] . this guideline referenced two systematic reviews on the diagnostic accuracy of cuff leak test [ , ] , published in and . both reviews demonstrated excellent specificity of the cuff leak test but disagreed with respect to sensitivity. in addition, there have been several studies of the diagnostic accuracy of cuff leak test published after these reviews were completed. consequently, we conducted a systematic review and meta-analysis to assess the diagnostic accuracy of the cuff leak test for predicting post-extubation airway obstruction and subsequent reintubation. the conduct and reporting of this systematic review followed the prisma-dta statement [ ] . our review protocol was registered at prospero (crd ). we searched medline, embase, scopus, isi web of science, and the cochrane library for eligible studies from inception to march , , without language restrictions [ ] . our search strategy was developed with the help of a medical librarian (additional file : table s ). we hand-searched the references of included articles for potentially relevant studies. we examined the diagnostic accuracy of cuff leak test in intubated adult patients awaiting extubation in critical care settings. the index test was cuff leak test regardless of the type of cuff leak test (quantitative or qualitative) and threshold used. the reference standards included post-extubation airway obstruction determined by the original authors and subsequent reintubation. we included observational studies (cross-sectional and cohort studies) that examined the diagnostic accuracy of cuff leak test in critical care settings if: ( ) the data were extractable into a × table from the reported data, ( ) post-extubation airway obstruction after extubation or reintubation was explicitly reported as the reference standard. we considered both published studies and conference proceedings; however, we included the abstracts from conference proceedings only when they provided data in enough detail to be extractable. we considered interventional studies in critical care settings that examined the efficacy of systemic corticosteroids to prevent post-extubation airway complications; however, we excluded patients to whom systemic corticosteroids were administered after they were judged at high risk of postextubation airway complications. two authors (ak and jk) independently screened titles and abstracts obtained from the search and selected potentially relevant articles. disagreement was resolved through discussion. the first author (ak) and one of the other authors (jlj and jk) in duplicate and independently extracted the following data from each study: ( ) patient demographics (age, sex); ( ) study characteristics (country, study population; duration of mechanical ventilation; mode of ventilation; observation period after extubation); ( ) the type of cuff leak test (quantitative or qualitative); ( ) numbers of true-positive, false-positive, true-negative, and falsenegative; and ( ) the reference standards used. quantitative cuff leak test measures the air leak volume with a cuff deflated and judges the post-extubation airway obstruction based on its absolute volume or proportion in comparison with the expiratory tidal volume against a certain threshold [ ] . qualitative cuff leak test examines the presence or absence of audible expired air around an endotracheal tube, which indicates the pass or failure of the test [ ] . in this study, a lack of a cuff leak, having a risk of post-extubation complications, was considered a positive test, while having a leak, suggesting low risk of post-extubation complications was a negative test [ ] . two authors (ak and jlj) independently assessed the risk of bias using the quality assessment for diagnostic accuracy studies- (quadas- ) tool [ ] . inconsistency was resolved through consensus. we had two primary outcomes: ( ) post-extubation airway obstruction and ( ) reintubation due to post-extubation airway obstruction. the reference standards for post-extubation airway obstruction included stridor (audible high-pitched inspiratory wheeze) [ ] , or laryngeal edema defined by the study authors (including confirmation with bronchoscopy [ ] or laryngoscope [ ] ). we pooled the data using a generalized linear mixed model approach to bivariate random-effects meta-analysis to calculate summary estimates of sensitivity, specificity, and likelihood ratios as well as the associated % confidence intervals (cis) [ ] . we pooled prevalence using a random-effects model, with exact binomial estimates of standard deviation and the freeman-tukey transformation for zero cells [ ] . to examine the sources of heterogeneity, we examined the receiver operating characteristic (roc) curves, assessed the correlation between sensitivity and specificity, and analyzed whether sensitivity and specificity of cuff leak changed with the type of cuff leak test (qualitative or quantitative), the proportion of women, inclusion or exclusion of reintubated patients in a study, and the length of intubation, using subgroup or meta-regression analysis [ , ] . we also calculated the sensitivity and specificity of cuff leak test using a cutoff of ml, a value that is frequently used in clinical practice [ ] . we tested for publication bias using deeks' method [ ] . we created a fagan's nomogram, which determines the posttest probability according to the pretest probability and the calculated positive and negative likelihood ratios [ ] . we followed standard diagnostic meta-analytic approaches in focusing on the sensitivity, specificity, and likelihood ratios instead of positive and negative predictive values because predictive values are dependent on the population prevalence of post-extubation complications, which can vary considerably. the threshold of statistical significance was set at p < . . all analyses were performed with stata se, version . (stata corp; college station, tx). our literature search produced studies. after application of inclusion and exclusion criteria, studies involving extubations were included in the analysis ( fig. ) [ , , [ ] [ ] [ ] . among the included studies, were published in english and one in korean [ ] . twenty-seven studies ( %) were prospective [ , , - , - , - ] . nine studies and ten were conducted in medical [ , , , , - , , ] and mixed intensive care units [ , , , , , , , , , ] , respectively ( table ). the included studies were published between and . all but one were published studies and the remaining one an abstract in a conference proceeding. eight studies were conducted in the usa, four each in france and taiwan, three in thailand, two in egypt, one each in australia, belgium, india, iran, italy, south korea, and turkey. the median sample size was , ranging - (interquartile range - ). the reported mean/median duration of mechanical ventilation ranged from to . days. five studies used a qualitative cuff leak test (auscultation of airflow) [ , , , , ] , and used a quantitative measurement of the cuff leak [ , , , , , , - , - , , , , ] (table ). one study reported the results from both qualitative and quantitative cuff leak tests examined in a single cohort [ ] . the remaining study reported on the data of patients who underwent either qualitative or quantitative cuff leak test [ ] . the most frequent cutoff values for quantitative cuff leak tests ranged from to ml (median, ml) in volume and from to % in proportion. twenty studies used assist control ventilation [ , , , , , , - , - , , , ] , and four used spontaneous breathing including pressure support ventilation [ , , , ] . another study examined either of these two ventilation modes [ ] . one study applied the ambu bag, while the cuff leak was tested [ ] . one study performed a qualitative cuff leak test during spontaneous breathing via t-tube and during cough while still intubated [ ] . the remaining one did not report the mode of ventilation used [ ] . twenty-four studies used stridor [ , , , - , - , - ] and three used direct visualization of the airway following extubation as reference standards [ , , ] for airway obstruction. one study used either of these reference standards [ ] . three of the studies were at low risk of bias for all quadas- risk of bias domains (table ) . seventeen studies ( . %) were deemed at low risk of bias for the domain of patient selection. eight out of studies that assessed quantitative cuff leak prespecified the cutoff of cuff leak; fourteen studies ( %) were deemed to have adequately assessed the index test. a reference standard was adequately assessed in studies ( . %). study participants were adequately followed up in studies ( . %). the prevalence of post-extubation airway obstruction ranged from to % (pooled estimate %; % ci - ; i = . %). the pooled sensitivity and specificity of cuff leak test for post-extubation airway obstruction were . ( % ci . - . ; i = . %) and . ( % ci . - . ; i = . %), respectively. the forest plots are shown in additional file : figure s . the pooled positive and negative likelihood ratios were . ( % ci . - . ) and . ( % ci . - . ), respectively. the area under the summary receiver operating characteristic (sroc) curve was . ( % ci . - . ) (fig. ) , and the pooled diagnostic odds ratio (dor) was . ( % ci . - . ) (additional file : table s ). there was no evidence of publication bias (p = . ). subgroup analysis suggested that the specificity was similar between the qualitative and quantitative cuff leak tests ( a nomogram based on the pretest probability of % (the incidence of stridor in the studies included in our study) is provided (fig. ) . the prevalence of reintubation varied from to % (pooled estimate: %; % ci - ; i = %). the pooled sensitivity and specificity of the cuff leak test for reintubation were . ( % ci . - . ; i = . %) and . ( % ci . - . ; i = . %), respectively. the forest plots of the sensitivity and specificity of the cuff leak table s ). there was no evidence of publication bias (p = . ). our study found that the cuff leak test has excellent specificity but moderate sensitivity for post-extubation airway obstruction. the cuff leak test thus works better to rule in than to rule out potential post-extubation airway obstruction. however, the false-negative rate of nr not reported % suggests that the cuff leak test may fail to identify some patients with post-extubation airway obstruction. our study found that the specificity of the cuff leak test for post-extubation airway obstruction was excellent, which is consistent with two previous systematic reviews [ , ] . in contrast, ochoa et al. and zhou et al. concluded that the sensitivity of cuff leak testing for postextubation airway obstruction was % and %, respectively [ , ] : our pooled sensitivity was %, which fell between those two findings. we included nearly double the number of studies that their reviews did. furthermore, the additional studies we included were higher quality, potentially making our findings more reliable. our analysis found that the qualitative cuff leak test had low sensitivity ( %) in predicting post-extubation airway obstruction. this has been consistently found in recent studies. the most likely explanation is the subjective nature of this test. in addition, since schnell et al. provided data from three different methods of qualitative cuff leak testing [ ] , the sensitivity of which were all around %; this study may have been overweighed, although repeat analysis limiting schnell's study to a single data contribution did not change the sensitivity of the qualitative test. in contrast, the specificity of both qualitative and quantitative cuff leak tests was high, nearly %, while there was a statistically significant difference between two methods, clinically both performed equally well. a cutoff of ml also had a low sensitivity ( %) and high specificity for predicting post-extubation airway obstruction. we thus conclude that the cuff leak test has high specificity and can be used to select patients to consider treating with systemic corticosteroids, but its low sensitivity suggests that the traditional practice of closely observing all patients in the immediate post-extubation period should be continued. consistent with these findings, the nomogram suggested that while a negative cuff leak test represents low possibility of post-extubation airway obstruction, a positive test still provides a relatively low posttest probability. the guideline by ats/accp provided a conditional recommendation regarding cuff leak test [ ] , because failing the cuff leak test might lead a delay in extubation and an increase in complications such as barotrauma and ventilator-associated pneumonia. the guideline weakly recommended that the cuff leak test be reserved for highrisk patients, who experienced a traumatic intubation, were intubated more than days, have a large endotracheal tube, are female, or were reintubated after an unplanned extubation [ ] . our analysis found that the length of intubation had a small impact on the specificity of cuff leak test. female sex and reintubation had no impact of the accuracy of cuff leak test. since the original studies included in our review examined non-selected patients with respect to the risk of post-extubation airway obstruction and the sensitivity of cuff leak test is moderate, we support the idea of the ats/accp guideline to reserve cuff leak test for high-risk patients. our study suggested that the cuff leak test has moderate sensitivity and excellent specificity for reintubation. although the sensitivity in our study was similar to those of previous meta-analyses, the specificity in our study was slightly higher [ , ] . the area under the sroc curve and dor were also greater than previously reported [ ] . thus, a failed cuff leak test may serve as a good marker for those at risk of reintubation, if postextubation airway obstruction is not treated adequately. the limitation of cuff leak test has been repeatedly discussed. cuff leak test can be susceptible to relationship of tube size to laryngeal diameter [ ] , respiratory system compliance and resistance, inspiratory flow, expiatory flow and time, and airway collapse [ ] , and clinicians should bear in mind that the ability of cuff leak test may vary according to the condition or type of patients [ ] . additionally, coughing during cuff deflation test hinders accurate measurement of the leak volume and lowers the reproducibility. a previous physiological study suggested that while patients were sedated and paralyzed, the cuff leak volume was reliably measurable [ ] . an adequate amount of sedatives and opioids can suppress coughing during the airway suctioning before cuff leak test or cuff deflation during the test. further, cuff leak testing is recommended several hours before extubation, which allows the arousal of patients from sedation by the time of extubation. thus, we may be able to at least attempt to increase the reliability of cuff leak measurement. few tests are available to estimate the risk of postextubation airway complications. a case series of three patients suggested that video laryngoscopy enabled visualization of laryngeal edema prior to extubation [ ] , but its clinical efficacy in estimating post-extubation airway complications is yet to be determined. several studies have examined the role of laryngeal ultrasonography in adult patients. laryngeal air column width difference is the difference between width of airway at the level of the vocal cord with cuff inflated and deflated. its reported sensitivity and specificity varied across studies, ranging from to % and to %, respectively [ , , ] . laryngeal air column width ratio is the ratio of air column width before extubation over that after intubation. it has been examined in only one study [ ] and needs further validations. thus, no single available options can correctly estimate the risk of post-extubation airway complications. clinicians should not overly rely on one single test in predicting the success or failure of extubation. our study had several strengths and limitations. strengths included a comprehensive search in five databases without language restrictions. this allowed us to conduct relevant subgroup analyses with a larger number of studies. further, inclusion of non-english studies facilitates the generalizability of our findings in various clinical settings [ ] . our study had some limitations. first, the definition of post-extubation airway obstruction differed across studies. stridor was more frequently used as the reference standards than laryngeal edema (as assessed with endoscopy). laryngeal edema may be more frequent than stridor, because stridor and respiratory distress occur when laryngeal edema narrows the airway by ≥ % [ ] . however, laryngeal edema is not always screened for in extubated patients, and the presence of stridor is an accepted sign of respiratory distress that triggers a concern for airway obstruction. thus, the finding of our study is generalizable to the clinical practice. second, although we attempted to include in the analysis the incidence of stridor due to post-extubation airway events, some patients might have had a concurrent clinical state that necessitated high minute ventilation or tachypnea through an edematous airway, which manifested as 'stridor. ' therefore, we might not have been able to completely separate stridor due to post-extubation airway events from stridor due to other etiologies, such as respiratory insufficiency. this limitation also applies to reintubation. third, whether to reintubate patients is subject to treating physicians' discretion and the effect of treatment to abort post-extubation stridor. therefore, the value of cuff leak test in predicting the need for reintubation in clinical practice may be limited along with the third limitation. however, prevention of post-extubation airway obstruction is more important than reintubation per se. once the cuff leak test identifies patients at high risk of postextubation airway obstruction, prophylactic systemic corticosteroids are indicated [ , , ] . fourth, out of studies that assessed the quantitative cuff leak test determined the cutoff with the knowledge of the results of the reference standards. it is known that data-driven optimization of the cutoff can lead to overestimation of test performance [ ] . thus, the pooled accuracy of quantitative cuff leak test in our study can be an overestimation; the optimal cutoff is still unknown. fifth, the quantitative cutoff for a positive test varied between the studies. since we had aggregate data from each included study, we failed to determine the optimal cutoff of cuff leak test. finally, there was substantial statistical heterogeneity in the pooled sensitivity and specificity for both outcomes. the presence of statistical heterogeneity is a common issue intrinsic to the the prediction region illustrates the extent of statistical heterogeneity by depicting a region within there is % confidence that the true sensitivity and specificity of a future study should lie meta-analysis of diagnostic accuracy of a test, given the clinical and methodological diversity in original studies as well as the possible relationship between sensitivity and specificity, as exemplified in roc curves in which more sensitive cut points have lower specificity (and vice versa). our subgroup analyses suggested that the type of cuff leak test (quantitative versus qualitative) and length of intubation might have been the cause of statistical heterogeneity of sensitivity and specificity, respectively, for post-extubation airway obstruction. the cuff leak test has excellent specificity but moderate sensitivity for post-extubation airway obstruction. the cuff leak test is a useful tool in the decision-making about extubation, but the low sensitivity suggests that a negative test cannot completely exclude post-extubation airway obstruction and that patients still need to be closely monitored post-extubation. the higher specificity suggests that clinicians should consider intervening in patients with systemic corticosteroids in response to a positive test. continued research to find better modalities to rule out post-extubation airway obstruction is needed. postextubation laryngeal edema and stridor resulting in respiratory failure in critically ill adult patients: updated review re-intubation increases the risk of nosocomial pneumonia in patients needing mechanical ventilation outcome of reintubated patients after scheduled extubation independent effects of etiology of failure and time to reintubation on outcome for patients failing extubation effect of failed extubation on the outcome of mechanical ventilation the outcome of extubation failure in a community hospital intensive care unit: a cohort study the effect of extubation failure on outcome in a multidisciplinary australian intensive care unit outcomes of extubation failure in medical intensive care unit patients prophylactic corticosteroids for prevention of postextubation stridor and reintubation in adults: a systematic review and meta-analysis when to extubate the croup patient: the 'leak' test cuff" test for safe extubation following laryngeal edema the cuff leak test to predict failure of tracheal extubation for laryngeal edema post-extubation stridor in intensive care unit patients. risk factors evaluation and importance of the cuff-leak test practice guideline: liberation from mechanical ventilation in critically ill adults. rehabilitation protocols, ventilator liberation protocols, and cuff leak tests cuff-leak test for the diagnosis of upper airway obstruction in adults: a systematic review and meta-analysis cuffleak test for predicting postextubation airway complications: a systematic review preferred reporting items for a systematic review and meta-analysis of diagnostic test accuracy studies: the prisma-dta statement the accuracy of google translate for abstracting data from non-english-language trials for systematic reviews the cuff leak test: does it "leak" any information? respir care group q-: quadas- : a revised tool for the quality assessment of diagnostic accuracy studies association between reduced cuff leak volume and postextubation stridor the cuff-leak test is a simple tool to verify severe laryngeal edema in patients undergoing long-term mechanical ventilation the "cuff-leak" test for extubation bivariate meta-analysis of sensitivity and specificity with sparse data: a generalized linear mixed model approach transformations related to the angular and the square root the performance of tests of publication bias and other sample size effects in systematic reviews of diagnostic test accuracy was assessed diagnostic tests : likelihood ratios the cuff-leak test as a predictor of postextubation stridor: a prospective study evaluation of the cuff-leak test in a cardiac surgery population measurement of endotracheal tube cuff leak to predict postextubation stridor and need for reintubation how to identify patients with no risk for postextubation stridor? high body mass index and long duration of intubation increase post-extubation stridor in patients with mechanical ventilation the endotracheal tube cuff-leak test as a predictor for postextubation stridor intravenous injection of methylprednisolone reduces the incidence of postextubation stridor in intensive care unit patients risk factors of extubation failure and analysis of cuff leak test as a predictor for postextubation stridor dexamethasone to prevent postextubation airway obstruction in adults: a prospective, randomized, double-blind, placebo-controlled study the role of the cuff leak test in predicting the effects of corticosteroid treatment on postextubation stridor the cuff leak test is not predictive of successful extubation risk factors evaluation and the cuff leak test as predictors for postextubation stridor cuff-leak test predicts the severity of postextubation acute laryngeal lesions: a preliminary study intra-individual variation of the cuff-leak test as a predictor of post-extubation stridor cuff leak volume as a clinical predictor for identifying post-extubation stridor cuff leak tests at the time of extubation correlate with voice quality assessment predicting laryngeal edema in intubated patients by portable intensive care unit ultrasound cuff leak test and laryngeal survey for predicting post-extubation stridor ultrasound-guided laryngeal air column width difference and the cuff leak volume in predicting the effectiveness of steroid therapy on postextubation stridor in adult. are they useful? laryngeal ultrasound versus cuff leak test in prediction of post-extubation stridor cuff leak test for the diagnosis of post-extubation stridor laryngeal ultrasonography versus cuff leak test in predicting postextubation stridor clinical risk, cuff leak test and laryngeal ultrasound based scoring system to predict postextubation stridor in intensive care unit patients determinants of the cuff-leak test: a physiological study the cuff-leak test: what are we measuring? is the leak test reproducible? use of video laryngoscopy and camera phones to communicate progression of laryngeal edema in assessing for extubation: a case series laryngeal air column width ratio in predicting post extubation stridor how often do systematic reviews exclude articles not published in english? tracheoesophageal compression associated with substernal goitre. correlation of symptoms with cross-sectional imaging findings adverse events associated with prophylactic corticosteroid use before extubation: a cohort study bias in sensitivity and specificity caused by data-driven selection of optimal cutoff values: mechanisms, magnitude, and solutions publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations we would like to sincerely thank ms. elizabeth suelzer, mlis, ahip for her help with literature search. supplementary information accompanies this paper at https ://doi. org/ . /s - - - .additional file : figure s . forest plot of the sensitivity and specificity of the cuff leak test for predicting post-extubation upper airway obstruction.additional file : figure s . forest plot of the sensitivity and specificity of the cuff leak test for predicting reintubation.additional file : table s . search strategy. table s . the pooled diagnostic accuracy of cuff leak test for post-extubation airway obstruction and reintubation. authors' contributions ak and jlj substantially contributed to conception of the study design, data acquisition, data analysis, interpretation, and the writing and critical revision of the manuscript. jk substantially contributed to data acquisition, interpretation, and critical revision of the manuscript. all authors read and approved the submission of the final manuscript. there was no funding source for this study. all data generated or analyzed during this study are included in this published article and its supplementary information files. this study is a systematic review and an ethics approval was not necessary. not applicable. the authors declare that they have no competing interests. received: july accepted: october key: cord- - zapcw authors: wilder, bryan; mina, michael j.; tambe, milind title: tracking disease outbreaks from sparse data with bayesian inference date: - - journal: nan doi: nan sha: doc_id: cord_uid: zapcw the covid- pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. while standard methods exist, they work best at coarse-grained national or state scales with abundant data, and struggle to accommodate the partial observability and sparse data common at finer scales (e.g., individual schools or towns). for example, case counts may be sparse when only a small fraction of infections are caught by a testing program. or, whether an infected individual tests positive may depend on the kind of test and the point in time when they are tested. we propose a bayesian framework which accommodates partial observability in a principled manner. our model places a gaussian process prior over the unknown reproduction number at each time step and models observations sampled from the distribution of a specific testing program. for example, our framework can accommodate a variety of kinds of tests (viral rna, antibody, antigen, etc.) and sampling schemes (e.g., longitudinal or cross-sectional screening). inference in this framework is complicated by the presence of tens or hundreds of thousands of discrete latent variables. to address this challenge, we propose an efficient stochastic variational inference method which relies on a novel gradient estimator for the variational objective. experimental results for an example motivated by covid- show that our method produces an accurate and well-calibrated posterior, while standard methods for estimating the reproduction number can fail badly. a key goal for public health is effective surveillance and tracking of infectious disease outbreaks. this work is motivated in particular by the covid- pandemic but the methods we describe are applicable to other diseases as well. a central question is to estimate the empirical rate of transmission over time, often formalized via the reproduction number r t , t = ...t . r t describes the expected number of secondary infections caused by someone infected at time t. accurate estimates of r t are critical to detect emerging outbreaks, forecast future cases, and measure the impact of interventions imposed to limit spread. r t is typically estimated using daily case counts, i.e., the number of new infections detected via testing each day. standard methods, including prominent dashboards devel-oped for covid- , provide accurate estimates under idealized conditions for the observation of cases and have been successfully used at a national or state level where many observations are available and sampling variation averages out flaxman et al. ; systrom, vladek, and krieger ) . however, successful reopening will require programs which track spread at the level of particular colleges, workplaces, or towns, where partial observability poses several challenges. first, only a small number of infected people may be tested. it is estimated that only about % of sars-cov- infections in the us result in a confirmed test (havers et al. ) and we could expect even fewer in populations with a high prevalence of asymptomatic or mild infections (e.g., college students). second, the biological properties of the test play an important role. for example, a pcr test which detects viral rna will show positive results at different times than an antibody or antigen test. further, there can be substantial heterogeneity across individuals. third, testing programs may collect samples in a particular way which impacts the observations. for example, one suggestion for schools and workplaces to reopen is to institute regular surveillance testing of a fraction of the population in order to detect outbreaks and catch asymptomatic carriers (larremore et al. ) . the observations will depend on the fraction of the population enrolled in testing (potentially small due to budget constraints) along with the sampling design (e.g., cross-sectional vs longitudinal). this paper presents gprt, a novel bayesian approach to estimating r t which accounts for partial observability in a flexible and principled manner (illustrated in figure ). this method yields well-calibrated probabilistic estimates (the posterior distribution). our model places a gaussian process (gp) prior over r t , allowing it to be an arbitrary smooth function. then, we explicitly model the sampling process which generates the observations from the true trajectory of infections. while this substantially improves accuracy (as we show experimentally) it creates a much more difficult inference problem than has been previously considered. specifically, our model contains tens or hundreds of thousands of discrete latent variables, preventing the application of out-of-the-box methods. moreover, the values of many variables are tightly correlated in the posterior distribution, further complicating inference. to make inference computationally tractable, we propose a novel stochastic figure : illustration of our gprt method. top row: the generative model gprt posits for the observed data. bottom row: the inference process to recover a posterior over r t . variational inference method, enabled by a custom stochastic gradient estimator for the variational objective. extensive experiments show that our method recovers an accurate and well-calibrated posterior distribution in challenging situations where previous methods fail. there is a substantial body of work which attempts to infer unknowns in a disease outbreak. a frequent target for inference is the basic reproduction number r (majumder and mandl ; riou and althaus ; wilder et al. ) ; by contrast, we attempt the more challenging task of estimating a reproduction number which can vary arbitrarily over time. there is a literature of both classic methods for estimating r t (wallinga and teunis ; cori et al. ; campbell et al. ) and newer methods developed for the covid- pandemic and implemented in popular dashboards systrom, vladek, and krieger ) . none of these methods incorporate partial observability and we empirically demonstrate that gprt improves substantially over methods in each category. another strand of literature develops maximum likelihood or particle filter estimates of the parameters of an epidemiological model (king et al. ; dureau, kalogeropoulos, and baguelin ; cazelles, champagne, and dureau ) . however, their work focuses on accommodating a complex model of the underlying disease dynamics; by contrast, we develop methods for probabilistically well-grounded inferences under a complex observation model. there is also a great deal of computational work more broadly concerned with disease control. examples include optimization problems related to vaccination or quarantine decisions (saha et al. ; zhang and prakash ; zhang et al. ) , machine learning methods for forecasting (without recovering a probabilistic view of r t ) (chakraborty et al. ; rekatsinas et al. ) , and agent-based simulations of disease dynamics (barrett, eubank, and marathe ) . our work complements this literature by allowing inference of a distribution over r t from noisy data, which can serve as the input that parameterizes an optimization problem or simulation. we now introduce a model for a disease process with a time-varying reproduction number. subsequently, we introduce example models for how the observations are generated from the disease process which our framework can support. we use a standard stochastic model of disease transmission similar to other r t estimation methods (wallinga and teunis ; cori et al. ; campbell et al. ); our contribution is a more powerful inference methodology which can accommodate complex observation models alongside a gp prior. let r = [r ...r t ] be the vector with r t for each time. from r, the disease model defines a distribution over a vector n = [n ...n t ] with the number of people newly infected each day. the main idea is that, over the course of a given individual's infection, they cause a poisson-distributed number of new infections with mean determined by r. specifically, if on day t individual i has been infected for h i days the expected number of new infections caused by i that day is here w h i gives the level of infectiousness of an individual h i days post-infection. w is normalized so that h w h = . for later convenience, we will define φ t = n i= w h i to be the total infectiousness in the population before scaling by r t (n is the total population size). each day, each infected individual i draws n i t ∼ poisson(λ i t ) other individuals to infect. we also incorporate infections from outside the population, with a mean of γ such infections per day. we assume the rate of external infection is constant with respect to our time but our model could be extended to a time-varying γ. we treat γ mostly as a nuisance parameter: our true objective is to infer r, but doing so requires accounting for the potential that some detected cases are due to infections from outside the population. we define n t = n i= n i t + poisson(γ) to be the total number of new infections. since φ is fixed given the time series n, we denote it as a function φ(n). we denote the probabilistic disease model induced by a specific choice of r and γ as m (r, γ) and the draw of a time series of infections from the model as n ∼ m (r, γ). we now depart from the standard disease model used in previous work and describe a wide-ranging set of examples for how our framework can accommodate models of the process which generates the observed data from the latent (unknown) true infections. previous work assumes either perfect observability or else the simplest of the three observation models we describe below (uniform undersampling). our focus is where observations are generated by a medical test which confirms the presence of the pathogen of interest. individuals have some probability of being tested at different times (depending on the testing policy adopted) and then test positive with a probability which depends on the biological characteristics of the disease and the test in question. the kind of test employed determines when an individual is likely to test positive during the course of infection. for example, for covid- , pcr tests are commonly used to detect sars-cov- rna. they are highly sensitive and can detect early infections. most infected individuals become pcr-negative within the week or two following infection as viral rna is cleared (kucirka et al. ) . by contrast, serological tests detect the antibodies produced after infection. an individual is not likely to test serologically positive until a week or more postinfection, but may then continue to test serologically positive for months afterwards (iyer et al. ) . the observable data generated by a serological testing program is likely quite different than a pcr testing program since the time-frame and variance of when individuals test positive differs strongly. a range of other examples are possible (e.g., antigen tests) and can be easily incorporated into our framework. our model adopts a generic representation of a particular test as a distribution d over t convert , the number of days post-infection when an individual begins to test positive and t revert , the number of days post-infection when they cease to test positive. for an infected individual i, we write t i convert , t i revert ∼ d. our method only assumes the ability to sample from d, meaning that we can directly plug in the results of lab studies assessing the properties of a test. t i convert , t i revert are unobserved: we only get to see if an individual tests positive at a given point in time, not the full range of times that they would have tested positive. next, we describe a series of example models for how and when individuals are tested, which reveal observations depending on the status (t i convert , t i revert ) for each person who is tested. for convenience, we let t i convert = ∞ for an individual who is never infected. note however that we can model false negatives by having d sometimes set t i convert = ∞ for an infected individual, or false positives by returning finite t i convert for an uninfected individual. we denote the number of observed positive tests on day t as x t . an observation model is a distribution over x given n, denoted x ∼ obs(n). each setting below describes one such distribution. uniform undersampling in this setting, each individual who is infected is tested independently with some probability p test (e.g., if they individually decide whether to seek a test). to model this process, we introduce two new sets of latent random variables. first, a binary variable z i ∼ bernoulli(p test ), indicating whether individual i is tested. second, a delay c i , giving the number of days between t i convert and when individual i is tested. we can integrate out the z i and obtain the following conditional distribution for the observed number of positive tests x t : denotes the indicator function of an event. however, we cannot analytically integrate out t convert and c. cross-sectional testing here, a uniformly random sample of s t individuals are tested on each day t. this models a random screening program (e.g., testing random employees each day as they enter a workplace). in this case, we have this expression provides the likelihood of x after conditioning on the latent variables t i convert , t i revert , though there is no closed-form expression conditioning only on n. longitudinal testing in this setting, a single sample from the population is chosen up front and every individual in the sample is tested every d days. we again denote the total number of individual tested on day t as s t , but note that now the group of individuals who are tested repeats every d days. longitudinal testing offers different (and potentially more revealing) information than cross-sectional testing since when an individual first tests positive, we know that they did not test positive d days ago. however, it complicates inference by introducing correlations between the test results at different time steps. let a t denote the set of individuals who are tested at time t. we assume that the complete sample d t= a t is chosen uniformly at random from the population, with the chosen individuals then randomly partitioned between the d days. we have where t i convert > t−d captures that i was not positive on their previous test. this introduces correlations between x t and x t−d , so there is not a simple closed-form expression for the distribution of the time series x even after conditioning on t i convert and t i revert . (as there is in the cross-sectional case). we will instead build a flexible framework for inference which can just as well use a kind of sample of the log-likelihood. we will place a gaussian process (gp) prior over r, resulting in the following generative model: where gp( , k) denotes a gaussian process with constant mean and kernel k and exp(γ) is an exponential prior on γ with meanγ. given the observation x, our goal is to compute the resulting posterior distribution over r and γ. however, is complicated by the fact that x is determined by a large number of discrete latent variables, primarily n (the time series of infections) and {t i convert , t i revert } n i= , the times when each individual tests positive. a typical strategy for inference in complex bayesian models is markov chain monte carlo (mcmc). however, mcmc is difficult to apply because of tight correlations between the values of variables over time: due to the gp prior, we expect values of r to be closely correlated between timesteps, and successive values of n are highly correlated via the model m . formulating good proposal distributions for high-dimensional, tightly correlated random variables is notoriously difficult and has presented problems for gp inference via mcmc in other domains (titsias, lawrence, and rattray ) . the other main approach to bayesian inference is variational inference, where we attempt to find the best approximation to the posterior distribution within some restricted family. modern variational inference methods, typically intended for deep models such as variational autoencoders (kingma and welling ) , use a combination of autodifferentiation frameworks and the reparameterization trick to differentiate through the variational objective (kucukelbir et al. ). this process is highly effective for models with only continuous latent variables. however, our model has many thousands of discrete latent variables which cannot be reparameterized in a differentiable manner. typical solutions to this problem would be to either integrate out the discrete variables or to replace them with a continuous relaxation (jang, gu, and poole ; vahdat et al. ) . neither solution is attractive in our case -the structure of the model does not allow us to integrate out the discrete variables analytically, while a continuous relaxation is infeasible because our latent variables have a strict integer interpretation (every infection requires in a particular individual becoming testpositive at particular points in time). the last resort to differentiate through discrete probabilistic models is the score function estimator (paisley, blei, and jordan ) , which is often difficult to apply due to high variance. gprt uses a combination of techniques which exploit the structure of infectious disease models to develop an estimator with controlled variance. first, we develop a more tractable variational lower bound which is amenable to stochastic optimization. second, we hybridize the reparameterization and score function estimators across different parts of the generative model to take advantage of the properties of each component. third, we develop techniques to sample low-variance estimates of the log-likelihood for each of the observation models introduced earlier. these techniques are introduced in the next section. we now derive gprt, a novel variational inference method for r t estimation. gprt approximates the true (uncomputable) posterior over (r, γ) via a multivariate normal distribution with mean µ and covariance matrix Σ. µ t is the posterior mean for r t while Σ t,t gives the posterior covariance between r t and r t . µ γ is the mean for γ and Σ γ,· gives its covariance with r. the diagonal Σ t,t gives the variance of the posterior over r at each time, capturing the overall level of uncertainty. the aim is to find a µ and Σ which closely approximate the true posterior. let q(r, γ|µ, Σ) denote the variational distribution. let p be the true generative distribution, where p(r, γ, x) is the joint distribution over x and (r, γ), p(r, γ) is the prior over (r, γ), and p(r, γ|x) is the posterior over (r, γ) after conditioning on x. the aim of variational inference is to maximize a lower bound on the total log-probability of the evidence x: where the right-hand side is referred to as the evidence lower bound (elbo). our goal is to maximize the elbo via gradient ascent on the parameters µ and Σ. this requires us to develop an estimator for the gradient of each term in the elbo. the first term is the negative cross-entropy between q and the prior p(r, γ). because both q and p have simple parametric forms, this can be easily computed and differentiated. the last term is the entropy, which is similarly tractable. the middle term is the expected log-likelihood. developing an estimator for the gradient of this term is substantially more complicated and will be our focus. in fact, for computational tractability we will actually develop an estimator for a lower bound on the expected log-likelihood; substituting this lower bound into the elbo still gives a valid lower bound on log p(x) and so is a sensible objective. the essential problem is that computing the log-likelihood of r requires integrating out the discrete latent variable n induced by the disease spread model, which is computationally intractable. the aim of this section is to develop the following stochastic estimator: theorem . let l be the cholesky factor of Σ, ξ ∼ n ( , i), there exists a function g(µ, Σ) with e r,γ∼q [log p(x|r, γ)] ≥ g(µ, Σ) ∀µ, Σ and e[∇] = ∇g(µ, Σ). essentially, theorem states that∇ is an unbiased estimator for a lower bound on the expected log-likelihood, exactly what we need to optimize a lower bound on log p(x) by stochastic gradient methods. moreoever, as we will highlight below, we can efficiently compute the terms of∇ via a combination of leveraging the structure of the disease model to apply autodifferentiation tools and novel sampling methods for the observation model. we now derive∇. proof. expanding the dependence of x on n we can rewrite the log-likelihood as it is not clear how to develop a well-behaved gradient estimator for this expression because we wish to differentiate with respect to the parameters governing two nested expectations, one within the log. however, via jensen's inequality, we can derive the lower bound pushing the log inside the expectation. we will substitute this bound into the elbo, obtaining a valid lower bound to maximize. the key advantage is that our new lower bound admits an efficient stochastic gradient estimator. we start with the inner expectation and attempt to compute a gradient with respect to r (which controls the distribution of the simulation results n). using score function estimator gives which expresses the gradient with respect to (r, γ) in terms of the gradient of the probability density of the disease model m with respect to (r, γ). it turns out that log m (n, φ|r, γ) can be easily computed. recall that n using the poisson superposition theorem, we have that n t ∼ poisson( n i= r t φ i t + γ) (while φ t is a deterministic function of n ...n t− ). accordingly, we have that where the second line substitutes the poisson log-likelihood. this expression can be easily differentiated with respect to r and γ in closed form. accordingly, we obtain an unbiased estimate of the gradient of our lower bound by sampling n ∼ m (r, γ) and computing ∇ r,γ log m (n|r, γ) log p(x|n). this suffices to estimate the gradient with respect to (r, γ). however, our goal is to differentiate with respect to µ and Σ, which control the distribution over (r, γ). fortunately, r and γ are continuous. so, we can exploit the reparameterization trick by writing (r, γ) as a function of a random variable whose distribution is fixed. specifically, since Σ is positive semi-definite, it has a cholesky decomposition Σ = ll t (for convenience, we actually optimize over l instead of Σ). sampling a standard normal variable ξ ∼ n ( , i) and letting r γ = µ + lξ is equivalent to sampling r, γ ∼ n (µ, Σ). we rewrite the lower bound as where µ and l appear only as parameters of the deterministic function expressing r and γ in terms of ξ, instead of in the distribution of a random variable. taking a sample from each of the expectations and substituting the score function estimator now gives the desired expression for∇. using theorem , our final gradient estimator will sample b values for ξ, run the model m once for each of the resulting values of r to sample n, and then compute b b k= ∇ µ,l log m (n(k)|r(ξ(k)), γ(ξ(k))) log p(x|n(k)), easily accomplished with standard autograd tools given the closed-form expressions for r(ξ), γ(ξ), and log m (n|r). in practice, we also use the mean log p(x|n(k)) as a simple control variate to reduce variance (sutton and barto ) . we now turn to the task of computing the log-likelihood function log p(x|n), which measures the log-likelihood of observing the sequence of positive test results x given n new infections per day. unfortunately, the log-likelihood is not available in closed form for any of the settings that we consider because it depends on additional latent variables (e.g., t convert , t revert , c, or a). we will show that it suffices to develop an estimator which lower-bounds the log-likelihood and that such estimators can be efficiently implemented for each of the observation models we consider. specifically, denote the collection of latent variables used in a particular observation model as α. then, we have which presents a similar difficulty as in developing our earlier lower bound: sampling α to approximate the inner expectation does not result in an unbiased estimator due to the outer log. using jensen's inequality in the same way gives and so substituting the right-hand side into our variational objective preserves validity of the lower bound. the rhs has the crucial advantage that we can now develop an unbiased estimator by drawing a single sample of α, which can then be substituted into the stochastic gradient estimator of theorem . that is, for each of the simulation results n( )...n(b) we sample a corresponding value for the latent variables, α( )...α(b) and use the gradient estimator ∇µ,l log m (n(k)|r(ξ(k)), γ(ξ(k))) log p(x|n(k), α(k)) this works without issue for the uniform undersampling and cross-sectional models where we can obtain a closed form for the log likelihood after conditioning on the appropriate latent variables. however, the longitudinal testing model presents additional complications. in particular, after sampling the latent variables t convert , t revert , and a t , the number of positive tests becomes deterministic quantity. denote this simulated trajectory of positive testsx. if x = x, then p(x| t convert , t revert , a) = and otherwise p(x| t convert , t revert , a) = . this renders the above gradient estimator useless because log p(x|n(k), α(k)) = −∞ unless the simulated trajectory exactly matches the observed data (a very low-probability event). while −∞ is technically a valid lower bound for the variational objective, it is not very useful for optimization. essentially, we need to develop a lowervariance estimator where the lower bound is more useful. we now present one such improved estimator. the intuition is that we can marginalize out a great deal of the randomness in the naive estimator by only revealing the results of random draws determining a t a single individual at a time. we start by sampling t convert and t revert . note that we can expand log p(x|n, t convert , t revert ) = t t= log p(x t |x ...x t− , n, t convert , t revert ) and consider the likelihood at each day t after conditioning on the results observed on previous days. to compute an estimate for this table : mean absolute error of each method averaged over instances and time points for each setting, along with standard deviation of the absolute error. "pcr" and "serological" denote settings where the observations are generated by the respective testing method. individual column headings give the percentage of the population enrolled in testing. sum, we introduce a new object, the series of matrices c t . at each time t, c t [t , t ] denotes the number of individuals who have t convert = t , t revert = t , and have not yet actually tested positive by time t. since a t is selected uniformly at random from the population, independent of the infection process, the x t individuals who test positive on day t are drawn uniformly at random from the set of all individuals who converted between days t − d and t, and who have not yet reverted. let n draws denote the number of individuals in a t who have not yet tested positive by time t and n conv = t t =t−d t t =t+ c t [t , t ] denote the number of individuals who are "eligible" to test positive at time t. now x t |x ...x t− , n, c t follows a binomial distribution with n draws draws and success probability nconv n − t− i= xi . accordingly, the log-likelihood log p(x t |x ...x t− , n, c t ) can be computed in closed form. after this, we can sample c t |c t+ by selecting a uniformly random individual to remove from c t+ . we can view this as iteratively revealing the test-positive members of a t after conditioning on the se-quence of previous test results, instead of sampling the entire set up front as in the naive method. we test the performance gprt vs standard baselines on a wide variety of settings. we choose three baselines which have been recommended by leading epidemiologists as methods of choice for covid- (gostic et al. ) . first is the wallinga-teunis (wt) method (wallinga and teunis ) , which uses the distribution of the time between an infected person and their secondary infections to simulate possible who-infected-who scenarios, each of which induces a particular r t . wt assumes that cases are observed exactly and that there is no delay in observation. second is the method of figure : observed x t and the distribution over r t returned by each method on an example in the outbreak setting with longitudinal sampling, d = , and a % sample. the green line gives the ground truth r t . we test each method in an array of settings, with different distributions for both the true value of r t and the observations. we include two different settings for the ground truth r t . first, the outbreak setting where r starts below and rises above at a random time. second, the random trend setting where r follows a linear trend which changes randomly at multiple points in time. details of the settings and other experimental parameters are in the appendix. we also include different observation models characterized by the test used, the sampling method, and the sample size. we include both pcr and serological tests, using previously estimated distributions for d (kucirka et al. ; iyer et al. ) . we also include three sampling models introduced earlier: uniform underreporting, cross-sectional, and longitudinal. finally, for each of the four combinations of tests and sampling method, we include four different sample sizes. many sizes model a challenging setting with sparse observations, representing highly limited testing capacity. note that the sample sizes evaluated are different for each method because they have different interpretations, e.g. % in the cross-sectional case means sampling % of the population each day while in the longitudinal case it would mean % every d days. for each setting, table shows the mean absolute error between the posterior mean r produced by each method and the ground truth. each entry averages over instances. for longitudinal testing we use d = ; results for other values are very similar (see appendix). across almost all settings, our method has lower mae than any baseline, often by a substantial margin (reducing error by a factor of - x). notably, gprt performs well even with extremely limited data (e.g., when testing . % of the population per day or when % of infections are observed). performance improves with more data, but the gains limited (e.g., . - . mae), indicating that our method is able to make effective use of even very sparse data. figure shows a representative example. the observed data is quite sparse, with - positive tests observed per day. our method recovers a posterior which closely tracks the ground truth. wt produces an estimate which is correlated with the ground truth but has many fluctuations and overly tight confident intervals. cori is not appropriate for data this sparse and produces a widely fluctuating posterior. epinow does not return an estimate for much of the time series, only estimating the part with denser observations (we gave the baselines an advantage by only evaluating their mae where they returned an estimate). moreoever, even in the higherobservation portion, it is less accurate than gprt. finally, figure shows calibration, a metric which evaluates the entire posterior (not just the mean). intuitively, calibration reflects that, e.g., % of the data should fall into the %-credible interval of the posterior. calibration is critical for the posterior distribution to be interpretable as a valid probabilistic inference, and for it to be useful in downstream decision making. figure shows the fraction of the data which is covered by the credible intervals of each method. this figure shows cross-sectional testing in the outbreak setting, but results for other settings are very similar (see appendix). gprt is close to perfectly calibrated (the dotted diagonal line) while the baseline methods are not well calibrated. the baselines suffer from two problems. first, as to be expected from their higher mae, they are biased and so their credible intervals often exclude the truth. second, they are over-confident: paradoxically, their calibration worsens with increased data since the larger sample size makes them more confident in their erroneous prediction. we conclude that gprt offers uniquely well-calibrated inferences. estimating the time-varying reproduction number of sars-cov- using national and subnational case counts an interaction-based approach to computational epidemiology bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models forecasting a moving target: ensemble models for ili case count predictions a new framework and software to estimate timevarying reproduction numbers during epidemics capturing the time-varying drivers of an epidemic using stochastic dynamical systems estimating the effects of nonpharmaceutical interventions on covid- in europe practical considerations for measuring the effective reproductive number seroprevalence of antibodies to sars-cov- in sites in the united states dynamics and significance of the antibody response to sars-cov- 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overlapping transformations different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures modeling between-population variation in covid- controlling propagation at group scale on networks dava: distributing vaccines over networks under prior information key: cord- -uora qcb authors: ruland, sebastian; lochau, malte; jakobs, marie-christine title: hybridtiger: hybrid model checking and domination-based partitioning for efficient multi-goal test-suite generation (competition contribution) date: - - journal: fundamental approaches to software engineering doi: . / - - - - _ sha: doc_id: cord_uid: uora qcb in theory, software model checkers are well-suited for automated test-case generation. the idea is to perform (non-)reachability queries for the test goals and extract test cases from resulting counterexamples. however, in case of realistic programs, even simple coverage criteria (e.g., branch coverage) force model checkers to deal with several hundreds or even thousands of test goals. processing each of these test goals in isolation with model checking techniques does not scale. therefore, our tool hybridtiger builds on recent ideas on multi-property verification. however, since every additional property (i.e., test goal) reduces the model checker’s abstraction possibilities, we split the set of all test goals into different partitions. in test-comp , we applied a random partitioning strategy and used predicate analysis as model checking technique. in test-comp , we improved our technique in two ways. first, we exploit domination information among control-flow locations in our partitioning strategy to group test goals being located on (preferably) similar paths. second, we account to inherent weaknesses of the predicate analysis by applying a hybrid software model-checking approach that switches between explicit model checking and predicate-based model checking on-the-fly. our tool hybridtiger is integrated into the software analysis framework cpachecker. the hybridtiger algorithm is implemented within the software verification framework cpachecker [ ] . cpachecker utilizes the eclipse cdt c-parser . if ( n == ) return ; return fib (n - ) + fib (n - ) ; } (a) c-program cpachecker allows developers to easily integrate new algorithms like hybrid-tiger, which may use other algorithms implemented in cpachecker, such as counterexample-guided abstraction refinement (cegar) [ ] . additionally, new reachability analyses can be integrated as configurable program analyses (cpas) [ ] . each cpa consist of an abstract domain with the operators post, merge, and stop. multiple cpas can also be combined into one cpa. hybridtiger uses the coveritest [ ] algorithm to sequentially combine test-case generation runs utilizing different verification techniques. each test-case generation run applies the cpa/tiger-mgp (tiger multi-goal-partitioning) algorithm, which utilizes the cegar algorithm. hybridtiger first extracts test goals from input programs and repeatedly executes reachability analyses provided by cpachecker until every reachable test goal is covered by at least one test case. to this end, test goals are encoded into (non-)reachability properties. if a test goal has been reached, cpachecker thus returns a counterexample and hybridtiger extracts a test case (i.e., a vector of input values), writes the test case to disk and marks the test goal as covered. hybrid test-case generation. hybridtiger receives as inputs a c program and a property specification (i.e., a set of test goals). next, hybridtiger transforms the c program into a control-flow automaton (cfa) [ ] . figure shows an example c program and the corresponding cfa. after cfa generation, the coveritest algorithm as configured in hybridtiger (see fig. ) is executed. in every new iteration, each analysis of our configuration first (re-)partitions the set of uncovered test goals (e.g., partitions p , p , p and p for cpa/-tiger-mgp-value and p and p for cpa/tiger-mgp-predicate in fig. ). in each iteration, cpa/tiger-mgp-value is performed first using explicit model checking and is stopped after s. after that, cpa/tiger-mgp-predicate is partitioning. hybridtiger utilizes domination information of test-goal locations according to the respective cfa paths. this meta-information is retrieved from the generated cfa: each cfa node (i.e., basic block of program locations) in fig. is annotated with a post-order id such that a node will only be reached after all nodes on the same path with a larger id have been reached at least once. hence, we use the ids of predecessor nodes related to the cfa edges of test goals as sorting criterion for the overall set of test goals before splitting this set into partitions of predefined sizes. in this way, test goals sharing similar paths are more likely to be assigned to the same partition thus facilitating reuse potentials of reachability-information during reachability analysis. hybridtiger has three main strengths. first, the directed generation of test cases aiming at covering particular test goals significantly reduces the overall number of test cases. additionally, most test cases produced by hybridtiger effectively increase the overall coverage (i.e., hybridtiger produces mostly correct and nonredundant test cases). second, hybridtiger uses control-flow information to partition test goals which potentially enhances efficiency of test-case generation due to information reuse among similar test goals. lastly, hybridtiger uses combinations of different analysis strategies (i.e., value analysis and predicate analysis) to cope with structural diversity of input programs. one weakness of hybridtiger is that the partitioning approach does not improve performance of a goal-by-goal approach if being applied to programs with a small number of test goals (e.g., reaching one single error location as demanded in the cover-error category). results. in test-comp , hybridtiger has participated in all categories and managed to reach the th rank in code coverage and the th rank in finding bugs, where hybridtiger performed better on tasks with many test goals. the version of hybridtiger submitted to test-comp is built from the tigerintegration branch revision of the cpachecker repository and is archived at https://gitlab.com/sosy-lab/test-comp/archives- . hybridtiger can be applied to a single file using the command where spec is the property file (e.g., coverage-error-call or coverage-branches) and file is the input c program. statistics of the analyses are printed to console and meta data on generated test cases as well as the test suite are written to files in the output folder. in order to run hybridtiger for the test-comp benchmarks a linux system with java , benchexec and the sv-benchmarks is required. finally, run benchexec with: the benchmark definition cpa-tiger.xml (archived at https://gitlab.com/sosylab/test-comp/bench-defs/tree/master/benchmark-defs), and the tool-info module cpachecker.py (archived at https://github.com/sosylab/benchexec/tree/master/benchexec/tools). cpachecker is maintained by the software systems lab at lmu munich as open-source project, contributed by an international group of researchers from lmu munich, university of passau, technical university of darmstadt and the institute for system programming of the russian academy of sciences.the branch tigerintegration from which hybridtiger is built is mainly developed at the technical university of darmstadt. additional information is available at https://cpachecker.sosy-lab.org/. software model checking via large-block encoding configurable software verification: concretizing the convergence of model checking and program analysis coveritest: cooperative verifier-based testing cpachecker: a tool for configurable software verification counterexample-guided abstraction refinement for symbolic model checking ), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons license and indicate if changes were made. the images or other third party material in this chapter are included in the chapter's creative commons license, unless indicated otherwise in a credit line to the material. if material is not included in the chapter's creative commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use acknowledgement. this work was funded by the hessian loewe initiative within the software-factory . project. key: cord- -m yv qkm authors: demey, baptiste; daher, nagib; françois, catherine; lanoix, jean-philippe; duverlie, gilles; castelain, sandrine; brochot, etienne title: dynamic profile for the detection of anti-sars-cov- antibodies using four immunochromatographic assays date: - - journal: j infect doi: . /j.jinf. . . sha: doc_id: cord_uid: m yv qkm in order to fight the sars-cov- pandemic infection, there is a growing need and demand for diagnostic tools that are complementary and different from the rt-pcr currently in use. multiple serological tests are or will be very soon available but need to be evaluated and validated. we have thus tested immunochromatographic tests for the detection of antibodies to sars-cov- . in addition, we assessed the kinetics of antibody appearance using these assays in patients after they were tested positive by rt-pcr. we observed great heterogeneity in antiboy detection post-symptom onset. the median antibody detection time was between and days according to the manufacturers. all the tests showed a sensitivity of to % on day and % on day . in addition, a single cross-reaction was observed with other human coronavirus infections. thus, immunochromatographic tests for the detection of anti-sars-cov- antibodies may have their place for the diagnostic panel of covid- . in order to fight the sars-cov- pandemic infection, there is a growing need and demand for diagnostic tools that are complementary and different from the rt-pcr currently in use. multiple serological tests are or will be very soon available but need to be evaluated and validated. we have thus tested immunochromatographic tests for the detection of antibodies to sars-cov- . in addition, we assessed the kinetics of antibody appearance using these assays in patients after they were tested positive by rt-pcr. we observed great heterogeneity in antiboy detection postsymptom onset. the median antibody detection time was between and days according to the manufacturers. all the tests showed a sensitivity of to % on day and % on day . in addition, a single cross-reaction was observed with other human coronavirus infections. thus, immunochromatographic tests for the detection of anti-sars-cov- antibodies may have their place for the diagnostic panel of covid- . keywords: sars-cov- ; covid- , antibody, lateral flow assay since december , the world has been facing a pandemic of covid- , an infectious disease caused by sars-cov- , a virus that emerged in china (wu and mcgoogan, ) . although rt-pcr testing of sars-cov- has become the standard method for direct diagnosis, these real-time pcr tests have some limitations, primarily dedicated infrastructure to avoid any biorisk, limited capacity and a long turnaround time (y. . there is increasing pressure from the medical community and society to screen the population on a large scale. serological tests in elisa format or as immunochromatographic lateral flow assay (lfa) have recently become available from many manufacturers (z. (haveri et al., ) . these serological tests will be complementary to pcr tests both for screening and diagnosis of the population, for the purpose of population exits from containment in different countries and finally for future epidemiological studies. however, it is necessary to evaluate the analytical performance of these assays and also their place in clinical practice. thus, the objective of our study was to evaluate four immunochromatographic assays for the detection of igm and igg antibodies to sars-cov- and to evaluate the kinetics of their detection by these lfa. twenty two patients diagnosed positive in amiens university hospital for sars-cov- on a nasopharyngeal swab using a rt-pcr technique (national reference center in pasteur institute, paris, france) were included in our study. the date of reporting of the first symptoms was retrieved from the medical records. the samples were tested regularly during the hospitalization until the tests were positive, with an evaluation at most on day post-symptoms. in order to evaluate a possible crossreaction with the other human coronaviruses described to date (nl , hku , e and oc ), sera following such viral respiratory infection diagnosed in our lab were tested. this project was conducted in accordance with the reference methodology (mr- france) in accordance with article of the gdpr. we evaluated immunochromatographic tests for the detection of igm and igg directed against sars-cov- ( figure ). these tests were kindely provided by asian manufacturers, namely biotime biotechnology co, autobio diagnostics co, isia bio-technology co and biolidics. for the biotime, autobio, and biolidics tests the detection of igm and igg is performed on the same diagnostic cassette. for isia different cassettes are available. each test requires between and µl of serum, plasma or whole blood and is read to minutes after the sample and diluent have been deposited. for the biotime and biolidics assays, respectively and of the patients could be tested for lack of immunochromatographic tests. longitudinal immunochromatographic testing in all patients shows heterogeneity in the time to detection of antibodies after symptom reporting (figure ). the median antibody detection time was days since onset of symptoms for autobio and biotime (igm or igg), days for biolidics (igm or igg) and and days for isia igm and igg respectively (figure and supplementary data). igg was detected in all patients on day since onset of symptoms, while igm was not detected in patients with autobio and isia. igm was detected before igg in , , and patients with the biotime, autobio, isia and biolidics assays respectively. in the other cases, igm was detected at the same time as igg. thus, the diagnostic interest of detecting igm directed against cov- -sars appears limited. the clinical sensitivity of the different tests could be assessed longitudinally during follow-up and we observed an increasing sensitivity in the post-symptom period ( figure and table ). as described above, the clinical sensitivity of igm does not appear to be superior to igg for these immunochromatographic tests. with either igm or igg detection for a patient on days , and since onset of symptom, we calculated a clinical sensitivity between and %, and % and % respectively ( figure b and table ). the autobio test appears to have better sensitivity at day ( . %) versus . %, . % and . % for biotime, isia and biolidics respectively (not significant). in order to evaluate the specificity of these different immunochromatographic tests, particularly regarding previous infections to other viruses of the human coronavirus family, we evaluated sera from patients who had a rt-pcr diagnosis of respiratory infection by different coronaviruses in (table ) . of the tests performed, only one (autobio) was positive from the serum of a patient with a respiratory diagnosis days previously of hcov- e. the same test for the other three samples with hcov- e was negative each time. cross-reactions with these different coronaviruses therefore appear to be limited but may require further investigation. in this study we demonstrated the kinetics of detection of antibodies to sars-cov- using immunochromatographic lfa. these simple rapid unit tests are also easy to read (figure ). profiling early humoral response were already observed with elisa assay (guo et al., ) (zhao et al., ) . we calculated increasing clinical sensitivities over time from the onset of symptoms in patients. moreover, we did not observe any real added value in igm staining from these immunochromatographic tests. with this kind of test, it is very difficult to distinguish the very recent infection from the older one because some patients present early with igg without igm and for some a detectable igm threshold appears later. serological elisa tests from research laboratories or portfolios of in vitro diagnostic manufacturers may allow a clearer distinction between igm and igg kinetics and their respective interest. nevertheless, the value of these point of care tests seems obvious in countries with limited resources but perhaps also as the epidemic progresses in individuals in the form of self-homemade assay from a drop of blood on the fingertip. this type of test could be easily delivered to individuals and thus limit contact. in addition, in countries with strong health systems, these rapid detection tests may also find their way as doctor tests in emergency departments. during this covid- epidemic there is a rebound in symptoms on days to leading to a visit to a doctor or an emergency department. in figure and table , we have calculated a sensitivity of these tests between % and % during this post-symptom reporting period. even if symptom reporting remains very subjective and time-varying but if we add an average incubation period of days (linton et al., ) , we can say that at - days post-infection these tests seem reliable. finally, regarding specificity that we evaluated with respect to sera of other common coronavirus infections, we observed a single cross-reaction. however, we were unable to test serum from people formerly infected with sars-cov (tian et al., ) . we would probably have many more cross reactions between these very close viruses as already report. also, due to the lack of available tests, we could not test for specificity with samples containing antibodies to other viruses (hiv, hcv, hbv and others pathogens). in conclusion, we described the kinetics of detection of post-symptom antibodies in patients using immunochromatographic rapid tests and demonstrated the good performance of these tests for the detection of antibodies after sars-cov- infection. our results suggest that these rapid and simple tests should be seriously considered in this time of health and political crisis to monitor both symptomatic and non-symptomatic patients. profiling early humoral response to diagnose novel coronavirus disease (covid- ) serological and molecular findings during sars-cov- infection: the first case study in finland stability issues of rt-pcr testing of sars-cov- for hospitalized patients clinically diagnosed with covid- development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis incubation period and other epidemiological characteristics of novel coronavirus infections with right truncation: a statistical analysis of publicly available case data potent binding of novel coronavirus spike protein by a sars coronavirusspecific human monoclonal antibody characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention antibody responses to sars-cov- in patients of novel coronavirus disease key: cord- -pbfi c e authors: lyngse, f. p.; kirkeby, c. t.; halasa, t.; andreasen, v.; skov, r. l.; moller, f. t.; krause, t. g.; molbak, k. title: covid- transmission within danish households: a nationwide study from lockdown to reopening date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: pbfi c e background the covid- pandemic is one of the most serious global public health threats in recent times. understanding transmission of sars-cov- is of utmost importance to be able to respond to outbreaks and take action against spread of the disease. transmission within the household is a concern, especially because infection control is difficult to apply within the household domain. methods we used comprehensive administrative register data from denmark, comprising the full population and all covid- tests, to estimate household transmission risk and attack rate. results we studied the testing dynamics for covid- and found that the day after receiving a positive test result within the household, % of potential secondary cases were tested and % of these were positive. after a primary case in , households, % of potential secondary cases were tested within days, of which % tested positive as secondary cases, implying an attack rate of %. among primary cases, those aged - were underrepresented when compared with the total population. we found an approximately linearly increasing relationship between attack rate and age. we investigated the transmission risk from primary cases by age, and found an increasing risk with age of primary cases for adults, while the risk seems to decrease with age for children. conclusions although there is an increasing attack rate and transmission risk of sars-cov- with age, children are also able to transmit sars-cov- within the household. in late , increased numbers of severe respiratory infections were reported in the wuhan region in china caused by the sars-cov- virus (coronaviridae study group of the international committee on taxonomy of viruses, ). since its emergence, the virus has spread rapidly throughout all five continents affecting millions of people (world health organization, ) and causing massive economic losses (fernandes, ) . the effective reproduction number was estimated in different studies with different methods to range from . to . (boldog et al. ( ) ), revealing a high transmission potential. person-to-person transmission is a major transmission mode of sars-cov- , including transmission through aerosols or droplets on surfaces (chan et al., ; leclerc et al., ) . quantifying the transmission risk in different settings is essential for improving our understanding of the viral transmission dynamics, to implement effective preventive measures, to minimize economic damage, and to avoid overloading the healthcare system. close person-to-person contact is one of the main risk factors and transmission within the household is thus a major setting for virus transmission (prem et al., ; davies et al., ; cauchemez et al., ; leclerc et al., ) . furthermore, infection control and isolation are challenging in the (often crowded) household domain. quantifying the extent of transmission within the household can help improve our understanding of the effects of implementing quarantine for household members, physical distancing and improved hygiene. furthermore, these estimates are useful in constructing reliable prediction models for the spread of sars-cov- from households to the community. data from contact tracing and monitoring of individuals have been used to investigate household transmission of sars-cov- (he et al., ; jing et al., ; liu et al., ; li et al., ; madewell et al., ) . contact tracing is laborious and requires large resources when there are many new cases, as in the case of the sars-cov- pandemic. thus, these studies have been limited to include a maximum of a few hundred primary cases, selected mainly due to history of hospitalization or clinical disease (see a systematic review by madewell et al. ( ) ). the relatively small sample size as well as the selection and recall bias caused by contact tracing may limit the generalizability of these studies. in this study, we exploit national register data from denmark to investigate transmission patterns within households. to our knowledge, this is the first nationwide study that uses estimates of household attack rates and transmission risks that exploit sars-cov- test data from an entire population. the epidemic in denmark on february , , the first case of sars-cov- was diagnosed in denmark (reilev et al., ) . shortly thereafter, the number of cases began to rise with an estimated effective reproduction rate (re) of about . (statens serum institut ( )). on march , a comprehensive lockdown of the public sector was implemented by the government. moreover, the private sector was encouraged to work from home as much as possible. in figure a. (panel a) , key indicators of the epidemic are shown: number of tests, positive test results, hospitalized cases, and deaths for the early stage of the epidemic, the lockdown period and the two following stages of reopening. the figure shows a clear reduction in the number of positive test results, hospitalized cases and deaths over time. panel b shows a summary of the main measures for controlling the epidemic over time, including test and contact tracing strategy, and restrictions on public and private workplaces, education and childcare institutions, as well as in the community in general. all danish residents have access to tax-paid universal health insurance, and a test for sars-cov- is free of charge. furthermore, denmark has comprehensive social welfare insurance, and sars-cov- sick leave is fully reimbursed by the state. thus, financial reasons are not a major obstacle to obtaining a test. the test capacity has increased throughout the epidemic, and in the study period, the number of tests has been fairly stable since late april (figure a. ) . in the beginning of the epidemic, all suspected cases of covid- were tested and their contacts traced. however, soon after, due to capacity constraints on testing, only cases with severe symptoms (i.e., admitted to hospital) were tested and the overstretched contact tracing was halted. during reopening testing again became generally accessible, so that all residents could obtain a test without a referral (panel b of figure a. ) . in the current study, we used danish administrative register data. all residents in denmark have a unique personal identification number that allows a completely accurate linkage of information across different registers at the individual level. all microbiological data in denmark is registered in the danish microbiology database, from where we obtained individual level data on all national tests for sars-cov- for the period february , (the first positive test in denmark) to july , . information on the reason for being tested (e.g., symptoms, potential contact with infected persons etc.) was not available. from the danish civil registry system, we obtained information about the sex, age, and home address for all individuals living in denmark. all data management and analyses were carried out on the danish health data authority's restricted research servers with project number fseid- . we constructed households by linking all individuals living at the same address, and only considered households with six or fewer members, in order to exclude e.g., institutions. the data set captured . % percent of the danish population. person level data, which included information on the test result and date and time of sampling as well as time of the result, were linked to individuals within households. for each household, we identified the first positive test for sars-cov- ; this case was defined as the primary case and referred to as such throughout this paper. we considered all subsequent tests from other members in the same household as tests taken in response to the primary case. we defined secondary cases as those who had a positive test within days of the primary case being tested positive. primary examination of the data revealed that this cutoff provided a stable proportion of potential secondary cases (see figure b ). in addition, we assumed that the secondary household members were infected by the household primary case, although some of these secondary cases could represent co-primary cases. a longer cutoff time period could result in misclassification of cases among household members with somewhere else being the source of secondary infections. in order to investigate potential bias in our results in relation to time, due to changing test strategy and capacity over the epidemic period (see figure a . for an overview of test strategy and capacity), we separated the data into three data sets representing the three time periods based on the test date of the primary case, and analyses were performed separately on these data sets. the defined periods were: lockdown: march -april ; early reopening: april -may ; and late reopening may -july (see figure a . ). during lockdown, educational institutions were kept closed and the public sector with non-essential functions stayed at home. children's daycare was limited to children of employees in essential functions, such as doctors, nurses and police. employees in the private sector were encouraged to stay home if possible, and international travel was minimized by closing the borders except for essential activities. in the early reopening phase, children's daycare became available again, and schools were re-opened for classes up to th grade. in the late reopening, systematic contact tracing was resumed, schools ( - th grade) and higher educational institutions reopened, along with restaurants and smaller bars (with physical distancing). . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint to determine the probability that an additional household member would test positive after the primary case in the household was tested positive, we used all records for potential secondary cases within the household. we defined the attack rate as the proportion of additional household members that tested positive, whereas the transmission risk was the proportion of secondary cases per primary case. we did not exclude any potential co-primary cases in the main analysis. we further conducted a sensitivity analysis for the robustness of the time cutoff of transmission from the primary case to potential secondary cases. we used sas . to manage and analyze the data (sas, ) . in order to reach sufficient sample sizes, we separated all records into age groups of five-year intervals. to investigate the testing dynamics, we took an event study approach (ball & brown, ) . following this method, we used the date of diagnosis of the primary case in each household as an event and observed all other household members for five days before until days after the event. in the case of two or more primary cases detected on the same date, we randomly assigned one of them as the primary case. we estimated the probability of being tested (β τ ) for each day relative to the first positive test result within the household, using the following equation: where y i,t is a binary variable for individual i being tested at time t. τ is days relative to the date of the primary case's positive test result. i τ =t denotes indicators for time since the primary case's positive test result. β τ represents parameters estimating the probability of being tested on day τ relative to receiving the primary case's test result in the household. ε i,t denotes the error term, clustered on the household (event) level. we used the same equation to estimate the probability of y testing positive conditional on being tested. furthermore, to estimate the proportion of potential secondary cases that had been tested on day τ or previously, we estimated the absorbing probability, using the following equation: where i τ ≥t = if individual i was tested on day τ or previously, and zero otherwise. we also used the same equation to estimate the probability of y ever being tested positive. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint to investigate the proportion on positive tests originating from households, we defined new cases that live in a household with another case that tested positive within the preceding days as a case originated from the household domain. we used a seven day rolling average in order to take account of variation in testing rates across the weekdays. to estimate the attack rate, we estimated the proportion of potential secondary household members who received a positive test within days after the test date of the primary case. we estimated attack rates using the following equation: where y i,t = if the individual had a positive test within the days after the primary case, and zero otherwise. γ denotes a vector of fixed effects for the three periods. female is a binary variable for sex. β measures the day attack rate. ε i,t denotes the error term, clustered on the household (event) level. to investigate the age structure of the attack rate for potential secondary cases and transmission risk from primary cases, we used a non-parametric approach. we separated the data into five-year age groups. we estimated the attack rate using the following equation: where y i,t = if the potential secondary case i had a positive test within the days after the test date of the primary case, and zero otherwise. agegroup s is five-year age groups of the potential secondary cases. α is a vector that measures the age structured attack rate. ε i,t denotes the error term, clustered on the household (event) level. we estimated the transmission risk using the following equation: where agegroup p is five-year age groups of the primary cases. β is a vector that measures the age structured transmission risk. we estimated the age structured interaction between the attack rate and transmission risk using the following equation: . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . where γ is a vector that measures the age structured interaction between attack rate and transmission risk. to quantify the effect of age on attack rate, we estimated the approximately linear relationships between attack rate and age using equation: where β measures the probability of being infected as a linear function of age. φ is a vector of fixed effects for each time period (see "robustness of estimates over time" in section . ). δ measures the differential age gradient for each period. π measures the effect of sex for each period. in order to investigate the potential difference between male and female cases, we explored the age dependent attack rate separately for each sex. we also separated the data into households where the primary cases were children (below years of age) and adults (above years of age). these thresholds were chosen to ensure the primary cases were either children or adults. we estimated the attack rate stratified by the number of household members for households with one to six members. furthermore, we estimated the proportion of households with n number of positive cases, conditional on the size of the household being greater than or equal to n (with a maximum household size of six). in total, we obtained positive test results from , household primary cases and , positive secondary cases, see table . further summary statistics are presented in appendix b. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint appendix figure a. presents the probability of being tested and testing positive over the epidemic for five-year age groups. we found that all age groups are being tested, though children generally had a lower probability. the increase in test capacity over time was approximately equally distributed across ages. in late june, we saw an increase in the probability of children being tested. appendix figure b. shows summary statistics of the primary cases compared to the overall danish population. panel (a) shows the age distribution and panel (b) shows the household size distribution. there were proportionally fewer children as primary cases than in the total population. the household sizes of the primary cases generally matched the household sizes of the population. in this section, we focus only on the testing dynamics during the late reopening, where test capacity was stable. (in appendix d, we illustrate changes over all three periods.) figure panel (a) shows that after receiving a positive test result in the household (t = ), % of potential secondary cases were tested (blue) the day after the positive test result (t = ) of the primary case was available and % of these % were positive (red). on the day preceding the test result (t = − ), % were tested and % of these tests were positive. panel (b) shows the proportion of individuals that were tested (blue) and those that tested positive (red), daily up to days after the primary case was tested (t = ). % of potential secondary cases were tested on the same day as the primary case and % of potential secondary cases tested positive on that day. within days after the primary case was tested, % of the potential secondary cases were tested and % tested positive. there were % who tested positive on the same day (t = ) as the primary case. these may represent co-primary cases, and therefore do not represent household cases. under this assumption, in order to estimate the attack rate, one should exclude these cases (by subtracting percentage points (pp) from %), thereby resulting in an attack . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint rate of %. similarly, cases detected within one day of the primary case may represent co-primary cases (t ≤ ). this leaves an attack rate of % (by subtracting pp from %). (appendix f provides robustness analysis on the definition of co-primary cases.) on the day preceding the result (t = − ) % were tested and % of these tested positive. the day after the households received their first positive test result (t = ), % were tested and % of these tested positive. in panel b, t = denotes the time the first positive test was taken (not when the test result was given). % of all potential secondary cases were tested on the same day as the primary case (t = ) and % of all potential secondary cases tested positive. this implies a % probability of testing positive conditional on being tested on the same day as the primary case. days after the day of the first positive test, % had been tested and % tested positive. shaded areas show the % confidence bands clustered on household level. figure shows the proportion of positive tests originating from households within the days after the primary case tested positive. after a rapid decrease immediately after lockdown, there was an increasing proportion of new cases originating from households during lockdown, and a decreasing proportion after reopening. the last day of school was june , and many families start their vacation at that time. after this date, the proportion started to increase again. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint we found an approximately linearly increasing relationship between attack rate and age. panel a of figure shows the probability of having a test (blue) and the probability of having a positive test (red) (unconditional on being tested) across -year age groups. the shaded areas show the % confidence bands. panel b shows the transmission risk from primary cases by age group, i.e., the probability of infecting others. the figure shows an increase with age for adults, while the risk seems to decrease with age for children. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint notes: panel a illustrates the probability of having a test (blue) and the probability of having a positive test (red) (unconditional on being tested) across -year age groups. panel b illustrates the transmission risk from primary cases by age group, i.e. the probability of infecting others. the shaded areas show the % confidence bands clustered on the household level. as figure shows an approximately linear relationship between attack rate and age, we estimated the linear relationship using equation (see table e . , column i). the results show that individuals had a baseline risk of . % of testing positive. the risk increased by . percentage points for each year of age. thus, a -year-old had a risk of . %, a -year-old had . %, and a -year-old had . %. the estimates were robust to different specifications, including period and sex covariates, table e . , column ii-iv. the attack rates conditional on the primary case being a child or an adult are presented in figure c. . when the primary case is a child (under years old), the attack rate seemed uniform, regardless of the age of the potential secondary case. when the primary case is an adult (over years old), the attack rate increased (linearly) with age. the attack rates by sex are presented in appendix c. . the results indicated no difference in attack rates between males and females. the interaction between the attack rate and transmission risk for each combination of age groups is presented in figure c . . the age range of the primary case is depicted on the horizontal axis and the age of potential secondary cases on the vertical axis. panel a shows the probability of being tested (for each age group combination); panel b shows the probability of obtaining a positive test result. the probability for potential secondary cases of being tested was generally highest when the primary case was a child (below years old). the probability of being tested was also high when the age difference between the primary case and the potential secondary case was small. the attack rate was highest when the primary and potential . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint secondary cases were above years of age. when children were the primary case, an increased attack rate was observed for all age groups. figure illustrates the proportion of cases by the number of household members for households with one to six members. for instance, in a household with two members (red), % of the households had one positive case, while % had two positive cases. similarly, in a household with three members (green) % of the households had one case, % had two cases, and % had three cases. (table e . .) this implies that in a three-person household, % have an attack rate of , % have an attack rate of %, and % have an attack rate of %. this amounts to an overall attack rate of % ( % × % + % × % + % × % = %). once a primary case was found within a household, the probability of at least one secondary case was %, regardless of household size, and consequently % of the primary cases do not generate any additional cases. in particular, the primary cases had a % probability of generating one additional case, % of generating two additional cases, % of generating three additional cases, and % of generating four additional cases. this pattern was consistent regardless of the number of persons in the household, showing a transmission pattern that was exponentially decreasing with the number members within the household. the pattern was consistent over the three phases of the epidemic examined here, indicating that it is not a result of the change in the testing strategy (figure d is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint the epidemic in denmark changed over time, both due to changes in policy response (e.g., lockdown), and changes in test capacity and strategy (see appendix a for an overview). in this section, we investigate the robustness of the previously described results over the three defined periods of the epidemic (see appendix d). the analyses show that despite the substantial changes in probability of being tested, the estimated attack rates were consistent over the epidemic. in appendix f, we investigate the sensitivity of the estimated attacks to the definition of co-primary cases. the analysis showed that the estimated age structured attack rates did not change noticeably by excluding secondary cases found within the same day, one day or two days of the primary case. we estimated an overall attack rate within households of % (table e . ), ranging from % during lockdown, % during early reopening, and % during late reopening (figure d. ) . this suggests that attack rates estimated early in the danish epidemic underestimated the true attack rate. this bias likely comes from the limited testing capacity . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint early on. these estimates are in line with the estimates from the literature; madewell et al. ( ) conducted a meta-analysis of household transmission of sars-cov- from studies and found an overall attack rate of . %, which is very close to our estimate. we studied the testing dynamics for covid- and found that the probability of obtaining a test relative to a primary case positive test result within the household peaked on the day after the primary case received the result, where % of all potential secondary cases were tested and % of these were positive (figure a) . interestingly, % of the potential secondary household cases were tested one day preceding the test result of the primary case, and % of these were positive. this could indicate that these individuals were tested for a reason other than the primary case result, e.g., for having symptoms themselves. the probability of being tested after a primary case in the same household increased from % on the same day as the primary case until it flattened out at around % on day six (figure b) . % of the secondary cases were found during the first three days after the primary case ( % / % = %). this highlights the importance of fast contact tracing, as most secondary cases are found in the first couple of days after the primary case, which is also concluded by moghadas et al. ( ) . the proportion of positive cases originating from households ( figure ) increased during the lockdown until the late reopening period when the borders reopened. thereafter, it increased again after the school holidays started. in other words, the school holidays (which also include three-weeks of annual leave for most parents) essentially functioned as another lockdown period, because families tend to stay together during the holidays. we suggest that this may have contributed to a low incidence of community transmission over the summer. when the testing capacity was relatively stable (from late april ), the proportion varies between % and % of total cases. this indicates that many cases originate within the household domain, and this should be taken into account when monitoring the epidemic as well as in national guidelines for covid- prevention. evidence from other countries also finds a substantial proportion of cases originating from households, as for instance, in israel, where % of all infections were found to have been originated at home (jaffe-hoffman, ). we estimated the age structured attack rate and transmission (figure ) and found a (linear) relationship between age and both the attack rate and transmission risk from primary cases. this suggests that susceptibility to infection increases with the age of the susceptible person. however, children (younger than year of age) also have an elevated transmission risk, likely due to closer contact with parents ( figure c. ), indicating that children may represent an overlooked risk. our findings correspond well with findings in the literature: madewell et al. ( ) found that susceptibility to infection increased with . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint age, and a large seroprevalence study in spain also found an increasing linear relationship with age (pollán et al., ) . similar findings were found by li et al. ( ) and bi et al. ( ) . we further estimated the attack rates conditional on the primary case being a child or an adult (figure c. ) . when the primary case is a child (under years old), the attack rate seemed to be uniform, regardless of the age of the potential secondary case. when the primary case is an adult (over years old), the attack rate increased (linearly) with the age of the potential secondary case. this suggests that transmission from children is fairly constant, and depends on close contact with susceptible cases, whereas transmission from adults is more effective the older the potential secondary case is. one could think that if a child is sick, caregivers are likely to have more even close contact with the child -and more so the younger the child is. the opposite may be true for adult cases, indicating that the susceptibility to covid- increases with the age of a person, reflecting immunological properties. although there is agreement that transmission from and between children is not the main driver in this epidemic (ludvigsson, ) , transmission from sick children to parents in the household domain may represent a hitherto overlooked risk factor. we also estimated the age structured attack rates by sex and found no difference in attack rates between males and females, corresponding to the findings of jing et al. ( ). we used a large administrative data set to investigate the attack rate and transmission risk from lockdown to reopening, comprising , primary cases and , potential secondary cases. exploiting this rich nationwide data, we were able to address several concerns regarding the sensitivity of our results. as the testing capacity and strategy (and hence access to obtaining a test) has changed remarkably over the epidemic, robustness of results are a primary concern when comparing positive test cases over the covid- epidemic. we addressed this by dividing our sample into three periods with different testing capacities (appendix d) and found that the probability of obtaining a test did increase remarkably across the periods. our results were, however, relatively consistent over time, suggesting that the findings are not due to changing testing strategies. there are no formal guidelines for defining co-primary cases. madewell et al. ( ) provided a review on household transmission of sars-cov- : most of the studies included in madewell et al. ( ) did not describe how co-primary cases were handled, several studies stated they assumed all secondary cases were infected by the primary case, one study excluded secondary cases if they developed symptoms before exposure to the primary case, . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint and another study randomly selected one primary case as the source of infection. we addressed this important question by showing the sensitivity for different specifications. we found that the attack rate is strongly dependent on the definition. for instance, in figure b we show that if one defines co-primary cases as individuals tested on the same day as the primary case, the secondary attack rate is reduced by % ( % / % = %). increasing the period for co-primary cases further caused the estimated attack rate to decrease even more. therefore, it is important to further investigate the dynamics of sars-cov- in homes, schools, workplaces and major places in the community in order to quantify their impacts on virus transmission and develop effective control measures. mathematical modeling is a widely used tool for researchers in order to understand and predict the spread of disease; and policy relies on proper results from these models when making decisions such as choosing between keeping some parts of society open and other parts closed. closing of childcare and schools has been widespread in most countries. the results from this study can be used as direct input in parameterizing such mathematical models in terms of virus transmission at home. furthermore, we estimated the age structured attack rate and transmission risk, as well as the interaction of these, which are important inputs in mathematical models, for instance, for contact matrices between age groups (davies et al., ; zhang et al., ) . when modeling the spread of covid- , many researchers assume that each contact has the same probability of transmission (conditional on time and distance of contact), i.e., a binomial process (e.g., jing et al. ( ); kucharski et al. ( ) ). our results, however, suggest that this should be modelled as a two-step procedure when simulating contacts between individuals: first, it should be determined whether a case is infectious or not (i.e., a bernoulli process), and second, conditional on being an infectious case, a binomial process should be used to represent actual transmission. this allows replicating the transmission dynamics of the virus more realistically and hence allows more realistic predictions from these models. in conclusion, to the best of our knowledge, this study presents the results of the first nationwide register-based study on household transmission of covid- . these results are important as they show differences in transmission pattern with the age of both the primary case and the potential secondary cases within households. a large proportion of transmission was found to occur within households, highlighting the severity of covid- transmission, and that preventative measures within households are urgently needed in order to prevent transmission. moreover, monitoring the proportion of positive cases originating from households may be an important tool for public health authorities to measure community transmission. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https: //doi.org/ . //doi.org/ . / appendix a is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint - - - - - - - - - - < - - -< -< - ---- - ---- ---- notes: this table provides summary statistics on the potential secondary cases included in the study. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint appendix c age structured attack rate notes: panel a shows the probability of being tested and panel b the probability of having a positive test. the age of the primary case is depicted on the x-axis and the age of potential secondary cases on the y-axis. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . appendix c. age structured attack rate by sex is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . appendix d dynamics over the epidemic appendix d. testing dynamics over the epidemic figure d . panel a-c presents the testing dynamics for the three periods of the epidemic. panel a shows that during lockdown only few percent of the other household members were tested and that there was a high positive rate of the ones tested. panel b shows that during the early reopening, more household members were being tested and the positive rate declined accordingly. lastly, panel c shows that in the late reopening even more household members were being tested and the positive rate declined further. panel d-f shows the proportion of household members ever being tested and ever being positive. during lockdown % of secondary household members were tested after days, during early reopening % were tested, and during late reopening % were tested. similarly, % had tested positive after days during lockdown, % during early reopening and % during late reopening. another aspect of testing is how long a person has to wait for the result after obtaining the test. table a . shows that % of all cases received the result within day during lockdown, within days during early reopening, and within day during late reopening. notes: shaded areas are % confidence bands clustered on the household level. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint appendix d. age structured attack rate over the epidemic figure d . illustrates the age structured attack rate separately for the three periods of the epidemic. the testing rate clearly increases during the epidemic, while the rate of positive test results is relatively constant. both rates increase with age of the case. notes: this figure illustrates the age structured attack rate separately for the three periods of the epidemic. figure shows the estimates for the pooled analysis. the testing rate clearly increases during the epidemic, while the positive rate is fairly constant. shaded areas are % confidence bands clustered on the household level. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint notes: the estimates are calculated from households with at least one potential secondary case, i.e., households with two to six members. the estimate for two secondary cases is calculated from households with at least two potential secondary cases, i.e., households with three to six members. estimates are in percentages. standard errors in parenthesis, clustered on the household level. . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint notes: this table provides estimates on the robustness of the estimates for the attack rate depending on the definition of co-primary cases. column (i) corresponds to column (ii) in table e . . in column (ii) we exclude secondary cases that test positive on the same day (t = ) as the primary case. in column (iii) we exclude secondary cases that test positive within one day (t ≤ ) of the primary case. in column (v) we exclude secondary cases that test positive within three days (t ≤ ) of the primary case. standard errors in parenthesis, clustered on the household level. *p< . , **p< . . . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint notes: this figure illustrates robustness for the definition of co-primary cases with respect to the age structured attack rate. panel a has no restrictions and is the same as figure . panel b excludes secondary cases testing positive the same day as the primary case (t = ). panel c excludes secondary cases testing positive within day of the primary case (t ≤ ). panel d excludes secondary cases testing positive within days of the primary case (t ≤ ). . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint an empirical evaluation of accounting income numbers epidemiology and transmission of covid- in cases and of their close contacts in shenzhen, china: a retrospective cohort study. the lancet infectious diseases risk assessment of novel coronavirus covid- outbreaks outside household transmission of pandemic influenza a (h n ) virus in the united states a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- age-dependent effects in the transmission and control of covid- epidemics economic effects of coronavirus outbreak (covid- ) on the world economy temporal dynamics in viral shedding and transmissibility of covid- early dynamics of transmission and control of covid- : a mathematical modelling study. the lancet infectious diseases what settings have been linked to sars-cov- transmission clusters? the characteristics of household transmission of covid- secondary attack rate and superspreading events for sars-cov- . the lancet children are unlikely to be the main drivers of the covid- pandemic-a systematic review household transmission of sars-cov- : a systematic review and meta-analysis of secondary attack rate the implications of silent transmission for the control of covid- outbreaks prevalence of sars-cov- in spain (ene-covid): a nationwide, population-based seroepidemiological study projecting social contact matrices in countries using contact surveys and demographic data coronavirus disease (covid- ): situation report changes in contact patterns shape the dynamics of the covid- outbreak in china : robustness for definition of co-primary cases key: cord- -javbnjrg authors: gupta, prateek; maharaj, tegan; weiss, martin; rahaman, nasim; alsdurf, hannah; sharma, abhinav; minoyan, nanor; harnois-leblanc, soren; schmidt, victor; charles, pierre-luc st.; deleu, tristan; williams, andrew; patel, akshay; qu, meng; bilaniuk, olexa; caron, ga'etan marceau; carrier, pierre luc; ortiz-gagn'e, satya; rousseau, marc-andre; buckeridge, david; ghosn, joumana; zhang, yang; scholkopf, bernhard; tang, jian; rish, irina; pal, christopher; merckx, joanna; muller, eilif b.; bengio, yoshua title: covi-agentsim: an agent-based model for evaluating methods of digital contact tracing date: - - journal: nan doi: nan sha: doc_id: cord_uid: javbnjrg the rapid global spread of covid- has led to an unprecedented demand for effective methods to mitigate the spread of the disease, and various digital contact tracing (dct) methods have emerged as a component of the solution. in order to make informed public health choices, there is a need for tools which allow evaluation and comparison of dct methods. we introduce an agent-based compartmental simulator we call covi-agentsim, integrating detailed consideration of virology, disease progression, social contact networks, and mobility patterns, based on parameters derived from empirical research. we verify by comparing to real data that covi-agentsim is able to reproduce realistic covid- spread dynamics, and perform a sensitivity analysis to verify that the relative performance of contact tracing methods are consistent across a range of settings. we use covi-agentsim to perform cost-benefit analyses comparing no dct to: ) standard binary contact tracing (bct) that assigns binary recommendations based on binary test results; and ) a rule-based method for feature-based contact tracing (fct) that assigns a graded level of recommendation based on diverse individual features. we find all dct methods consistently reduce the spread of the disease, and that the advantage of fct over bct is maintained over a wide range of adoption rates. feature-based methods of contact tracing avert more disability-adjusted life years (dalys) per socioeconomic cost (measured by productive hours lost). our results suggest any dct method can help save lives, support re-opening of economies, and prevent second-wave outbreaks, and that fct methods are a promising direction for enriching bct using self-reported symptoms, yielding earlier warning signals and a significantly reduced spread of the virus per socioeconomic cost. dct, however, is not free of disadvantages. due to a wide range of privacy concerns about smartphone communications, dct suffers from poor adoption by the public [ ] . additionally, most countries using dct have adopted a simple form which informs and recommends quarantine to all digitally-recorded contacts of cases confirmed through testing. we call these systems binary contact tracing (bct) because they recommend users either to quarantine or not (binary decisions) based on whether a past contact took place with a confirmed index case (binary input feature). covid- is a challenging disease to mitigate with bct for two primary reasons (i) bct currently relies on reverse transcriptase pcr (rt-pcr) tests which have high disease phase-dependent false negative rates. to make it worse, these tests are expensive, and may require a long time to obtain results [ , ] (ii) the majority of transmissions of sars-cov- take place before the infector shows any symptoms, thereby reducing the likelihood that a potential infector would have been tested before transmission [ ] . we observe that there are a wide variety of clues potentially available to a contact tracing app that would allow for non-binary, individualized recommendations, thereby offering significant improvements to bct. we call these methods feature-based contact tracing (fct), and hypothesize they could provide an important and effective means of reducing the spread of the disease, perhaps even more effectively than bct at lower adoption rates. recognizing this potential, we propose covi-agentsim -a software testbed to design, evaluate and benchmark dct methods using cost-benefit analysis in terms of lives saved, reduction in effective reproductive number (r t ) of the virus, disability-adjusted life years (dalys) averted, and productive hours lost. by using an agent-based model (abm) as the foundation of this testbed, we are able to simulate a rich set of individual-level input features. covi-agentsim can be adapted to a region of interest by providing appropriate demographics and contact pattern information for that region. it can then be calibrated to match published data for that region of interest. we calibrate covi-agentsim to reproduce covid- case and hospitalization data for the region of montreal, canada. in order to ensure the simulator is a fair and reliable testbed, we also check that the relative ordering of methods is preserved across wide ranges of simulator parameters and over several metrics. we propose a simple rule-based fct method which leverages individual-level features to make non-binary recommendations, and compare this approach to bct and compare both to no-dct via cost-benefit analyses. we find that both bct and fct methods are able to reduce spread of the disease, and our results echo those of recent research [ ] suggesting that dct methods can still save lives even at low adoption rates. we find evidence that fct approaches, which leverage rich individual-level features to make graded recommendations, are promising for improving dct even further. additionally, by stratifying dalys over age groups, we observe the most dalys averted per person for those over years of age, even with low app adoption rates in that age group, thus showing the protective effects of younger people using dct. these results are conservative in estimating the benefits for the most vulnerable populations, since we randomly assign dct app usage proportional to smartphone usage, yet more vulnerable people (or those close to more vulnerable people) may be more likely to use dct. our results thus strongly support the usage of dct methods as a component of effective public health strategies, and we hope covi-agentsim will be a useful resource for development, benchmarking, evaluation, and improvement of dct methods. agent-based models (abms) are frequently used to study geospatial and other patterns of disease which vary at an individual level (e.g. [ , ] ). they are thus often useful for studying differential effects of policy decisions and interventions on different subgroups of the population; for instance [ ] use an abm to study which post-lockdown measures most effectively protect the most vulnerable, in terms of disease incidence, mortality, and icu occupancy, and [ ] and [ ] study patterns of covid- spread in different representative locations (university, workplace, and highschools), and the impact of different intervention scenarios in each of these locations. one of the interventions studied by these works is dct, and both find evidence that it can reduce icu admissions and help curb the spread of the disease. abms are also useful for modeling the impact of outlier individuals or events such as super-spreading, e.g. [ ] , which are not easily captured by mathematical models of population-level spread. several works have studied the use of smartphone apps in epidemic management, e.g. [ , ] , and some work has begun specifically on covid- . for instance, ferretti et al [ ] propose a mathematical model of infectiousness based on early epidemic data in china and compare binary contact tracing to manual tracing. they quantify the contribution of different transmission patterns (infection through symptomatic individuals, presymptomatic individuals, and from the environment) and the requirements for effective contact tracing. assuming a -day delay in notification (and thereby quarantine of the individual), the authors demonstrate mct could not bring r t below and hence, could not control the epidemic. instantaneous contact tracing by a digital tracing application on smartphones could do so (r t < ). shamil et al. [ ] follow a similar approach, but with an abm taking into account realistic contact patterns, studying the potential efficacy of bct in controlling the spread of the disease. they find strong dependence of the efficacy of digital contact tracing on app adoption, suggesting that bct alone is insufficient to control a pandemic unless over % of the population is using the app. [ ] find similar results, emphasizing however that even at very low adoption rates dct is able to save lives. this suggests that dct should be considered an important component of public health strategy for mitigating covid- . we find similarly that bct and fct are unlikely to control a pandemic on their own at low adoption rates (see section ) , showing that even at % adoption rate these methods must be combined with other strategies to contain the disease. perhaps most similar to our work is hinch et al. [ ] , who also propose an open-source abm which allows manual and digital contact tracing methods to be compared, with benefits stratified across age. developed concurrently to our simulator, similarities between the two approaches highlight the importance of several design decisions made independently but converging to the same solutions, e.g. the use of abms, a python interface, and the need for empirical testbeds of this nature. a key difference in our simulator is the rich set of individual-level features (including e.g. pre-existing medical conditions), which allow us to benchmark feature-based contact tracing methods, and also allow for stratification over a larger variety of subgroups. the cost of this level of detail is computation; our simulator models smaller populations at higher fidelity for the same computational budget. we perform a scaling analysis (appendix k) in order to ensure the dynamics we produce on these smaller populations are representative of larger populations. however, the simulator of [ ] may be preferable for studying binary-only contact tracing methods, or when faster computation is needed relative to individual-level detail. the simulator is an agent-based compartmental model [ ] implemented in python [ ] and c [ ] , using simpy [ ] , a process-based discrete-event simulation framework. for each agent the simulator tracks transitions through susceptible, exposed, infectious, and recovered (seir) states, as well as a variety of individual characteristics, including pre-existing medical conditions, self-reported symptoms, and test results. this rich set of individual features enable the simulation of contact tracing apps which make use of such features. at the same time, we parameterize our simulator using real-world data when available, and when no data is available we make weak assumptions and investigate the sensitivity of our results with respect to these assumptions (see section . ). covi-agentsim simulates the spread of the sars-cov- virus in a city through contagion events between agents. simulator is initialized with a synthetic population along with the mobility and contact patterns informed by census and empirically derived data. it can be configured easily for any region of interest (see appendix f). each agent i in the simulation has individual characteristics (e.g. age, sex, pre-existing medical conditions) denoted x i . dwelling characteristics, workplace association, and contact patterns are derived from age-stratified surveys and empirical studies (see appendix e. ). at start of a simulation, a fraction α of the agent population is randomly exposed to covid- . infection spreads through communities via contagion events at households, workplaces, schools and other random locations. agents move around the city transitioning between locations like households, workplaces and other locations. the pattern of each individual's mobility (i.e., which locations they visit, how often they visit them, and how they interact with other individuals at these locations) is set according to [ , ] . while at a location, agents sample contacts according to age-stratified contact matrices derived from [ ] . a detailed discussion of agents' mobility patterns and location dependent contact pattern is provided in appendix e. figure compares simulated age-stratified contact patterns with surveyed matrices. virus transmission takes place anytime an infectious and a susceptible individual are within meters of each other for at least minutes, thereby possibly transmitting viral load to a newly infected agent. we model the probability of covid- transmission p according to [ ] . borrowing notation from the authors, briefly, this probability is proportional to age-dependent susceptibility s a of the susceptible agent with age a, location-dependent multiplicative factor b n (for location n), symptom status (asymptomatic, mild, severe) dependent ratio a s of the infectious agent, and a surrogate for cumulative viral load (evl) transmitted from the infectious agent for duration δt. we discuss evl in the next section. a proportionality factor r is used to calibrate the reproductive number of the disease spread. for the sake of completeness, a mathematical form of this transmission model is presented in eq and eq . where p (δt, s a , a s , n) is the probability of the contagion event. we use the same values for constants as used by authors in their open-sourced code . after such a contagion event, we sample for the infected agent the variables controlling the course of the disease, including symptoms and severity. additionally, we sample a time-series of a quantity proportional to viral load as measured by [ , ] , which we call effective viral load ev l; this quantity represents the interaction of the virus with the host's immune system. we further discuss (ev l), its dependence on age and preexisting conditions, and how it is sampled in appendix b. a model for sampling symptoms for each agent conditional on whether the agent has cold, flu, or covid- is discussed in details in appendix j. in covi-agentsim, we model rt-pcr testing and its relation to contact tracing applications. as discussed earlier, the disease trajectory for each agent depends on their age and preexisting conditions. thus, there are agents who experience symptoms on a spectrum from none (asymptomatic) to severe: agents who experience more severe symptoms are more likely to seek an rt-pcr test. given the limited testing capacity at the onset of the pandemic, we model a testing facility with a fixed maximum capacity. for an infectious agent, the outcome of a test is modeled according to disease phase dependent false negative rates as per [ ] . as an example, days after a sars-cov- infection, the infected agent will have a false negative rate of %. upon receiving a positive test result, the agent is put to self-isolation for d max days with a probability of not following such interaction modeled via dropout parameters. we discuss details about testing in appendix c and hospitalization in appendix d. unlike existing covid- abms, our agents are designed to follow varying levels of contact patterns. for example, number of contacts sampled by an agent in level k at location l corresponds to a fraction (γ l k ) reduction in contacts with respect to pre-pandemic number of contacts for that location. these pre-pandemic number of contacts are available through surveyed studies [ ] which we discuss in appendix e. thus, if there are n + such levels ranging from , , ..., n, an agent at location l in level will draw contacts using pre-pandemic number of contacts (γ l k = ), and an agent at location l in level n is in quarantine i.e. samples no contacts (γ l k = ). fraction γ l k for intermediate levels k ∈ { , ..., n − } are obtained by interpolation scheme (e.g. linear) between γ l and γ l n . our choice is motivated by the desire to have a simple model grouping together the effect of choices individuals can make to reduce their likelihood of becoming infected like washing hands, wearing a mask, and physical distancing. each of these levels are further associated with a dropout parameter that represents the fraction of time an agent in level k will drop to level , returning to a higher level of activity (specifically, pre-pandemic numbers of contacts). covi-agentsim can be configured to quarantine individuals due to any of the following triggers (a) confirmed positive test (b) self-reporting of symptoms, (c) recommended by the app, and (d) household member of any of the above cases. additionally, in order to model population-wide mobility restrictions we use a bernoulli distribution with parameter β ∈ [ , ] to sample contacts. thus, an agent that usually draws contacts will now draw β * contacts on average. this modeling choice is a simplification of the varying degrees of government imposed mobility restrictions, controlled by a population-wide β. dct methods rely on capturing high-risk contacts and communicating risk information. the population-level app adoption rate is a key parameter because the fraction of contacts captured by this system will be proportional to the square of the app-using fraction of the population. to distribute apps throughout our simulated population, we use an age-dependent distribution across smartphone owners. we use an age-based breakdown of smartphone users as in [ ] , and use an u p t ake parameter to vary the population-level adoption rate. if an agent is assigned an app, there is a provision to report individual characteristics like age and preexisting conditions as well as daily symptoms. we further model dropout rates for reporting symptoms as well as a "drop-in" rate for falsely reporting symptoms to account for malicious users and other confounding factors that produce symptom inputs, such as colds or flu. when app users i and j have a significant encounter on day d (which can lead to contagion) the ct method can exchange messages between them, on the same day or later. we have considered two kinds of messages: a contact message exchanged on day d allows i and j to keep track of the encounter event (such as when it happened) as well as a handle allowing them to send each other messages later (potentially via some server), while minimizing breaches in privacy. a contact message could also contain information about the current degree of contagiousness risk they pose to each other on day d. later, if i observes new clues suggesting their contagiousness on day d was actually higher, i can send an update message to j, with information which can help j update their own evaluation of contagiousness. we denote m d i,j (t) the risk message sent on day t by i to j regarding their encounter on day d. if t = d this is the initial (contact) message, whereas for t > d this is used to update the information j will have at day t about their encounter with i on day d. note that i may send multiple update messages to j, as they acquire more information about having been infectious on day d. additionally, we restrict the frequency of communication: if t is the time of the last risk message sent by i about some encounter, the next message is sent the clues which agent i may use to come up with its risk messages include symptoms, test results, pre-existing conditions and received risk messages. the way to come up with these risk messages, as well as how to adjust behavior based on estimated risk, is specified by the ct method, such as those described below. in digital contact tracing we have two goals: to reduce the individual's spread of disease (by recommending a reduction in mobility to risky individuals), and to inform contacts of additional risk. agent's adherence to a recommendation level k entails sampling location specific contact patterns according to that level (see section . ). we denote agent i's behavior level on day d by ζ i d such that for a total of n + behavior levels, ζ i d ∈ { , , ..., n}. determination of this recommendation level is done via a risk estimator that uses a rich suite of features to evaluate agent i's risk history on day t. that risk history is denoted r i t , where we constrain risk levels to be non-negative integers with a maximum value of r max . we use r i t,d to denote estimated risk of agent i for day d such that t − d max < d < t. if an agent i had an encounter with an agent j on day d such that t − d < d max , r i t,d is sent to the past contacts as a risk message m d i,j (t) = r i t,d if j was a contact of i on day d (see section . ) . this determines what information is available to agent's contacts such that they may modify their own behavior or to propagate risk further. useful notations we use n (i) to denote a set of agent indices that had at least one digitally recorded contact with agent i in the past d max days. further, we use the colon symbol (:) to iterate through all possibilities for the variable at that position. for example, m d i,: (:) represents risk messages from agent i to all agents j ∈ n (i) for encounter on day d, if there was one. similarly, m : i,: (:) represents risk messages sent by agent i to agent n (i) within the past d max days. we the most common class of digital tracing methods, binary contact tracing (bct), can be viewed as a binary classifier with final decision (behavior recommendation) being whether the agent should quarantine or not. most often, the decision boundary is simple: did the individual had a recent contact with someone who received a positive rt-pcr test? we refer to these methods as test-based bct, which we describe formally next. in test-based bct method, for an agent i with test d i = + , agents j ∈ n (i) are notified and recommended to quarantine themselves as discussed in section . we call this particular method bct because it only affects the immediate contacts (and their household members) of individuals with positive test results; in section . we show results for this baseline, bct , where second order contacts may also be quarantined. we describe a class of methods we call feature-based contact tracing (fct), which leverage the potentially rich set of features available on a smartphone to make graded recommendations. as discussed earlier, we make use of following available information on an app to update an agent i's estimated risk history r i d on day d: i,: (:), and (e) previous estimated risk history r i d− . the agent's estimated risk for the past d max days is then propagated as discussed in section . . in addition to risk estimation, the agent's behavior is set to a level ζ i d based on the estimated risk for that day i.e. r d,d . in this section, we describe one such rule-based implementation of fct -heuristic-fct which forms the basis of our experiments. with the help of available information about how covid- spreads and manifests itself in an individual in the form of symptoms, we designed a rule-based fct method. specifically, for every available aforementioned feature type, we determine the agent's risk history for the past d max days. the agent's risk history on each day d is taken as the maximum across these per-feature estimated risks. broadly, heuristic-fct uses the following rules: • test results, t i d : the agent's risk is set to r max = r max if there is a positive test result in the past d max days. this rule takes priority over any other rules (assuming that a positive test gives us maximum certainty about being in the top risk level). • symptoms, s i d : we identify three categories of symptoms based on how indicative they are of covid- . the presence of a highly informative symptom in s i d results in a high risk level r high ; a moderately informative symptom results in a moderate risk level r moderate ; and a mildly information symptom results in mild risk level r mild . we assign these risk level values for the past d max / days in r i d , similarly to [ ]. • risk messages, m : i,: (:): the risk of an agent receiving a risk message r max is estimated to be ρ = r high , while one receiving r high is estimated to be at ρ = r moderate , and so on. the rationale is that the level of risk decreases rapidly as we move away from one agent to its contacts, to the contacts of these contacts, etc. we then compute the duration of time when agent i could have been infectious if this contact had caused their infection as d + < d < d. thus, we set the agent's risk to this value ρ until d days in the past. • other rules: there are some rules that are designed to override the above rules. for example, an agent with a negative test on day d is assigned a risk of from that day onwards. further, an agent is estimated to be at risk level if there had been no positive test in d max days, no symptoms in the last d max / days, and no high, moderate of medium risk messages in a certain past time horizon. we present a formal description of this risk estimator in appendix i. in this section we seek to provide following evidence: ( ) our simulator is producing a reasonable approximation of real-world covid- dynamics, and ( ) it is a reliable testbed for comparing contact tracing methods. we address ( ) by checking the output epidemiological characteristics match published literature (see figure and table ), and by checking that the hospitalization and mortality statistics are well-aligned with those found in real world data ( figure ). we address ( ) by performing a sensitivity analysis of the simulator to a wide range of parameters, and checking that the ranking between contact-tracing methods is preserved over these settings, for different metrics. we calibrate the simulator so that the observed statistics in the simulator are similar to what is observed for covid- , plotting seir curves in and comparing statistics to published data in . simulator reported numbers are average µ in days and corresponding standard deviation σ, computed over random seeds on a population size of . it is important to note that these statistics are a result of the many processes happening within the abm; there are no parameters that specifically encode these values. we run simulations using random seeds and plot the mean and standard deviation of the hospitalization and mortality statistics over days. we compare these results to the real data reported in montreal from the same time period. our simulations use , people and we report results as a proportion of population. we see that under these settings the proportion of the population that is hospitalized or deceased aligns with the data from montreal (see figure ). a primary contribution of this work is the creation of an abm which can act as a testbed for comparing covid- contact tracing methods. while the majority of the parameters in our abm are chosen according to published literature, much about covid- is still unknown or uncertain. for this reason, we conduct a sensitivity analysis of some key parameters which exhibit high variance across different studies. specifically, we study the impact of the asymptomatic proportion of the population (see figure ), which is a difficult to measure without widespread serological testing, and the initially infected proportion of the population ( figure ). we observe that the relative efficacy of different methods (i.e. the ranking of methods) holds across a wide range of settings, a desirable characteristic for a comparison testbed. we compare against the real hospitalization and mortality data (as a percentage of population) during the first wave of covid- in quebec. it is important to note that we only report a post-lockdown scenario. we report results with our simulator from runs with a population of , people. figure : sensitivity to asymptomaticity: these figures show a comparison between contact tracing methods (including the no tracing setting) and varying the proportion of the asymptomatic population between and %. we plot two views of the same data with different y-axes: fraction infected andrt. the relative performance between the methods are consistent across rates of asymptomaticity and choice of y-axis. we report the mean and standard deviation across seeds with a population of people. on the right, we see a counter-intuitive result: thert at the end of the simulation is lower for simulations which started with a larger initially infected population. this can be explained by noting thatrt in some sense reports the instantaneous change in rate of spread of the disease while the fraction infected reports the absolute extent of the spread. crucially, the ranking between the methods remains similar across choice of visualization and initially infected population. we report the mean and standard deviation for runs under each condition with a population of people. we focus our analysis on the region of montreal for the period between march and june. our agents are initialized with dwelling and workplace characteristics informed from publicly available census data [ ] . we use n + = recommendation levels γ i , with γ = (full pre-pandemic mobility), γ = (full quarantine), γ as per post-lockdown contact patterns reported in [ ] , and rest of the levels as γ k = γ k+ / . given a memory intensive infrastructure required for managing risk messages, we run simulations on a smaller population size of people. we initialize each simulation with . % of the population as infected ( infections), and run different seeds for each value of β ∈ { . , . , . , ..., . } resulting in a total of runs. these values are chosen so that we can get estimates ∆r of the change in the reproduction number of the virus, as discussed in section . . we compare the heuristic-fct method proposed in section . with the test-based bct method discussed in section . , and a no tracing scenario. the scenario of no tracing corresponds to agents initialized at level (post-lockdown contacts with some restriction advised) instead of level (pre-pandemic contacts), in order to compare our methods in the context of the scenario where economies are gradually reopening. we use test-based bct and test-based bct to distinguish between the two variants when necessary, otherwise we use test-based bct to imply test-based bct which is the method being considered by most of the countries. we compute the following metrics to evaluate various scenarios: • average number of contacts per day per human (c): we empirically compute the average number of daily contacts per agent in simulation. • proxy r (r): we use an empirical calculation to estimate the reproductive number r, we call this estimater. at any timepoint in the simulation we may approximate r t byr t , by computing the infection tree and taking the ratio of number of children number of parents , where parents are recovered agents. this ratio gives an approximate rate of growth of the tree. we user t at the end of the simulation as ourr. • daily cases (%): percentage of population exposed, i.e., new cases on any given day of a simulation. • cumulative cases (%): percentage of agents in exposed, infectious, or recovered state up until a particular day of a simulation. • prevalence (%): percentage of population in infectious or exposed state on any given day of a simulation • incidence (%): number of agents exposed per susceptible agents on any given day of a simulation. it is also referred to as attack rate. as the contact tracing methods proposed in this paper change agents' behaviour to varying degrees, it is crucial to compare different methods across similar social mobility restrictions. for example, bct can only use levels and n while fct can use all levels from to n. therefore, at the same value of β, bct will likely under perform as it can not reduce infections by using intermediate levels. thus, for a fair comparison of bct with fct, we run simulations with varying values of β ∈ ( , ) and match them for average number of contacts. to compare the performance of different methods for the same mobility restriction we empirically compute pairwise difference in meanr for a fixed number of contacts c. this is achieved by obtaining the performance in terms ofr of a method across a spectrum of values of c (by varying β), and fitting a gaussian process (gp) regression [ ] to obtain a functional dependence for each method between c andr. we denote this fitted regression for method a byr gp a . to compute the advantage of method a over b, we find note that r = is the threshold between exponential growth and exponential decay of the virus and serves as a good point of interest when comparing methods since the objective is to choose a method which brings r below , all else being equal (e.g., general restrictions on social mobility). figure shows a comparison of the gp regression fits between aforementioned dct methods at % adoption rate, and a no tracing scenario, across a range of values of c. we observe that heuristic-fct significantly improves over test-based bct by reducingr by . %. of note is the region around c = . ± . wherer = . for no tracing. we compare the performance of dct methods in this region to set our comparisons in the context of current scenarios (partial lockdown) where government-imposed restrictions keep r under control. to further investigate the reason for the improvement of heuristic-fct over test-based bct, we peek into the simulations in the concerned region of c. figure shows that on average, heuristic-fct exhibits lower incidence as well as prevalence on any given simulation day. this is expected as heuristic-fct makes use of far richer features as compared to binary test results used by test-based bct to evaluate individual's risk of infecting others. finally, due to network effects, it is likely that adoption rate plays an important role in the performance of dct methods. thus, we evaluate dct methods at various adoption rates. to do this, we run simulations of dct methods at different adoption rates in a similar way as explained in section . , and concern our analysis on simulations chosen according to the selection criterion described above. figure shows the performance of the considered dct methods at different adoption rates. as expected, the performance diminishes with lower adoption rates, for all the methods. however, we observe that heuristic-fct retains its advantage over bct methods even at the lower adoption rates. at the same time, we also note that poor adoption brings both the dct methods close to no tracing, figure : pareto front. we compare dct methods at % adoption rate, and a no tracing scenario. for each method, a gp regression is fit as discussed in section . , approximating a trade-off between mobility and spread of disease. we plot the mean fitted function along with % confidence intervals. relative to the no tracing scenario, we observe a statistically significant . % reduction inr by heuristic-fct as compared to . % by test-based bct method. figure : case curves. we investigate the dynamics of the simulations chosen as per the criterion mentioned in section . to compare the performance of dct methods at % adoption rate in the context of partial-lockdown. shown are the mean with one standard error band of the metrics described in section . . simulations under heuristic-fct exhibit lower attack rates (incidence) as compared to test-based bct method, thereby explaining the advantage visible in figure . thereby making it more difficult to measure significant advantages over the partial lockdown scenario. thus, we argue that by continuity while at any adoption rate dct methods can save lives, adoption rate is crucial for their efficacy. figure : effect of adoption rates. performance of dct methods is heavily dependent on adoption rates. however, heuristic-fct retains its advantage over test-based bct across this spectrum. covid- has been a challenge for health agencies and economic policy decision makers alike. countries around the world have taken unprecedented measures to prevent the collapse of health and economic welfare of people. yet, at times, these two objectives have seemed to be at odds with each other in efforts to contain the pandemic. therefore, we acknowledge that the evaluation of dct methods should also stand on sound assumptions of utility maximization in economic theory. in this section, we attempt to relate simulation dynamics to economic outcomes that policy makers can use for decision making. to assess the socio-economic burden of covid- , we examine the following metrics: (a) disability-adjusted life years (dalys) averted [ ] , a measure of lost years of healthy life, and (b) temporary productivity loss (tpl), a measure of economic cost to society of restrictive measures. of particular interest is the trade-off between these two measures. we use tpl per daly averted to compare the cost-effectiveness of dct methods with respect to the no tracing baseline. this can be thought of as an incremental cost-effectiveness ratio (icer), which answers the following question: how much more does each unit of additional benefit (in averted dalys) cost with respect to the no tracing baseline? a breakdown of the methodology used to calculate dalys and tpl can be found in appendix l. one assumption made in computing tpl is that total foregone work hours due to quarantine are scaled by a factor of . [ ] to account for the proportion of agents able to work from home. to assess the impact of the aforementioned ct methods on dalys and tpl, we run simulations of agents for each method. for a reliable economic analysis, it is necessary to have data on the full trajectory of simulations reaching a post-epidemic steady state comprised of agents that are either susceptible or recovered. such a trajectory would help assess whether the dct methods actually avert the loss of life years, or simply delay them. since ct methods are used to stop individuals from spreading the disease, it is important to know whether the ct methods have successfully reduced the overall proportion of individuals, or if they have simply delayed these infections. if the simulations are only run for days with . % infections seeded at the start, then the epidemic has still not reached a post-pandemic steady state, resulting in a possible overestimation of the benefits of the aforementioned ct methods. thus, we run longer simulations of days with % infections seeded at the start of simulations. this particular choice lets us draw preliminary insights into the cost-effectiveness of ct methods without having to scale up the simulations which are extremely compute intensive. as a first step towards understanding simulation dynamics in terms of healthcare and economic costs, we compute dalys averted and tpl for each scenario considered in section under the conditions described above. we use no tracing as a reference scenario to independently evaluate differential benefit of dct methods over doing nothing. icer for no tracingunder the assumptions discussed at the onset of this section, our experiments (results in table ) suggest that heuristic-fct saves almost six times more dalys than test-based bct, a significant number of life years saved. however, we note that the tpl of implementing test-based bct is % that of heuristic-fct: higher proportions of agents are quarantined under heuristic-fct. finally, we note that the cost per daly averted ofheuristic-fct is % of that of test-based bct. thus, the cost per healthy year of life saved by heuristic-fct is lower than the test-based bct method. icer for test-based bct to quantify the cost-effectiveness advantage that heuristic-fct provides over test-based bct, we also calculate the icer of heuristic-fct over test-based bct. on average, heuristic-fct saves ( . − . ) = . more dalys than test-based bct. however, it costs ($ k − $ k) = $ k more as well. therefore, the icer of heuristic-fct over test-based bct is k . = $ k per daly averted. dalys per age group since there is evidence in the literature that covid- disproportionately affects the elderly [ ] , we stratify the dalys per person by age in figure . it is highest among people aged - years for both ct methods, which is consistent with the literature. it is worth noting that the mean of heuristic-fct performs at least as well as test-based bct across all age ranges, and notably better for agents aged and over. figure : impact of different ct methods on dalys, binned by age group. dalys per person are total dalys per age group over the size of each group. heuristic-fct consistently outperforms test-based bct across older age groups, most vulnerable to covid- . we attempted to create an easily configurable platform to assist in evaluation of dct methods and variants thereof. further, we proposed an fct method that has a potential to improve upon bct methods, that is widely used in practice. however, we would like to point out some of the limitations our work. first, although most of the parameters in covi-agentsim are informed from published literature, there are assumptions we had to take in the absence of available data. in this paper, we have enlisted most of these parameters and corresponding references that informs them. it is important to note that as more about covid- will be known these parameters are subjected to change, thereby affecting results in section . additionally, we introduced intermediate levels of user behavior to contrast fct with bct. this is done with the help of introducing a factor γ n for level n that represents fraction reduction in number of contacts relative to pre-pandemic number of contacts (γ ), empirical estimates of which have been widely used in epidemiological modeling. to obtain intermediate levels, we used interpolation such that γ k = γ k+ / . although it is trivial to experiment with various interpolation schemes, in the absence of user-behavior research, there is not enough that can be done in this regard other than providing the sensitivity analysis of the parameters involved therein. in addition to this, we foresee the use of such assumptions to be translated into government policies such that resulting number of contacts can approximate these assumptions. second, our modeling framework of fct relies on certain assumptions of technology which might not hold in practice. for example, our assumptions of proximity detection using bluetooth signals (appendix g) might be unrealistic. however, [ ] 's work on improving the reliability of bluetooth signal can be a way to address this. further, we assume the app to be active (in foreground) to be able to communicate with nearby phones all the time, an assumption that might not hold depending on the app design. there are a variety of such technological and ethical considerations which are discussed in [ ] to design a successful peer-to-peer fct app. covi-agentsim incorporates most of the technological assumptions in [ ] , however, with additional effort, other assumptions can also be incorporated in covi-agentsim to evaluate dct methods in different settings. third, we designed the heuristic-fct method using rules that were informed by domain knowledge about covid- 's spread characteristics. at this point, we acknowledge that there should be room for improvement in these rules which can be brought upon by amalgamation of ideas in disciplines such as epidemiology, user behavior research, computer science, and statistics to name a few. alternatively, machine learning methods could be used to learn such rules. thus, we think that a unified mathematical framework to analyze fct methods might help further in development of better fct methods. this work presents covi-agentsim, a simulation testbed for evaluation of dct methods. covi-agentsim is an agent-based compartmental model that is initialized with a synthetic population sampled from the census data. daily activities as well as interactions for each agent are sampled according to the empirically derived contact matrices. we calibrate covi-agentsim to approximate the spread of covid- virus to the region of montreal, however, the simulator can be easily configured for other regions via change of an appropriate configuration file. finally, we propose the fct class of contact tracing methods that utilize a richer set of input features as compared to bct methods (which rely on binary signals like presence or absence of a positive test result). in doing this, we aim to provide infected individuals with a warning signal earlier than bct methods. to put fct in practice, we designed heuristic-fct which uses hand-designed rules to inform an individual's risk of infection and infectiousness to others. our empirical results show that heuristic-fct results in . % improvement in r t over bct methods, and both the methods themselves provide a significant improvement over a partial lockdown scenario. experiments with varying adoption rates suggest that the efficacy of dct methods is heavily dependent upon adoption rates. it is, however, observed that heuristic-fct retains its benefit over test-based bct method across the adoption rate spectrum, but this advantage was not statistically significant in the face of very low adoption rates, at the scale of our simulations. using an agent-based compartmental model as the foundation of this testbed allows us to simulate a rich set of individual-level features, which we show can potentially be leveraged by dct methods to improve over the existing bct methods. we hope that the baselines established in this work will encourage and enable the informed development of dct methods as a first step in their responsible deployment as an epidemic intervention tool, potentially saving lives at lower economic cost during deconfinement and/or second-wave prevention. finally, this work joins a growing body of work in considering novel methodologies for rigorous evaluation of interdisciplinary technologies. epidemiology is fundamentally an intersectional science, touching sociology, biology, behavioural psychology, geography, political science, ecology, mathematical and computational modeling, and many other fields, in a society which is increasingly digitized and globalized. by working together across fields, with careful empirical study, we have hope in dealing with the important issues we face. a major direction for future work is to benchmark a wider variety of ct methods, including probabilistic and machine-learning based methods which could make even better use of the features our simulator provides than the heuristic-fct proposed here. the data generated by our simulator are potentially of interest for training such models to estimate individual-level characteristics which are predictive of the spread of the disease. our cost-benefit analysis using dalys and tpl is a first step towards an integrated framework to help policy makers in their decision process. we see imbuing economically sound decisions in our simulated agents as a step in creating an integrated framework for richer evaluation of dct methods. although covi-agentsim is designed to evaluate dct methods, we foresee directions for the simulator to investigate the impact of a gamut of non-pharmaceutical interventions on containing covid- . for example, with some work and expertise in manual ct methods, one can compare and evaluate various variants thereof. another example is to analyse various covid- testing strategies in conjunction with dct methods. studies of this nature could potentially help public health agencies as well as policy makers in their decision process. a far cry, though worth mentioning, is the fact that covi-agentsim has essential components for simulating an outbreak, thereby enabling adaptation to other infectious diseases like influenza or tuberculosis. [ ] giulia cencetti, gabriele santin, antonio longa, emanuele pigani, alain barrat, ciro cattuto, sune lehmann, and bruno lepri. using real-world contact networks to quantify the effectiveness of digital contact tracing and isolation strategies for covid- pandemic. medrxiv, . [ ] yunhwan kim, hohyung ryu, and sunmi lee. agent-based modeling for super-spreading events: a case study of mers-cov transmission dynamics in the republic of korea. a test, this agent is added to the queue. for different symptom severities, we assign a different probability of seeking a test. at some points during the pandemic, montreal experienced a restricted testing capacity. in order to model that setting, we limit the daily testing capacity to a proportion of the population (generally set to . %). to determine which people get tested under such a restriction, we allocate tests to people with more severe symptoms and app-based recommendations. after a test has been conducted, there is a delay before results are returned ( days in our experiments). during this period, the individual who is being tested is isolated, and if the test returns positive then an additional days of isolation is recommended. any quarantine which is applied to the person receiving the test is also applied to other members of their household. we adopt a simple model of hospitalization and interaction within them. to simulate post-lockdown scenarios, we assumed no infections in hospitals. we adopt a probabilistic model of hospitalization where likelihood of being admitted to the hospital or icu depends on symptom severity and age. mortality rates are conditioned on age-group following data from quebec public health (date?) [ ] . the duration of a hospitalization, likelihood of requiring critical care, and mortality rate given critical care by age follow nationally conducted surveys available publicly . the number of hospitals is defined in relation to the population, using the same ratio of hospitals to people as are found in quebec ( . hospitals per , people). the number of hospital beds per capita, and occupancy ratios are taken from , and the number of icu beds per capita and occupancy ratios are taken from . hospitals are staffed by doctors and nurses, who are modelled as people with a profession that requires they work at the hospital and have protected interactions with patients. literature on the link between underlying medical conditions and covid- encompasses risk of being hospitalized due to covid- , risk of severe complications (e.g. mechanical ventilation) and risk of mortality. preexisting medical conditions were used to model: ) hospitalizations and deaths outcomes and ) conditional probability of symptoms. to model hospitalizations and deaths in the population, we used risk ratio estimates from studies focusing on risk of hospitalisation and risk of death as outcomes. risk ratios adjusted for other individual characteristics were preferred over crude estimates. to inform the hospitalisation and death outcome model from the simulator, we selected the following risks ratios: diagnosis of heart disease, . [ ] , stroke history, . [ ] , asthma with recent oral corticosteroid use, . [ ] , copd, . [ ] , cancer (excluding haematological malignancy), . [ ] , diabetes, . [ ] , obesity stages and (body mass index (bmi) = - . kg/m ), . , obesity stage (bmi > kg/m ), . [ ] , ckd, . [ ] , immuno-suppressed because of asplenia, . and because of immunosuppressive conditions (excluding asplenia and haematological malignancy), . [ ] . given the uncertainty on the association between smoking and covid- prognosis [ ] , we did not consider this risk factor in the simulator. in this section we describe contact patterns in pre-pandemic situation. scenarios of lockdown and contact patterns in intermediate behavior levels are a modification by a factor γ n as discussed in the section . we use empirically derived matrices in from [ ] for canada that we further project on to montreal's demographical structure. projection of country-wide matrix to a regional matrix is done via method described in [ ] . however, abm can be configured to bypass the step of regional projection of contact matrices. given a discrepancy between population wide mean daily contacts inferred from projected matrices and montreal's number of contacts reported in a survey [ ] , we scale the projected matrices appropriately. we ran simulations with no infected agent i.e. α = to observe the pre-pandemic contact patterns to yield simulated contact patterns in this section. additionally, the simulated contact patterns shown in this section are descaled with the same multiplicative factor that is used to scale the projected matrices. as discussed in the main section, agents are grouped into houses according to census data [ ] . thus, we simulate dwelling characteristics of the city of montreal. however, it can be configured easily for any other city by using appropriate parameter values. we consider house of sizes ranging from to . age distribution of agents living solo also follows census data. further, house sizes ranging from to consider three broad categories of dwelling characteristics -(a) couple with x kids, (b) single parent with x kids, (c) random allocation, where x represents number of kids required to complete the house size. for example, for a house with single parent and of size , x = . the distribution of these characteristics also follow from census data. finally, we also consider senior residencies where a proportion of agents above age live. we inform this proportion from the census data as well . we explicitly model older adults living in assisted care resulting in oversampling of contacts in that age group. we discuss it further in the appendix e. as a result of housing allocation discussed above, we yield a contact pattern as shown in figure e . . we make two observations (a) there is an oversampling of contacts towards the older age groups: it is because older agents grouped in collectives like senior residencies are modelled explicitly. this choice was motivated from [ ] which suggests inclusion of collectives in proper response to the covid- pandemic. (b) a slight discrepancy we observe in the intensity of the main diagonal is due to insufficient social gatherings at households. we consider an age-dependent workplace allocation such that agents in each age group have a probability of attending a school or a workplace. we consider schools for the following age groups (a * ) - years old (y.o) (b) - y.o (c) - y.o (d) - y.o (e * ) - y.o: (f * ) - y.o (g * ) - y.o, where * marks the age group in which only a fraction (informed by census data) of agent population was allocated schools. further, we assume % employment so that all agents older than y.o and younger than y.o. were allocated a workplace. agents in senior residencies are allocated a common room as their workplace where they get together during working hours. such allocation of younger agents to schools give a contact pattern as shown in figure e to model infections at locations other than workplace and house, we consider locations where agents remain for a relatively shorter duration as compared to house and workplace. specifically, we model interactions at locations like restaurants, grocery stores, and parks. note that this category of locations is also termed as "other" in [ ] . further, as the mean number of contacts at house are greater than the number of residents, it was important to consider socializing activities organized at houses. to do this, we maintain a pool of agents that an agent interacts with, and bring them together for a social activity at either a restaurant or at the agent's house. we discuss scheduling of these activities next. a contact pattern resulting at these random locations is shown in figure e. . we consider adult supervision for agents below y.o i.e. except for when agent goes to school, at least one adult agent (older than y.o) has to be present all the time. thus, we pre-plan the schedule of agents older than y.o at the start of the simulation, and plan the schedule of agents younger than y.o during the simulation. planning the schedule takes into account workplace opening hours as well as regularly scheduled activities like social gatherings , exercising, and grocery shopping . thus, an agent who has gone to a grocery store or a restaurant on one day will be less likely to go again during that same week, and so on. the schedule additionally depends on the day of the week. for instance, agents with school as workplaces are scheduled to be at school on weekdays, whereas most of their time will be spent at home on weekends. on the day of activity, however, these activities might stand cancel due to sickness, quarantining requirements, or hospitalization. in these situations, location of activity is appropriately changed for a required duration. at the same time, if an agent requiring adult supervision is sick, has to quarantine, or is hospitalized, an adult from the same house has to cancel the activity to stay with the agent. of note, agent's mobility i.e. presence in locations other than house is reduced when they are experiencing symptoms (to a degree proportional to symptom severity). note that we do not change the schedule unless the agent is quarantining i.e. normal mobility is maintained all the time unless the agent is put in the level n. figure e. show a breakdown of contacts at each location on weekdays and weekends. we implement age-stratified contact sampling as informed from empirically derived contact matrices as described in appendix e. . specifically, for each agent we draw number of contacts as per the location-specific agestratified number of contacts obtained from the contact matrices. we use a negative binomial distribution [ ] to draw number of contacts. further, we use these matrices to infer probability of interaction with other agents in each age group, thereby, implementing location dependent assortativity in interactions. we call these interactions as encounter. finally, we also figure e. : simulated mean daily contacts on weekdays and weekends broken down by age groups. agent activities are scheduled such that the mean number of contacts on work and non-work days follow surveyed data as reported in [ , ] draw amount of time spent in each encounter as per the survey conducted in california [ ] standardized to the demographics of montreal. thus, we obtain an aggregated contact pattern as shown in figure e. . we briefly describe the required steps for customization of the simulator. location-specific demographic and contact data may be modified simply by adding a new configuration file to the configs folder. configuration files are written using yaml, a human friendly data serialization standard. essentially, these files contain key-value pairs. the values for a new region must be specified and contained in the new configuration file. examples of modifications required to model a new region include: population-level distribution of age, housing distribution i.e. number of houses from size to , occupation characteristics including age for kids to go to schools, retirement age, etc. and, finally, how often people go out to stores, socialize, we provide details of the messaging protocol that uses bluetooth signals to exchange tokens. the privacy protocol which provides anonymous message exchange between phones which have exchanged these tokens is covered in more depth in another paper . in the context of the current work, we focus on the description of how we model the bluetooth communication range of phones and on the description of the clustering algorithm we use to prepare received messages for input to a risk prediction model. given a ground-truth distance and duration for our encounter, we want to determine if two app-users should exchange encounter messages. we only exchange encounter messages if the perceived distance is below meters and the duration greater than minutes. to compute this, we use a naive model of the bluetooth noise which uses a per-person noise and a per-encounter noise. each smartphone has a different noise sampled uniformly between and . each encounter takes the mean of this value across both users. we then apply a relative offset to the real encounter distance by multiplying the combined user noise and a uniform random variable centered at with range [ . , − . ]. the magnitude of the distance offset is up to metres when the real distance is metres, and up to . metres when the ground truth distance is metre. an encounter message m enc is composed of the day the encounter occurred d and the sender's quantized risk at the time of the encounter r d . the formal definition of a risk message is: an app user (say "alice") receives new encounter messages four times per day in batches; we call the set of new encounter messages on day d, m new . the risk messages which alice has already clustered are noted m enc (which is an empty set when alice first installs the app). it is useful to think of encounter messages as database records. alice inserts records into her database whenever she encounters other app users ("bobs") with their current risk estimate. update messages are like database update statements, and are used to change the risk values in old encounter messages. full citation to be provided in the camera-ready version if a user (say "bob") had many encounters with alice, and bob subsequently receives a positive test result, becomes sick (reporting symptoms), or otherwise re-evaluates his risk, then bob will send risk update messages to alice. similar to encounter messages, these risk update messages may be sent through the server up to four times per day. more specifically, if bob updates his estimate of his risk on some previous day d old , then bob will construct a risk update message for every encounter message that he had on d old and these messages are sent to the users with whom bob had a contact. if this update message is sent on day d, it is composed of the current day d, his new risk r new , his previous risk estimate for that day r old and the day of the encounter d old . therefore, the formal definition of a risk update message is: m update = (r new , d, r old , d old ) ∈ m updates by virtue of the strong privacy protocol in place, we are not able to create message clusters that correspond the true chains of contacts for the encountered users. the only information we have to create clusters is the day and risk level of the encounters. our hypothesis is that a user's contact patterns can provide a rough idea on the number of individual people they encounter on each day. all encounter messages received on a given day with a similar risk level are put into the same cluster. given that there are risk levels, it is only possible to create new clusters on a given day, unless the user receives update messages. every update messages is created for exactly one encounter message. if there are fewer update messages for a given day / risk combination than there are encounter messages for that day / risk, then we split the existing cluster for that day / risk into two, with one cluster containing newly updated encounter messages, and another containing the rest of the messages. we do not claim that this clustering algorithm is optimal, that the input format to the neural network is optimal, or that this messaging protocol is optimal. there exists an interesting trade-off between privacy and risk precision which we hope will be explored in future work. agent-agent transmission all encounters are assumed to be at a distance equal or less than two meters. transmission events can only take place between infectious and susceptible individuals. although the abm models all encounters taking place between individuals, a susceptible individual is only considered exposed (i.e. the model considers that an effective contact has taken place) when the encounter lasts a minimum of minutes and bernoulli distribution with probability determined via equation gives . the likelihood of viral transmission during a given effective contact is proportional to the time duration of the encounter, and depends broadly on characteristics of both the infected and susceptible individual. we use the transmission model as explained in [ ] . thus, encounters taking place in certain locations (i.e. senior residencies and households) are also inherently more prone to result in a transmission event, all other factors being equal. this is modeled via b n . at the same time, characteristics affecting infectiousness (of the infected individual) include progression of the disease (i.e. effective viral load) (ev l), whether (and to what extent) they are symptomatic (a s ). susceptibility of the exposed individual depends notably on age (s a ). environment-agent transmission please note, that the probability of environmental transmission is not supported by any published study, and we consider environmental transmissions in the experiments in this paper. however, abm can be configured to simulate environmental transmissions. empirical estimates of such transmissions stands at % as per [ ], therefore, we consider a transmission model that models environmental infections in pre-pandemic scenario. given the lack of such estimation in post-lockdown scenario, we do not consider any such transmissions. we model these transmissions by considering a linearly time-decaying probability of location being contaminated which is triggered by the presence of an infectious individual. initial magnitude of contamination is dependent on the agent's current phase of the disease. further, the duration of such contamination is informed from experimental study [ ] , which lists surfaces and the duration for which virus survives on them. we consider an experimental environment transmission model that estimates probability of infecting agent as proportional to (a) contamination strength of the location, and (b) susceptibility of an agent. the proportionality factor being the environmental transmission control knob which lets us model the disease spread as per the observed data. we denote s high as the row indices in s i d ∈ { , } nsymptoms×dmax such that the symptom at those indices are highly informative symptoms (see sec. j. ). similarly, we obtain sets of indices s moderate and s mild . we used n + = recommendation levels, thereby allowing an agent behavior level to be either of { , , , }. we also denote the set of days {d , d , ...d max } as d. the heuristic-fct algorithm is implemented as algorithm . we next describe each function of the heuristic-fct. in each of the following sections we detail the probability of a given symptom in each of phases of the disease. the probability of a person having fatigue as a symptom is given in the first column, while the probabilities of having the other symptoms given that this person has fatigue are given in the columns following the fatigue column. in order to have unusual symptoms, the person must also be over years of age; that is, the probabilities in the table given for unusual symptoms are the probabilities of having unusual symptoms given this person is over years of age and is experiencing fatigue. the probability of having trouble breathing as a symptom is given in the tb column for the corresponding covid- phases. for an individual to experience severe chest pain (scp), the individual must also be extremely sick; that is, the probabilities given for having scp as a symtpom are the probabilities of having scp given an individual has trouble breathing and is extremely sick. the probability of having light/moderate/heavy trouble breathing is given by the probability of an individual having light/moderate/severe symptoms of covid- and the probability of having trouble breathing as a symptom. the probability of having loss of taste as a symptom of covid- is % during the onset phase, % during the plateau phase, and % for all other phases of covid- . aches are not caused by covid- in this simulator, but are caused by the flu. the probabilities of having aches on the first and last days of the flu are % and % respectively, while the probability of having aches for all other days with the flu is %. we wish to verify that the dynamics of the simulator at the population sizes we model are representative of larger populations. because of the computational demands of an agent-based model, particularly with messaging between agents, it is more efficient to model smaller populations, as long as the dynamics remain reprsentative. as shown in figure k . , we find that population sizes above k to be representative of the dynamics of larger populations across a range of metrics. we thus ensure all experiments are run with populations of k and over. disability-adjusted life years (dalys) are a summary measure of the public health burden associated to a specific cause's premature mortality and morbidity. to calculate dalys, we individually compute the years of life lost due to premature mortality (ylls) [ ] for agents that died during the simulation, as well as the years of life lost due to disability (ylds) [ ] for agents that were infected and symptomatic. disability weights (dw) are taken from the global burden of disease study [ ] : they represent health preferences such that a dw of is perfect health and a dw of is equivalent to death. hence, the higher the amount of dalys, the worse health outcomes are. dalys are calculated without discounting or age-weighting, following the who methodology [ ] . for each agent i, tpl temporary productivity loss (tpl) is the loss in productivity due to absenteeism from work. to calculate tpl, we extract from the simulator the number of work hours that agents aged to years had to forego due to quarantine, taking care of a dependent (supervision), or illness to the point of being unable to work. we then multiply this quantity of foregone work hours by the average hourly wage in montreal [ ] to obtain total tpl. we follow the methodology for calculating tpl presented in [ ] . disability weights covid- is a novel disease, and there are no published disability weights for different levels of severity of the disease. therefore, we use similar conditions as proxies for different health states of the agents. agent hospitalization status is used as a proxy for actual health status, and can be divided into three categories: agents that are symptomatic and not hospitalized, agents that are hospitalized but not in critical are, and agents that are in critical care. the disability weights, as well as their equivalent causes in the gbd study can be found in table l. . full trajectory due to the computational strain of the message-passing within the simulations, observing the full trajectory under binary contact tracing and feature-based contact tracing is currently unfeasible. future work will consider longer simulations that reach a post-pandemic steady state.. ppl in addition to temporary productivity loss (tpl) due to absenteeism from work, cost-benefit analyses following the human capital model (hca) [ ] typically include a permanent productivity loss (ppl) due to premature mortality component. when longer simulations become possible, future work will take into account ppl. . to properly evaluate the impact of different tracing strategies on the socio-economic burden of a disease, it is important to evaluate whether the proposed strategies avert dalys, or simply delay them [ ] . such evaluations require a longer trajectory to arrive at a postpandemic steady state, which we will consider in future work. . the focus of this paper is not the cost-benefit analysis of the outcomes of the simulator, but rather the simulator itself, a sensitivity analysis of the cost-benefit results has been relegated to future work.. table l . : yll, yld and dalys × for different ct methods. in all three cases, the bulk of dalys is due to years of life lost due to premature mortality (yll), rather than years of life disabled (yld). women are also disproportionately affected in all three scenarios. as can be seen in figure l . , under no tracing, the total dalys is . , and the tpl is $ . m. test-based bct slightly affects the health and economic outcomes: the tpl is $ . m and the total dalys is . . however, heuristic-fct has a comparatively large effect on the total dalys, which drops to . . however, this is contrasted by a rise in the tpl to $ . m: health outcomes are drastically improved at the cost of a greater drop in productivity. of note is the difference in impact of both tracing methods: whereas test-based bct has very little effect on the health and economic outcomes, heuristic-fct reduces total dalys by . % at the expense of an increase in tpl by . %. bootstrapping dalys and tpl are computed for each seed separately before being aggregated to obtain a mean and standard error. when measures are calculated across subgroups of the simulation's population, such as across age groups, bootstrapping is used to capture todo figure l. : impact of different ct methods on dalys and total foregone work hours. no tracing foregoes the least amount of work, but results in a high amount of dalys. test-based bct foregoes more work, but still results in a large loss of health. heuristic-fct foregoes even more work than no tracing does, but results in a large decrease of dalys, alleviating the health burden. total foregone hours due to quarantine, aggregated across individuals, are scaled by a factor of . 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: a systematic analysis for the global burden of disease study global, regional, and national incidence, prevalence, and years lived with disability for diseases and injuries for countries and territories, - : a systematic analysis for the global burden of disease study global burden of disease collaborative network. global burden of disease study (gbd ) disability weights world health organization. who methods and data sources for global burden of disease estimates weekly and hourly earnings of employees by sex, montréal and all of québec covid- and the health policy recession: whatever it takes, grandma or the economy or what makes sense? information on the montreal population regarding age, sex and occupation distribution was retrieved from canadian census data [ ] . prevalences of selected medical conditions considered as covid- infection and prognosis risk factors were determined based on prevalence estimates from nationally representative surveys or medical surveillance programs in canada: heart disease [ , , , ] , stroke [ ] , asthma [ , ] , chronic obstructive pulmonary disease (copd) [ , , ] , cancer [ , , ] , diabetes [ , , , ] , obesity [ , , , , ] , chronic kidney disease (ckd) [ , , , ] , immuno-suppressed conditions [ ] and smoking [ , ] . national prevalence estimates were extracted based on age group (< , - , - , - , - , - , - , - and > years of age) and sex.we determined conditional probability of developing covid- in abm based on symptoms and risk factors associated with covid- in published literature. a mathematical modelling study of the epidemic with canadianspecific estimates [ ] was used to model covid- susceptibility in the pediatric population of the simulator. we model inoculum, the amount of virus transmitted during an exposure event, as a random variable uniformly distributed between . and .. the magnitude of inoculum is used to determine the type and severity of symptoms.we sample parameters for a piece-wise linear model of what we call effective viral load (evl) . we think of evl as a piecewise linear function, attributes of which are sampled for each individual separately. this approximation follows empirical studies on viral load progression [ , ] . figure b . is the mean of sampled effective viral load curve. we model rt-pcr test allocation as a priority queue. when an agent experiences symptoms, or is advised by a contact tracing application to seek key: cord- - wpxm of authors: van walle, i.; leitmeyer, k.; broberg, e. k.; group, the european covid- microbiological laboratories title: meta-analysis of the clinical performance of commercial sars-cov- nucleic acid, antigen and antibody tests up to august date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: wpxm of we reviewed the clinical performance of sars-cov- nucleic acid, viral antigen and antibody tests based on test results from published studies and new test results from eu/eea member states. pooling the results and considering only results with % confidence interval width [≤] %, we found nucleic acid tests, among which point of care test, and antibody tests with a clinical sensitivity [≤] % for at least one target population (hospitalised, mild or asymptomatic, or unknown). analogously, nucleic acid tests and antibody tests, among which point of care tests, had a clinical specificity of [≤] %. three antibody tests achieved both thresholds. evidence for nucleic acid and antigen point of care tests remains scarce at present, and sensitivity varied substantially. study heterogeneity was low for / ( . %) sensitivity and / ( . %) specificity results with confidence interval width [≤] %, and lower for nucleic acid tests than antibody tests. manufacturer reported clinical performance was significantly higher than independently assessed in / ( . %) and / ( . %) cases for sensitivity and specificity respectively, indicating a need for improvement in this area. continuous monitoring of clinical performance within more clearly defined target populations is needed. testing is one of the central pillars of public health actions in epidemic and pandemic situations to allow timely identification, contact tracing, and isolation of infectious cases to reduce the spread of infectious diseases. in addition, it allows e.g. estimating disease incidence, disease prevalence, and prevalence and duration of humoral immunity. reliable testing for severe acute respiratory syndrome coronavirus (sars-cov- ) and timely reporting of the data to public health authorities is therefore key for management of the coronavirus disease pandemic. this requires appropriate and accurate diagnostic tests, with sufficient availability, for both identifying individuals that are currently infected with sars-cov- as well as those that have been infected in the past. timely access to testing, sufficient supply of testing materials, availability of tests and related reagents and consumables as well as high-throughput testing are pivotal in this context. a large number of commercial tests for sars-cov- rna (nucleic acid tests or nats) or viral antigen detection are currently available, as well as serological tests for sars-cov- specific antibodies. the various types of tests can be used for different purposes and many of these tests have the ce-ivd certificate that indicates compliance with the european in vitro diagnostics directive ( / /ec) and can thus be marketed within the eu/eea countries. in addition, the us food and drug administration has granted emergency use authorisations for use of many commercial tests in the us and the world health organisation maintains an emergency use listing of commercial tests. [ , ] it is however important to note that the ce-marking is based on a self-declaration of the test manufacturer, including the claims on performance of the test. independent information on the clinical performance of these tests in terms of sensitivity and specificity is still limited, and yet this is critical for proper interpretation of results. for this reason, the european centre for disease prevention and control (ecdc) launched a continuous call to eu/eea member states and the uk on april to provide any such clinical performance data for sharing with other member states. these data, provided by member states, are presented in this paper. in addition, publicly available data were added. finally, minimal performance criteria for different intended uses were gathered from public sources and aided by a survey conducted among eu/eea member states and the uk from may to june . studies containing potentially usable data on clinical performance of sars-cov- nucleic acid, antigen and antibody tests were first extracted from systematic reviews on this topic. these reviews were identified through an initial pubmed (medline) search for systematic reviews and meta-analysis for 'covid- ' and 'sars-cov- ', followed by snowballing using the 'find similar articles' feature. the selection was then extended with the studies listed in the foundation for innovative diagnostics (find) database and the european commission (ec) covid- in vitro diagnostic devices and test methods database. both databases attempt to exhaustively identify peer-reviewed as well as grey literature on clinical performance of covid- tests and are continuously updated. [ , ] results from the latter were further filtered on those with a description indicating that they contain clinical performance results. results produced by united states food and drug administration were also included. [ ] finally, pubmed was searched according to the query in supplementary figure s . the resulting studies were subsequently assessed for eligibility. at present there are virtually no clinical performance studies that can be judged as being at low risk of bias and low applicability concerns, and systematic reviews up to this point have not used risk of bias or applicability concerns as exclusion criteria. [ ] [ ] [ ] [ ] this was not done in this work either. instead, studies were excluded if they did not contain data on commercial tests, or if one or more of the authors were employed by the developer or manufacturer of the index test, to avoid possible conflicts of interest. studies with an ineligible design, such as blinded tests, analytical validation only, use of another threshold for positivity than in the instructions for use, comparisons between different specimen types or use of an antibody rather than nucleic acid test as reference test for any type of index test were subsequently excluded as well. further exclusions were done at sample level based on the reference test employed. samples classified as actual negatives, i.e. used for determining specificity, had to either (i) be taken before the covid- outbreak, in practice before , (ii) be taken from an individual without covid- compatible symptoms, or (iii) be taken from an individual with covid- compatible symptoms but who was confirmed with another respiratory illness. samples classified as actual negatives that were taken during the outbreak and were negative according to a nucleic acid test were therefore excluded. this was done to maximally reduce misclassification as actual negatives due to known issues with sensitivity of nucleic acid tests. such misclassified samples would artificially lower index test specificity in particular when the index test is more sensitive than the reference test. [ ] [ ] [ ] [ ] [ ] [ ] [ ] for the same reason the reported sensitivity of nucleic acid or antigen index tests, based on a nucleic acid reference test, was considered to be a positive agreement instead, calculated as part of a headto-head comparison between the two tests. for antibody index tests on the other hand, a nucleic acid test was considered to be a valid reference test to determine actual positive samples and sensitivity, in accordance with who interim guidelines. [ ] manufacturer reported clinical sensitivity and specificity data were extracted from instructions for use where available, or otherwise from the manufacturer's website. sensitivity results derived from contrived samples spiked with purified viral rna were excluded. primary clinical performance data generated by the covid- microbiological laboratories group's co-authors were assessed by ecdc according to the same criteria as those of the literature review. meta-analysis of the included clinical sensitivity and specificity results was performed per test and per target, i.e. the genomic region for nucleic acid tests and the antibody isotype for antibody tests. antigen targets were not distinguished further. antibody test sensitivity results below the threshold days after onset were excluded. sensitivity and positive agreement results were further stratified by case population: hospitalised cases, mild or asymptomatic cases or unknown. pooled sensitivity and specificity values were calculated using fixed effects analysis, i.e. separately summing and dividing the number of correct predictions by the total number of samples in the group. wilson % confidence intervals were calculated for pooled results. study heterogeneity was assessed through the i statistic, calculated through random effects analysis using r version . . and the metafor package. [ ] i values < . % were considered low heterogeneity, . - . % moderate and ≥ % high heterogeneity. as of june , minimum performance criteria for tests were publicly available from belgium, france, the netherlands and the united kingdom (supplementary table s ). all were applicable solely to antibody (ab) tests. the intended uses included diagnosis of covid- , determination of exposure to sars-cov- and determination of the immune status against sars-cov- . minimum clinical sensitivity for all of the specified intended uses ranged from to %, with a median of %. these thresholds applied to samples collected at least > days post onset of symptoms (dpo), taking into account the time to seroconversion. minimum clinical specificity for all of the specified intended uses was % in six countries and . % in one. for nucleic acid and antigen confirmatory tests, the draft who target product profiles for priority diagnostics to support response to the covid- pandemic state > % -> % sensitivity (acceptable/desired) and > % specificity. [ ] general thresholds of > % sensitivity and > % specificity were used for further analysis, together with a maximum % confidence interval (ci) width of ≤ %. for igm only results, an upper limit of ≤ dpo, or the highest dpo category having a lower limit ≤ dpo, was added as well since igm antibodies decrease fairly rapidly and such tests are not intended to be used long after exposure. [ ] primary clinical performance data eight systematic reviews were identified, including one by health technology assessment bodies not listed as a peer-reviewed study, and the primary studies included in the analysis extracted. [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] the full list of studies in the find and ec databases was retrieved on august . pubmed was searched on the same date. from the ec database, out studies were screened out since their description did not indicate that they would contain clinical performance data on commercial tests. analogously, out of studies were screened out from the pubmed results. from the combined list of studies, had no clinical performance data on commercial tests, were excluded due to a potential conflict of interest and were excluded due to an ineligible design, leaving a total included studies. a complete overview of the study selection is given in figure . after exclusion of antibody test sensitivity results ≤ dpo and ineligible specificity results, a total of and index test results remained for calculation of sensitivity and specificity, respectively. after addition of original, previously unpublished results provided by the authors of this study, this increased to and index test results, respectively, for tests (supplementary tables s -s ) . pooled estimates for clinical sensitivity and specificity per test, target and, for sensitivity, case population were made as described in methods. for antibody tests, results were restricted to those estimates that had a % ci width of ≤ % and were derived from at least two studies, to be able to assess study heterogeneity. based on the minimum performance criteria analysis, results above  % sensitivity and/or  % specificity for a particular population are highlighted (table ) . among these results, there were two clias, one elisa and no lfias/pocs, that had  % sensitivity. analogously, there were nine clias, four elisas and twelve lfias/pocs, that had  % specificity, among which the three with  % sensitivity. study heterogeneity was low for / ( . %) sensitivity and / ( . %) specificity results with ci width of ≤ %. there were few sensitivity results for igg for mild or asymptomatic cases, iga and total antibody, none of which had a ci width of ≤ % (table ) . compared to the same test used for hospitalised cases, drops in sensitivity were . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint observed of . %, . %, . % and . % for igg, . % for iga and - . % for total antibody. the latter negative value is likely due to low number of samples for both populations. for nucleic acid tests that were not point of care (poc) tests, results were restricted as for antibody tests (table ) . three tests had  % positive agreement with a ci width of ≤ %, and nine had  % specificity. study heterogeneity was low for all sensitivity and all specificity results with ci width of ≤ %. limited data were available for five poc antigen tests and five poc nucleic acid tests (table ) . large variability in positive agreement was observed. the best performing nucleic acid poc achieved a positive agreement of . % ( . - . %), i.e. with a ci width of ≤ %. virtually no data were available on specificity, but no false positives were observed among them for either antigen or nucleic acid pocs. the correlation between independently assessed clinical performance results and manufacturer reported results is shown in figure . only independently assessed results with ci width of ≤ % are included. a total of / ( . %) of sensitivity and / ( . %) specificity results were significantly different (p< . ). this review represents, to our knowledge, the most complete independent overview so far of clinical performance of commercially available covid- tests. a substantial amount of previously unpublished data from european countries are included as well. to date, there are numerous commercial tests for which sufficient performance data are available to allow calculation of clinical sensitivity or positive agreement, and specificity with narrow confidence interval ranges. reassuringly, the clinical performances of several nucleic acid and antibody tests exceeded the minimum performance criteria. as time progresses, the list of tests with sufficient available performance data is expected to increase. at the same time, the available evidence for point of care nucleic acid and antigen tests remains scarce, even though these tests can have substantial practical advantages for e.g. screening. we therefore recommend more emphasis on the validation of these tests, including as part of a testing algorithm, whereby the sensitivity and specificity of taking two tests with a number of days in between is assessed, and which can e.g. be useful to reduce the duration of a quarantine period. the comparison between the independently assessed clinical performance data and manufacturer reported clinical performance revealed that in particular sensitivity is frequently ( . % of the cases in this study) significantly overestimated by the manufacturer. at a minimum, this emphasises that such independent assessments are clearly necessary. in the longer term, an explicit and proactive regulatory mechanism in europe to compare available independently generated evidence on these tests with manufacturer reported values, coupled with appropriate regulatory action, could be useful. this could also be rewarding towards those manufacturers that do provide robust estimates of their product's performance. limitations of this paper include that most of the included studies have a substantial risk of bias in the sample selection, especially for the sensitivity panel, as established also in the assessments performed in the systematic reviews that were used as a source. results were mainly based on hospitalised cases or poorly defined populations, whereas the population of interest consists often of symptomatic cases in general or even asymptomatic cases, and differences in performance may exist depending on disease severity. while this review addresses a pressing need for actionable . cc-by . international license it is made available under a perpetuity. is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . clinical performance data, ideally, the clinical performance should be assessed through prospective studies or clinical trials with a guaranteed unbiased sample selection for a clearly defined target population and intended use of the test. given the difficulty of assessing and extracting the data from individual studies in a coherent way, we recommend that the standard for reporting of diagnostic accuracy studies (stard) should also be followed when publishing the results. [ ] in this context, the selection of the reference test is particularly important with respect to reference negative samples. as described in some of the assessed studies, it should be avoided that index test results are considered as false positives while the samples are from actual cases and for this reason we excluded nucleic acid negative samples from suspected covid- patients altogether. we expect therefore little bias in the specificity results, except potentially from under or overrepresentation of confounders. this is especially relevant for seroprevalence studies, where, in the current lowprevalence situation, in particular the specificity of the test needs to be well-defined and high. on the other hand, sensitivity results using a nucleic acid test as reference should be interpreted with caution, since the positive samples may exclude some actual cases. possibilities to improve the reference test can include testing -potentially only the false positiveswith a second reference nucleic acid test preferably targeting different genes, testing more than one sample from the same patient including for antibodies at a later time point, testing samples from both upper and lower respiratory tracts, and sequencing the sample. the handling of intermediate index test results is an issue that needs to be described in studies, and in general these should be considered as positive results rather than either negatives or being excluded from the validation, since they would normally require further follow-up to confirm the positivity of the sample. for the above reasons, the authors and organisations contributing to this study in no way recommend the use of the listed commercial tests over other not listed commercial or in-house tests. finally, it should be kept in mind that this study is a snapshot in time and that the clinical performance of tests may change over time as the virus population evolves. we therefore recommend a continuous monitoring of clinical performance both in europe and globally, which is key for reliable monitoring of the pandemic and which will also support vaccine and antiviral development. these results should be shared in a timely manner publically is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint is the author/funder, who has granted medrxiv a license to display the preprint in (which was not certified by peer review) preprint the copyright holder for this this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint centre for infectious disease control, national institute for public health and the environment, the netherlands), maaike j.c. van den beld (centre for infectious disease control johan reimerink (centre for infectious diseases research, diagnostics and laboratory surveillance ,centre for infectious disease control, national institute for public health and the environment unit of medical microbiology, star-shl medical diagnostic center jeroen bosch hospital, 's-references . united states food and drug administration. emergency use authorizations for medical devices world health organisation. coronavirus disease (covid- ) pandemic -emergency use listing procedure (eul) open for in vitro diagnostics joint research centre of the european commission. covid- in vitro diagnostic devices and test methods database find evaluation update: sars-cov- molecular diagnostics united states food and drug administration openfda dataset on covid- serological testing evaluations antibody tests for identification of current and past infection with sars-cov- the current role of antibody tests for novel coronavirus sars-cov- in the management of the pandemic diagnostic accuracy of serological tests for covid- : systematic review and meta-analysis rapid, point-of-care antigen and molecular-based tests for diagnosis of sars-cov- infection clinical evaluation of ausdiagnostics sars-cov- multiplex tandem pcr assay serological immunochromatographic approach in diagnosis with sars-cov- infected covid- patients combination of serological total antibody and rt-pcr test for detection of sars-cov- infections antibody responses to sars-cov- in patients of novel coronavirus disease sars-cov- viral load in upper respiratory specimens of infected patients clinical performance of sars-cov- molecular tests diagnostic performance of ct and reverse transcriptase polymerase chain reaction for coronavirus disease : a meta-analysis laboratory testing for coronavirus disease (covid- ) in suspected human cases: interim guidance conducting meta-analyses in r with the metafor package covid- target product profiles for priority diagnostics to support response to the covid- pandemic v. . of interpreting diagnostic tests for sars-cov- testing for sars-cov- (covid- ): a systematic review and clinical guide to molecular and serological in-vitro diagnostic assays systematic review with meta-analysis of the accuracy of diagnostic tests for covid- meta-analysis of diagnostic performance of serological tests for sars-cov- antibodies up to april and public health implications diagnostic characteristics of serological-based covid- testing: a systematic review and meta-analysis stard guidelines for reporting diagnostic accuracy studies: explanation and elaboration we would like to acknowledge the technicians in the european microbiology laboratories who work hard to support the control of covid- and supported the validations described in this manuscript.we would like to acknowledge the companies that made some of the kits available for evaluation to some of the laboratories. key: cord- - ddlh authors: peeling, rosanna w. title: diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date: - - journal: int health doi: . /inthealth/ihv sha: doc_id: cord_uid: ddlh diagnostics play a critical role in clinical decision making, and in disease control and prevention. rapid point-of-care (poc) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. a new generation of poc molecular tests that are highly sensitive and specific, robust and easy to use are now available for deployment in low resource settings. decentralisation of testing outside of the laboratory can put tremendous stress on the healthcare system and presents challenges for training and quality assurance. a feature of many of these poc molecular devices is that they are equipped with data transmission capacities. in a digital age, it is possible to link data from diagnostic laboratories and poc test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. data connectivity also allows control programmes to monitor the quality of tests and testing, and optimise supply chain management; thus, increasing the efficiency of healthcare systems and improving patient outcomes. 'without diagnostics, medicine is blind.' alain merieux. diagnostics and laboratory services have been labelled as the achilles heel of global health. in the past, low quality diagnostics and ineffective laboratory services resulted in a mistrust of laboratory results, which in turn led to a decreasing demand for laboratory services and a low priority for funding. the maputo declaration has called on governments, multilateral agencies, development partners, professional associations and academic institutions to address laboratory challenges that limit the scale-up of services for tb, malaria and hiv diagnosis and care. together with the us centers for disease control and prevention's call to end the neglect of laboratories, this has provided a major milestone on a pathway to place diagnostics and laboratory services as important pillars of a healthcare system. , recent outbreaks of influenza, middle east respiratory syndrome coronavirus (mers-cov) and ebola virus disease illustrate the importance of diagnostics in outbreak investigations. [ ] [ ] [ ] with rapid technological innovations in the last years and donor investments in the development of improved diagnostics for infectious diseases of public health importance, it is time to re-examine the achilles heel and explore the promises and challenges of diagnostics in a digital age. accurate diagnostic tests play a key role in clinician trust and patient management. diagnostic testing is traditionally considered as a tool to rule in or rule out a condition or infection when clinical presentation in a patient is non-specific. for diseases such as hiv and other sexually transmitted infections, most infections are asymptomatic but can cause serious long-term consequences. diagnostics are used to screen for infection so that treatment can be given to prevent the development of long-term complications and to interrupt the chain of transmission to sexual partners or to the fetus in the case of pregnant women. a test for the human papillomavirus helps to determine risk of disease progression to cervical cancer. for pathogens that have developed antibiotic resistance, such as neisseria gonorrhoeae, diagnostic testing is used to determine antibiotic susceptibility to ensure treatment efficacy. for hiv patients, a cd test result is used to determine if the patient is eligible for antiretroviral treatment and, for those on treatment, a viral load assay is used to determine treatment compliance and drug efficacy. a test of cure is used to determine when treatment can be stopped ( figure ). beyond patient management, diagnostics play a critical role in various aspects of public health through disease prevention and control. diagnostics are critical in surveillance, to monitor trends in disease and antimicrobial resistance and assess the impact of interventions. diagnostic tools 'of sufficient sensitivity and specificity to detect levels of infection that can lead to transmission' were identified as one of the three essential requirements for disease elimination or eradication. who has set eradication or elimination targets for a number of neglected tropical diseases (ntds), including guinea worm, polio, yaws, trachoma, schistosomiasis, lymphatic filariasis, onchocerciasis, human african trypanosomiasis, chagas' disease and visceral leishmaniasis (vl) and the elimination of mother to child transmission (emtct) of hiv and syphilis. mass drug administration (mda) is the main control strategy for many of these diseases, resulting in the need for highly sensitive tests to detect the few remaining cases in areas of low transmission intensity after multiple rounds of mda. highly specific tests are then needed to certify elimination and maintain post-elimination surveillance. there is often little commercial interest in the development of diagnostics that are used mainly for surveillance because of the low return on investment. for a ntd such as schistosomiasis, the chinese national control programme has defined stages for schistosomiasis control as morbidity control (prevalence over % as defined by stool examination), infection control (prevalence of - %), transmission control (prevalence lower than %), transmission interruption (no case detected in years successively) and elimination (no case detected in the e years after transmission was interrupted). diagnostics results are used to inform national and regional control policy, redirect resources and to transition to the next phase of the control and treatment strategy. the who targets for emtct and who/unaids - - targets for hiv by also include diagnostic test coverage as indicators for efficiency of service delivery that help countries with setting a course to have an aids free generation and to end the hiv epidemic by . diagnostic testing is usually performed in laboratories. in countries where the laboratory infrastructure is limited, who advocates for the use of a syndromic approach for patient management whereby patients are treated for all the major causes of that syndrome. this often leads to overtreatment and increases risk for the development of antimicrobial resistance. in the last decade, rapid point-of-care (poc) diagnostic tests fulfilling the assured criteria (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free and deliverable) have become commercially available and are widely used for infectious diseases such as malaria, hiv and syphilis. [ ] [ ] [ ] [ ] [ ] these tests have allowed control programmes to increase access to testing, identify those who need to be put on treatment, optimise disease control and save lives. however, the quality of these tests varies, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. a new generation of immunoassays, molecular and nanotechnology platforms has been developed in recent years that can improve patient management and disease surveillance. these platforms have superior performance and make use of optical readers, mobile phones and data transmission capabilities to improve reading of results and data transmission. such technologies provide real-time results to inform patient management decisions. data, linked to precise geographical locations using gps, can be transmitted to a central database to inform disease control programmes or to monitor progress towards elimination. many of these assays can also yield quantitative results to give estimates of pathogen copy number or, in the case of hiv, to monitor treatment compliance or efficacy. these technology platforms can also be used to detect multiple targets from a single specimen. for geographic areas with multiple diseases targeted for elimination, if surveillance is conducted in the same sentinel population, such as children under the age of years, using the same specimen, such as a blood sample, exposure to multiple ntds can be detected on a multiplex platform. this may be a more cost-effective means of conducting post-mda surveillance than collecting specimens and testing for a single ntd at a time, , although cost-effectiveness of using these platforms for multiple ntds remains to be demonstrated. increased sensitivity of detection using these advances has made it possible to have tests that detect antibodies from oral fluids. the use of these non-invasive specimens has made it possible to design hiv tests for self-testing or for home use. the availability of self-testing at home has allowed testing to be de-stigmatised and should help countries with achieving the first of the unaids/who - - targets. bead-based immunoassays bead-based technologies are more versatile and potentially offer higher sensitivity compared to traditional solid phase immunoassays. instead of using enzymatic amplification of a colorimetric substrate, bead-based assays can use a range of labels, including laser or fluorescence to detect the binding of the secondary antibody to an antigen or antibody target. the beads are in solution, offering more sites for ligand binding compared to a solid phase support. fluorescent intensities can yield quantitative results. protein arrays offer the potential of quantification of the antigen target as a surrogate measure of bacterial, parasite or viral load to inform treatment strategies. detection of multiple targets from the same pathogen can lead to increased efficiency over single-target assays. detection of targets from multiple pathogens using a single specimen can offer substantial cost and sample savings over traditional elisa measurements. the detection platforms are often equipped with data transmission capacities and allows near real-time surveillance of disease trends and monitoring the effect of special interventions. microfluidic devices offer many advantages, such as high throughput, short analysis time, small volume and high sensitivity, which make them an ideal immunoassay format for clinical diagnoses. the current microfluidic immunoassays have limited multiplexing capability compared to flow cytometric assays but are improving. immunoassays developed on a microfluidic platform that reproduce all the steps of a traditional elisa in a miniaturised format are now available. the microfluidic disc can fit into the palm of a hand and is rapid and inexpensive to manufacture. these platforms allow multiplexing, but have only been validated for antibody detection in blood samples. antigen detection from urine or stool samples will require multistep specimen processing and/or purification or concentration before being put into the antigen-antibody reaction within the microfluidic channels. a recent publication showed that it is possible to use the power of smart phones to power a microfluidic immunoassay reaction by plugging the reaction chamber into a smart phone using a dongle. over assays can be run before recharging is necessary. the results are interpreted and displayed on the phone and the data transmitted to a central database if required. a dual test to detect antibodies to hiv and syphilis has been designed on this platform and will have utility not only to improve access to prenatal screening but also to allow surveillance data for the dual elimination of mtct of hiv and syphilis to be available in real time. nanosensor assays a growing number of promising diagnostic tools are based on nanotechnology. the application of nanomaterials to detect host or pathogen biomarkers has the potential to yield ultrasensitive assays. quantum dots are fluorescent semiconductor nanoparticles typically between and atoms in diameter and the technology has been applied to the development of ultrasensitive tests for hiv and other viral infections. it is also possible to use these technologies to combine pathogen detection and speciation with genetic analysis, such as detection of single nucleotide polymorphisms. hence, they can be used for high throughput screening of drug mutation targets. quantum wires are being used in the development of a fully automated diagnostic test for malaria infection, speciation and drug resistance status in less than minutes. these nanosensors can ultimately be configured to a handheld pda-type device or a thin plate about the size of a small business card containing a tiny nanowire sensor. operationally, these tests are simple to use and give answers in less than minutes. they can be used during a doctor's visit or at home by a patient, or early detection of bioterrorism in a community setting. linking mobile connectivity and gps will enable anonymised disease data to be sent to a data cloud for real-time surveillance. advocacy to apply these novel technologies to ntds and antimicrobial resistance monitoring is an urgent priority. this requires precise engineering of nanomaterial surfaces as the interface between the nanomaterial and the specimen is where the reaction occurs. molecular assays offer superior diagnostic performance compared to the limit of detection of immunoassays. in the last two decades, nucleic acid amplification tests (naats) have become the 'gold' or reference standard to which the performance of other diagnostic tests is compared. until recently, they have remained largely laboratory based and are expensive and inaccessible. a number of poc molecular assays, with or without amplification, are now on the horizon that may transform the delivery of health services. , the first sample-in/answer-out real-time pcr platform that can be used wherever there is a source of electricity has been introduced for the diagnosis of tb and detection of rifampicin resistance. [ ] [ ] [ ] the genexpert real-time pcr platform has a large menu of test targets; thus, allowing polyvalency to test for different pathogens. it requires minimal onsite expertise and provides a result in less than hours. it has additional advantages of random access and remote quality control. however, the cartridges are expensive and not affordable or sustainable unless subsidised in most high burden countries. to maximise the impact of these novel technologies, it is critical that patient pathways be modified to take advantage of the speed to result and to find cost-efficient means of implementation compared to traditional laboratory testing. isothermal amplification platforms such as helicase dependent amplification (hda), cross priming amplification (cpa), recombinase polymerase amplification (rpa) and loop-mediated amplification (lamp) assays can be engineered into poc naats as there is no requirement for sophisticated equipment to perform thermal cycling. the details of these technologies have been described elsewhere. , poc naats based on these technologies have largely been applied to high burden diseases such as hiv and tb, but other technologies, such as lamp, have been developed and evaluated for the diagnosis of vl and hat. in the case of vl, the lamp assay for leishmania donovani is highly sensitive and specific for the diagnosis of vl (using a blood sample), and for the diagnosis of post-kala azar dermal leishmaniasis (pkdl) (using a skin biopsy). diagnosis of pkdl will be important for the elimination agenda since patients with this condition are an important source of infection. in the case of hat, the lamp assay was shown to have a sensitivity of . % ( % ci . to . %) and a specificity of . % ( % ci . to . %) compared to a pcr reference standard. advocacy and investments are needed to apply these technologies to the control and elimination of ntds. the promise of diagnostics in a digital age in a digital age, data from social media and poc diagnostics in communities can be used to provide early warning for infectious disease outbreaks, and timely information to inform disease control and elimination programmes. the isense project, an epsrc irc funded project in early warning sensing systems in infectious diseases, aims to create low-cost latent sensing systems to analyse self-reported symptoms on the web, including social networks and micro-blogging sites (twitter) and searches (bing, google). isense will develop a new generation of early warning sensing systems to identify outbreaks of deadly infectious diseases, such as flu, methicillin-resistant staphylococcus aureus (mrsa) and hiv, by linking self-reported symptoms on the web to a new sensor-enabled disease surveillance infrastructure for an early warning sensing system for infectious diseases (http://www.i-sense.org.uk/research). the simplest poc diagnostic tests that are widely used today are rapid diagnostics tests (rdts) in a lateral flow format. these are read with the naked eye, which is subjective and prone to human error and may be further exacerbated by poor lighting in health posts. in addition, rdts lack on-board quality control and are often used in remote areas where health workers receive minimal training. as a result, accuracy of rdts performed in the field can be quite variable. this may adversely affect patient care and the accuracy of the data gathered for surveillance. digital imaging technology in electronic readers and smart phones can be used to capture and interpret rdt results and transmit data. given the large number of brands of rdts for hiv, malaria and syphilis, it would be ideal to have diagnostic test readers that could accommodate a variety of test technologies (e.g., lateral flow, immunofiltration) and formats (e.g., strips, cassettes of various sizes and shapes). a number of rdt readers are already on the market and others are in the pipeline. given the widespread adoption of smart phones in resource-limited settings, rdt readers using this technology have the potential to combine high-resolution test images with the computing capability required to run image analysis software and transmit data. the readers range in price depending on the technical complexity of the instrument and their compatibility with the type of rdts. data collection for the emtct is difficult when testing is highly decentralised and data quality is difficult to verify. to track global progress towards elimination of mtct of hiv and syphilis many challenges need to be addressed. currently, data from antenatal screening need to be manually accessed from individual testing sites. electronic readers for rdts are able to capture and automatically transmit data and may, therefore, serve a critical purpose for strengthening data collection and surveillance in the context of monitoring and evaluation of dual elimination. , improving supply chain management real-time data monitoring via electronic readers could help to improve coordination of supply chain management by multiple partners. operational data on stocks, device usage and condition can be uploaded via wi-fi or cellular networks and transmitted to central databases. by linking the data to supply chain management software, stock-outs can potentially be avoided and health system efficiency improved. in recent years, rdts have been introduced to increase hiv and syphilis screening in antenatal clinics, enabling same day testing and treatment of infected mothers to prevent adverse outcomes of pregnancy and fetal loss. the emtct targets to be achieved are % of pregnant women access antenatal care, % of pregnant women at antenatal care tested for hiv and syphilis, and % of those testing positive receive treatment. to achieve these targets, countries will need to have a system to track progress the capacity for ongoing surveillance once the elimination target is achieved. studies have shown that the introduction of rapid rdts for syphilis for prenatal syphilis screening has strengthened health systems by improving access to diagnostics, health worker job satisfaction and reducing stillbirths and neonatal mortality. in peru, the introduction of rdts for prenatal screening has resulted in infected pregnant women being screened and treated in a single visit instead of - visits over days. , challenges of new technologies assuring quality of poc lateral flow tests and devices decentralisation of testing outside of the laboratory can put tremendous stress on the healthcare system and presents challenges for training and quality assurance. when testing is decentralised, programme managers are often unable to monitor testing coverage and quality, making it difficult to identify problems of sub-standard testing and stock-outs in a timely manner. international health for poc molecular devices, requirements for instrument calibration, ongoing maintenance and frequency of failure, power usage and environmental sustainability should also be considered. creation of a central database to collect surveillance data from village antenatal clinics all the way through to national and global databases is needed. this involves obtaining consensus on where to host the data, what data to collect, who has access to the data and finding affordable software. middleware solution that provides 'open access' will allow for rapid coordinated transmission of data to governments. technology is needed to ensure data is collected, transmitted and stored in a way that conforms to ethical and legal standards, maintaining patient privacy and confidentiality. these governance issues may be resolved by ensuring separate levels of access to operational data versus patient data. in addition, data storage should be in-line with country specific regulations. further discussion needs to take place around data ownership. an excellent example of a national database that informs critical programmatic decisions in real time is the kenyan national early infant diagnosis (eid) portal (www.nascop.org/eid), which has now been extended to cover hiv viral load and other diagnostics. this database is the result of a successful public-private partnership that involved the government of kenya ministry of health, usaid/president's emergency plan for aids relief (pepfar), the us cdc, the clinton health access initiative (chai), hewlett packard, safaricom and strathmore university. hewlett packard built a basic data centre at the national aids/std control programme (nascop) and at testing laboratories for early infant diagnosis. safaricom, the largest provider of mobile services in kenya, set up a short code service for sms. strathmore university students built the application. pepfar, cdc and chai rolled out the eid programme countrywide. the result is a national eid portal running on a government data centre-hosting all the testing and program data entered from computers in laboratories equipped with laboratory information systems (web-based applications). over health facilities that provide eid services have access to all the data and test results over sms, mobile web, web and email in near real time. data analytics include sample transport tracking, volume of testing at each facility, test results, including the number of rejected samples and indeterminate results. results are delivered via electronic and paper means (sms printer, email, courier, web) and real time eid/prevention of mtct programme analytics are available online by facility, and at regional and national levels. the new generation of diagnostics equipped with digital technologies are transforming the field of clinical decision-making and disease control and prevention. rapid poc tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests varies, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. electronic readers have the potential to provide fast, accurate, standardised rdt interpretation and real-time data reporting with a huge range of positive functions, including improving quality assurance, supply chain management and providing accurate timely data for surveillance. although countries need to consider data governance and confidentiality issues, data connectivity allows control programmes to monitor the quality of tests and testing, and optimise supply chain management; thus, increasing the efficiency of healthcare systems and improving patient outcomes. author's contribution: rp has undertaken all the duties of authorship and is guarantor of the paper. achilles heel" of global efforts to combat infectious diseases laboratory medicine in africa: a barrier to effective health care the maputo declaration on strengthening of laboratory systems. geneva: world health organization laboratory systems and services are critical in global health: time to end the 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syphilis. global guidance on criteria and processes for validation. geneva: world health organization point-of-care tests to strengthen health systems and save newborn lives: the case of syphilis rapid syphilis tests as catalysts for health systems strengthening: a case study from peru the costs of accessible quality assured syphilis diagnostics: informing quality systems for rapid syphilis tests in a tanzanian setting the author would like to acknowledge david mabey and debi boeras in providing helpful comments in the preparation of this manuscript.funding: none. ethical approval: not required. key: cord- -k adcls authors: döhla, m.; boesecke, c.; schulte, b.; diegmann, c.; sib, e.; richter, e.; eschbach-bludau, m.; aldabbagh, s.; marx, b.; eis-hübinger, a.-m.; schmithausen, r.m.; streeck, h. title: rapid point-of-care testing for sars-cov- in a community screening setting shows low sensitivity date: - - journal: public health doi: . /j.puhe. . . sha: doc_id: cord_uid: k adcls objective: with the current sars-cov outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. the gold standard is a quantitative polymerase chain reaction (qpcr)–based system taking several hours to confirm positivity. for effective public health containment measures, this time span is too long. we therefore evaluated a rapid test in a high-prevalence community setting. study design: thirty-nine randomly selected individuals at a covid- screening centre were simultaneously tested via qpcr and a rapid test. ten previously diagnosed individuals with known sars-cov- infection were also analysed. methods: the evaluated rapid test is an igg/igm–based test for sars-cov- with a time to result of min. two drops of blood are needed for the test performance. results: of individuals, tested positive by repeated qpcr. in contrast, the rapid test detected only eight of those positive correctly (sensitivity: . %). of the qpcr-negative individuals, were detected correctly (specificity: . %). conclusion: given the low sensitivity, we recommend not to rely on an antibody-based rapid test for public health measures such as community screenings. objective: with the current sars-cov outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. the gold standard is a quantitative polymerase chain reaction (qpcr)ebased system taking several hours to confirm positivity. for effective public health containment measures, this time span is too long. we therefore evaluated a rapid test in a highprevalence community setting. study design: thirty-nine randomly selected individuals at a covid- screening centre were simultaneously tested via qpcr and a rapid test. ten previously diagnosed individuals with known sars-cov- infection were also analysed. methods: the evaluated rapid test is an igg/igmebased test for sars-cov- with a time to result of min. two drops of blood are needed for the test performance. results: of individuals, tested positive by repeated qpcr. in contrast, the rapid test detected only eight of those positive correctly (sensitivity: . %). of the qpcr-negative individuals, were detected correctly (specificity: . %). conclusion: given the low sensitivity, we recommend not to rely on an antibody-based rapid test for public health measures such as community screenings. © the royal society for public health. published by elsevier ltd. all rights reserved. covid- is rapidly spreading worldwide, and the number of cases in europe is rising with increasing pace in several affected regions. while there is an urgent need to contain the pandemic to protect the elderly and vulnerable population, there are several obstacles to control the spread of new infections. the vast majority of sars-cov- einfected individuals appear to have only mild to moderate symptoms similar to the flu or other flu-like infections, e lacking defining symptoms. thus, while we start losing the ability to trace all sars-cov- einfected contacts, identification of potentially infected individuals becomes increasingly hard ( table , fig. ). to protect the vulnerable population, it is necessary to assess the infection status of potential contacts to patients with covid- rapidly but also to approve employees to work with at-risk individuals in the hospital or nursing homes. the current gold standard for sars-cov- detection is a sars-cov- especific, quantitative real-time polymerase chain reaction (rt-qpcr) testing from a nasal or pharyngeal swab, sputum or broncoalveolar lavage. , following standard protocols, rna needs to be extracted and the presence of viral rna confirmed by rt-qpcr. this requires several potentially erroneous steps and several hours for sampling and evaluation. even high-throughput laboratories require a minimum of e h from sampling to evaluation, and final information of the infection status may take up to h. this bears the risk of a potential further spread of sars-cov- in the meantime and hinders widespread testing of all potential contacts. there is currently no rapid method to detect potentially sars-cov- epositive individuals that would allow an assessment of their infection status in a reliable manner. there is an urgent need for immediate targeted detection of infected individuals to slow the pandemic. we therefore evaluated a rapid antibody igg/igmebased testing system in the community setting for its ability, specificity and sensitivity to reliably identify infected individuals. the german red cross had established a covid- screening centre in a high-prevalence area with more than confirmed cases among , inhabitants. the cluster outbreak occurred after a carnival celebration and secondary transmissions in the families and rural community. the medical personnel at the screening site perform e throat swabs for sars-cov- diagnostics every day on symptomatic individuals. thirty-nine randomly selected individuals at the centre were tested simultaneously using the sars-cov- rapid test and the gold standard rt-qpcr method (altona diagnostics). in addition, collected and stored serum samples of previously diagnosed individuals with known sars-cov- infection were analysed. all individuals accepted testing via written informed consent. the rapid test used for evaluation is a qualitative igg/igm detection system to test for a current or past infection of sars-cov- . the chemical coupling pad contains gold-labelled sars-cov- weak and strong is superior; the manufacturer's recommendation is also to interpret weak results as positive. lrþ: positive likelihood ratio; lr-: negative likelihood ratio; roc: receiver operating characteristics; ci: confidence interval. antigens and mouse igg controls. there are two detection bands (t ¼ igm and t ¼ igg) on the test strip, which are coated with mouse anti-human igm and igg antibodies, respectively. the control band (c) is coated with a goat anti-mouse igg antibody. after discarding the first drop of blood from a fingertip prick, two drops of blood are applied onto the rapid test chip. in addition, two drops of a provided solution are added. the test indicates positivity for igg after min and for igm after min. when a test sample is added to the sample-loading area, the antigen forms an immune conjugate with the gold-labelled antibodies and then move to the detection zone by a capillary action. the negative conformity rate has been described to be % for negative controls. the positive conformity rate has been described to be % at early stages of infection (day e ) and % at late stages of infection (day e ). the study population was well balanced in terms of age (median: years, interquartile range [iqr]: e ) and gender ( / female [ . %]). the majority described symptoms including dry coughing ( . %), fatigue ( . %) and a runny nose ( . %). only five individuals had no symptoms. twenty-two individuals were tested positive by repeated rt-qpcr, while were tested negative. positive individuals reported five symptoms in median (iqr: e ), while negative individuals reported only (iqr: e ) symptoms. we were able to identify the probable date of exposure of individuals ( . %). median time between exposure and test was . days (iqr: e ). all used rapid tests were valid; of ( . %) tests were negative. we saw a weak response in cases and a strong response in cases. there was no case of a singular igm response indicating acute or recent sars-cov- infection. the manufacturer recommends to classify weak responses as positive which was supported via receiver operating characteristics (roc) curve analysis. therefore, we defined tests as positive in our study. considering the pcr results, we found eight tests to be true-positive and to be false-positive, whereas tests were true-negative and tests were false-negative (table) there was no statistically significant correlation between rapid test results and time from potential exposure (exact test, p ¼ . ), presence of symptoms (exact test, p ¼ . ), age (exact test, p ¼ . ) or gender (exact test, p ¼ . ). the sars-cov- outbreak in / followed an unprecedented international response to contain the pandemic. high transmission rates and the vast majority presenting with only mild to moderate unspecific symptoms complicate the ability to contain the virus. moreover, laboratory methods to detect sars-cov- infection rely on rt-qpcr testing that require longer time for sample handling, preparation and diagnosis. while rapid point-ofcare testing is critically needed, the current evaluation of an antibody-based system demonstrates only low sensitivity and is therefore not recommendable to detect potential infections as a stand-alone test. indeed, studies demonstrated that seroconversion occurred sequentially for igm and then igg with a median time of and days, respectively. the presence of antibodies was < % among patients in the first days of illness and then rapidly increased to % at day after onset of symptoms, which appear to be too late from a public health perspective. in this real-life study setting at a community sars-cov- testing site after a cluster outbreak, we investigated the superiority of an antibody-based rapid test in comparison with the current sars-cov- rt-qpcr gold standard. we tested screened persons of an official screening centre that we had selected by chance. this is a scenario that already occurs and will more often occur in all european union (eu) member states within the next months. the rapid test was substantially inferior to the rt-qpcr testing and should therefore neither be used for individual risk assessment nor for decisions on public health measures. as there is an urgent need for a sufficient rapid testing system for sars-cov- , an antigen-based system may therefore be more appropriate. we recommend accelerating the development and evaluation of effective point-of-care testing systems. the study has been approved by the local institutional review board in march ( / ). none declared . european centre for disease prevention and control (ecdc) clinical characteristics of coronavirus disease in china scientists are sprinting to outpace the novel coronavirus imaging and clinical features of patients with novel coronavirus sarscov- evidence of sars-cov- infection in returning travelers from wuhan, china improved molecular diagnosis of covid- by the novel, highly sensitive and specific covid- -rdrp/hel real-time reverse transcription-polymerase chain reaction assay validated in vitro and with clinical specimens diagnosis of sars-cov- infection based on ct scan vs. rt-pcr: reflecting on experience from mers-cov epidemiology and transmission of covid- in shenzhen china: analysis of cases and , of their close contacts antibody responses to sars-cov- in patients of novel coronavirus disease none q declared. key: cord- -mbkrg v authors: jantzen, r.; noisel, n.; camilleri-broet, s.; labbe, c.; de malliard, t.; payette, y.; broet, p. title: epidemiological and socio-economic characteristics of the covid- spring outbreak in quebec, canada: a population-based study date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: mbkrg v background: by mid-july , more than , covid- cases had been diagnosed in canada with more than half in the province of quebec. to be prepared for a potential second wave of covid- in the fall, it seems of utmost importance to analyze the epidemiological and socio-economic characteristics of the spring outbreak in the population. method: we conducted an online survey of the participants of the cartagene population-based cohort, composed of middle-aged and older adults. we collected information on socio-demographic, lifestyle, health condition, covid-related symptoms and covid- testing. we studied the association between these factors and two outcomes: the status of having been tested for sars-cov- and the status of having received a positive test when having been tested. these associations were evaluated with univariate and multivariate analyzes using a hybrid tree-based regression model. results: among the , respondents from the cartagene cohort, were tested for covid- and were positive. medical workers and individuals having a contact with a covid- patient had the highest probabilities of being tested ( % and . %, respectively) and of being positive ( . % and . %, respectively) among those tested. . % of the participants declared that they have experienced at least one of the four covid-related symptoms chosen by the public health authorities (fever, cough, dyspnea, anosmia) but were not tested. results from the tree-based model analyzes adjusted on exposure factors show that the combination of dyspnea, dry cough and fever was highly associated with being tested whereas anosmia, fever, and headache were the most discriminant factors for having a positive test among those tested. during the spring outbreak, more than one third of the participants have experienced a decrease in access to health services. there were sex and age differences in the socio-economic and emotional impacts of the pandemic. conclusion: we have shown some discrepancies between the symptoms associated with being tested and being positive. in particular, the anosmia is a major discriminant symptom for positivity whereas ear-nose-throat symptoms seem not to be covid-related. the results also emphasize the need of increasing the accessibility of testing for the general population. epidemiological and socio-economic characteristics of the covid- spring outbreak in quebec, canada: a population-based study background by mid-july , more than , covid- cases had been diagnosed in canada with more than half in the province of quebec [ ] . the province of quebec confirmed its first case of covid- on february . with only seventeen confirmed cases, the state of emergency was declared by the quebec government on march the th with a shutdown of daycare facilities, primary and secondary schools, cegeps and universities followed by a more extensive shutdown of restaurants and bars, indoor sport facilities and non-essential economic activities. in early march, most cases could be traced to infected travelers returning to canada or to close contact with those travelers. by march , according to the public health agency of canada, nearly half of canadian covid- cases have been acquired through community spread [ ] . in mid-july, more than , covid- postive cases have been confirmed in the province of quebec with nearly half in the montreal metropolitan area and around one-third of the confirmed cases have been diagnosed among middle-aged and older adults. as in many countries over the world, the covid- testing strategy in canada has evolved over the first wave, taking into account each province's specific situation. in order to be prepared for a potential second wave of covid- in the fall, it seems of utmost importance to analyze the epidemiological and socio-economic characteristics of the spring outbreak in the population, together with the results of the public health policies that have been implemented. such information can provide useful knowledge for planning public health strategies for the next coming months. despite the impressive number of publications about covid- infection, most of them are hospital-based series, [ , , , ] to name a few, while population-based studies are scarce [ , , ] . however, population-based cohorts that have been established before the pandemic may yield unbiased estimates of the characteristics and consequences of the pandemic in the general population. it may also provide useful information about the effectiveness of public health interventions such as testing strategies. in this context, the existing population-based cohort cartagene (cag), composed of middle-aged and older adults, which was established before the covid- outbreak, offers a unique opportunity to analyze the characteristics and consequences of the outbreak among a population that seems to be at greatest risk. a large survey (hereinafter referred to as cag covid- ) was launched in early june. an online questionnaire was sent to the participants of the cag cohort for collecting information about covid- -related symptoms, diagnosis, comorbidities and social impacts of the spring outbreak. the aim of this survey was to analyze the demographic, clinical and socio-economic characteristics associated with the covid- pandemic in quebec in spring . we also investigated the risk exposure, pre-existing medical conditions and clinical features that led to being tested and to have a positive result among those who have been tested. cartagene is a population-based cohort composed of more than , quebec residents aged between and years at recruitment [ ] . original survey design . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint was defined by gender, age groups and forward sortation area (fsa -defined by the first -digit postal codes). participants have been recruited during two phases (phase a: - (n = , ) and phase b: - (n = , )) in metropolitan areas where nearly % of quebecers live and prospective follow-ups are conducted on a regular basis. with a rich collection of data including phenotyping and biological data, cag is the largest ongoing prospective population cohort and biobank in quebec, canada. the collected data includes a self-administered socio-demographic and lifestyle questionnaire (phase a and b), an interviewer-administered health questionnaire (phase a and b); non-invasive physical measurements (phase a) and biospecimen collection (blood (phase a and b) and urine (phase a)). more than , individuals have provided blood samples. the lifestyle questionnaires cover topics such as socio-demographic factors, lifestyle, mental state, psychosocial environment, personal and family history of disease, health care utilization, medication use, reproductive health and history and declared health conditions. a cohort-wide follow-up has been carried out in aiming at updating lifestyle and health information to years after the baseline data. cag is part of the canadian partnership for tomorrow's health (canpath, former called cptp) which is the canada's largest population health research platform [ ] . cag covid- online questionnaire for this study, we have developed a specific online questionnaire [ ] for collecting updated information on basic demographic variables (age, sex, household composition and postal code), covid- testing, test dates and results, whether participants suspect they had an undiagnosed covid- infection based on symptoms (cough, shortness of breath, fever, etc.). we also collected information on exposure status: health care or essential workers, contact with someone who has been diagnosed with covid- , international travel. those with confirmed covid- infection were asked if they were hospitalized along with details related to their care, treatment and outcome of the hospitalization. in addition, participants were asked to report existing chronic health conditions and medication use. finally, they were asked about the psychosocial and socio-economic impacts of the pandemic on their lives. this online questionnaire was unfolded in close collaboration with the canpath consortium for allowing future inter-provincial comparisons as well as other national and international research initiatives. a weblink to the consent and questionnaire was sent by email to all the cartagene participants with a valid email address, that is , . initial invitation was followed by up to emails reminders. the digital invitations were sent early in june and were valid for weeks. survey closed early july . a positive exposure status was defined as an individual being either medical or essential workers, having been in contact with a covid- positive patient or coming back from international travel. a medical worker was defined as either a physician, nurse, hospital/aged-care facility employee, first responder, pharmacist with patient exposure. an essential worker was defined as either a grocery store attendant, public transit, police, fireman. a contact with a covid- positive . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint individual was defined as being in the same room as a person who was told by a health professional that he or she has covid- . international travel was considered as a travel outside canada returning after the st of february. pre-existing conditions were defined as medical condition currently treated among the following list: cardiovascular diseases (hbp, coronary artery disease,...), autoimmune diseases, diabetes, infectious diseases, gastro-intestinal and liver diseases, cancers, renal diseases. the following list of symptoms were considered in the questionnaire: dry cough, wet cough, shortness of breath (dyspnea), fever (≥ • c), shivering, fatigue, runny nose, sinus pain (sinusitis), ear pain (otitis), sore throat, hoarseness, loss of taste (ageusia), loss of smell (anosmia), diarrhea, nausea, vomiting, loss of appetite, headache, general muscle aches and pains. the possible responses were: none, mild, moderate or severe. for the association studies, the following symptoms were considered as present only when being severe: fatigue, loss of appetite, sinus pain, ear pain, sore throat, hoarseness, headache, muscle pain, diarrhea. hereafter, we will refer to the symptom-based case definition chosen by the quebec public health authorities with at least one of the four major symptoms: fever (≥ • c), a new cough or a cough that gets worse, difficulty of breathing, anosmia with or without ageusia [ ] . two outcomes were studied. the first was the status of having been tested for sars-cov- (rt-pcr). the second was the status of having received a positive test when having been tested. confirmed covid- infection was defined as at least one positive result test. if multiple tests were performed, we considered the date of the first positive one. the participants' baseline characteristics have been reported and tested : demographic (age, sex, geographical location, level of education, financial resources, household income, dwelling type), health history (high blood pressure, cardio-vascular disease, pulmonary disease (chronic obstructive pulmonary disease (copd), asthma, ...), cancer, diabetes, autoimmune diseases, mental health, body mass index (bmi)), lifestyle behaviors (smoking status, alcohol intake,...). mean (or median) with standard deviations (or interquartile ranges) were reported for continuous outcomes. frequencies with % confidence intervals were reported for qualitative variables. for comparing means between groups, we used an anova test. for categorical variables, we used chi-squared test or exact test if needed. for the univariate association analyzes (between factors and studied outcomes), we used a chi-square test (qualitative) or a logistic regression model (quantitative). for each hypothesis test, we reported the p-values. moreover, in order to address the multiple testing problem, we also indicated those that are still significant for a fdr (the expected proportion of false discoveries among all discoveries) controlled at a level of % using the benjamini-hochberg procedure [ ] . . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint for the multivariate analyzes of exposure and risk factors, we used a multiple logistic regression model. for the multivariate analyzes of symptoms associated with the outcomes, we had to cope with complex interplay between clinical symptoms. thus, we considered a generalized partially linear tree-based regression (gpltr) model. gpltr models represent a class of semi-parametric regression models that integrate the advantages of generalized linear regression and tree-structure models [ ] . the linear part is used to model the main effects of confounding variables (e.g. exposure) while the nonparametric tree part is used to address potential collinearity and interactions between explanatory variables (e.g. clinical symptoms). this tree-based model provides a classification of individuals in homogeneous groups in terms of risk for the event of interest and identifies relevant combination of explanatory variables. the optimal gpltr tree is selected using a penalized maximum likelihood method with the bayesian information criterion (bic) [ ] . regression trees are prone to instability, especially when dealing with a low number of outcomes, making variable selection somewhat precarious. thus, for the analyzis of the positive status outcome, we constructed multiple trees using a bagging approach, which provides a way to assess the relevance of each variable across the set of trees using variables' importance measures. these later results provide us some arguments regarding the reliability of the selected optimal gpltr tree. we reported the depth deviance importance score (ddis) of each symptom that is computed for each gpltr model as the sum of the values of the deviance at each split based on this variable, weighted by the location of the split in the tree. these scores are summed across the set of trees, and normalized to take values between and , with the sum of all scores equal to . a set of gpltr models was done and we reported the symptoms as ranked by the ddis. we also evaluated in our dataset the discriminative power of the menni et al. logistic-based predictive model [ ] which is based on age, sex, loss of smell and taste, fatigue, persistent cough and loss of appetite. we reported the area under the roc curve (auc) together with the sensitivity and specificity applying the % probability threshold (as proposed by menni et al. and corresponding to the bayes rule). statistical analyzes were performed using r software [ ] . regression tree analyzes were performed with the 'gpltr' r package [ ] . estimation of the probability of being positive when experiencing a symptom since the tested participants are selected based on the symptoms being hypothesized to be associated with a positive test, the tested participants constitute a non-random set (ascertainment bias). thus, it is not possible to estimate directly the probability of being infected given that the person has experienced a particular symptom since non-selected (untested) individuals are unobserved. we can only estimate the probability of being positive given that the person has experienced a particular symptom and has been tested. instead, we propose to report the minimum, mean and maximum values that these probabilities can take using the law of total probability. more precisely, we . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint know that the probability of being positive given that the person has experienced a particular symptom (p (+|s)) can be expressed as: where p (+|s ∩ t ) (resp. p (+|s ∩t )) are the probabilities of being positive when the symptom is present and he/she has been tested (resp. not tested) and p (t |s) is the probability of being tested when having the symptom. from our data, p (+|s ∩t ) and p (t |s) could be directly estimated while p (+|s ∩ t ) could not. however, we know that this probability ranges from zero (complete dependence) to p (+|s ∩ t ) (independence between positivity and test). thus, we calculated the minimum, mean and maximum values that p (+|s) can attain for each symptom. survey respondents among the , participants of the cartagene cohort, we sent the questionnaire to , individuals. as compared to the non-respondents (n= , ), the respondents (n= , ) were slightly older (median age of . vs. . , p < . ), composed of more women ( . % vs. . %, p < . ), had a higher education level ( . % vs. . %, p < . ) and were more often living in montreal ( % vs. . %, p < . ). the same results were observed when comparing the individuals who answered the questionnaire to the whole cartagene cohort. of the , respondents, , had responded to the questions regarding covid- testing ("have you been tested for covid- ?" and "what was the result of your st covid- test?"). hereafter in this article, we analyzed this set of , respondents. both the proportion of tested participants for covid- and positive individuals among those being tested are consistent with those reported in quebec at the closure of our survey (tested: cag . % among the , individuals who experienced at least one covid-related symptom (as defined above), , declared that their first action was to call or consult their family doctor ( . %), to call the or a dedicated coronavirus hotline ( . %), to go to the pharmacy ( . %), to the hospital emergency room ( . %) or to a covid- screening clinic ( . %). among the , individuals who tried to contact a healthcare professional, . % ( ) were not able to reach someone on the phone or to see someone because of too much waiting. among the participants who experienced a covid- contact, the majority was at work ( ), in a health care facility ( ) or at home ( ). in the later case, covid- contacts were the spouse or partner. . % ( / ) were not tested. among the respondents, ( . %) have been tested for covid- and ( . %) were declared positive. among these tested individuals, had one test, had . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . when looking to the number of tests performed per day, we can see a low number of tested participants during april with a maximum at the end of may. this trend reflects the shortage faced by the province in early april followed by a rebound by end of may. in our series, the highest number of tests per day was may , consistent with the entire province [ ] (supplementary figure s ). among the tested individuals, were medical workers, were in contact with a covid- positive individual and had both risk exposures. individuals were essential workers including without other risk exposure. individuals declared an international travel, including having no other risk exposure. among the tested individuals with no declared risk exposure, declared no covidrelated symptom with patients having a chronic pre-existing medical condition (mainly cardio-vascular or respiratory disease). the proportion of positive cases varied widely across risk exposure status: . % ( / ) for the medical workers, . % ( / ) for essential workers, . % ( / ) for people in contact with a covid- positive individual without professional exposure, . % ( / ) for people having declared an international travel without other exposure risk and . % ( / ) for people having one of the major symptoms but without known exposure risk. none of the patients without risk exposure or covid-related symptoms were positive. there were individuals who declared that they have experienced at least one of the four covid-related symptoms chosen by the quebec public health authorities but were not tested. among them . % were medical worker, . % had a contact with a covid- patient. among those having none of these later exposure factors, . % declared an anosmia. moreover, the percentage decreased with the number of covid-related symptoms from . % (one symptom) to . % (all the four symptoms). among the individuals with at least one positive test, ( . %) participants had a first negative test followed by a positive test. twenty-three ( %) were working as a medical worker and ( . %) as an essential worker. seven ( . %) were in contact with a covid- positive individual without professional exposure and five ( . %) with no other risk exposure traveled outside of canada. three individuals have been hospitalized for covid- infection but none of them was hospitalized in icu. five were treated with an experimental therapy prescribed by a clinician for covid- . the colchicine was the only one prescribed treatment. none of them had chloroquine/hydroxychloroquine, remdesivir, lopinavir-ritonavir or tocilizumab. among the positive cases, ( . %) felt completely or mostly back to normal. eight ( %) were sick for seven days or less, ( %) between eight and fourteen days, ( %) between fifteen and thirty days, and ( %) more than thirty days. the two individuals who felt not really back to normal were at and days of symptoms. they had and different symptoms, respectively. among the positive individuals who responded to mental and emotional questions, / ( . %) had someone to help meeting their immediate needs. / . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint ( . %) received help, aid or support (including from friends, family, community or government). socio-economic, lifestyle and health early impacts of the covid- spring outbreak general and socio-economic impacts while the household income had substantially decreased for ( . %) of all the participants, there was a moderate or major impact on the ability to meet financial obligations or essential needs (e.g. rent or mortgage payments, utilities and groceries) for ( %). among the , individuals who regularly took public transit before march , ( . %) did not continue to take public transit after march, while ( . %) took public transit less frequently. individuals changed their transport habits because of the lockdown ( ), being afraid of covid- exposure ( ), quarantine/in self-isolation ( ) or covid- symptoms ( ) . regarding the relationship with the intimate partner during the lockdown, , ( . %) of the participants experienced no change, ( . %) declared that they became closer than before the pandemic, while ( . %) felt more distant or strained than before the pandemic. same trends were observed with friends and colleagues who became closer in , ( . %) and ( . %), respectively, while more distant in ( . %) and ( . %), respectively. the family relationship became more distant or strained than before the pandemic for , ( . %) of the participants while ( . %) became closer. during the spring outbreak, , ( . %) of the participants have experienced a change in access to health services. among them, ( . %) had a surgery canceled or deferred, ( . %) a medical procedure canceled or deferred, ( . %) a treatment canceled or deferred and ( . %) experienced a delay for seeing a healthcare professional about an preexisting problem and ( . %) about a new problem. however, , ( . %) have used virtual appointments with their health care provider. among the individuals who have initiated new use of mental health services, did for anxiety, for depression and for stress. overall, the mental/emotional health at the time of completing the questionnaire was good/excellent for , ( . %) participants. over the last weeks, some individuals have been bothered more than half of the days or nearly everyday by the following problems: trouble falling/staying asleep or sleeping too much ( . %), feeling tired or having little energy ( . %), feeling nervous ( . %), trouble relaxing ( . %), excessive worrying ( . %) or constant worrying ( . %). since march, the alcohol consumption increased for ( . %) of the participants. among the current smokers ( . % of the participants), ( . %) increased their consumption, ( . %) decreased their consumption whereas ( . %) did . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint not change. among the individuals who used cannabis in the past months ( . % of the participants), ( . %) increased their consumption, ( . %) decreased their consumption whereas ( . %) did not change. the physical activity decreased for , ( . %) of the participants. sleep duration and quality did not change for , ( . %) and , ( . %), respectively. the food intake increased for ( . %), while the food quality decreased for ( . %) of the participants. because of the pandemic, , of the participants ( . %) looked for support from family, ( . %) from general media (tv, internet, social media), ( . %) from the government, ( . %) from friends, ( . %) from provincial or federal health authorities, ( . %) from professional and ( . %) from colleagues. the covid- outbreak had different impact between men and women. the alcohol consumption increased more among women ( . % versus . %, p < . ). physical activity and quality of sleep decreased more for the women ( . % versus . %, p < . ; . % versus . %, p < . , respectively). the quantity of food intake increased ( . % versus %, p < . ) more for the women. since march, women accessed more mental health services for anxiety ( . % versus . %, p < . ), stress ( % versus . %, p < . ) and depression ( . % versus . %, p = . ). nevertheless, the current mental/emotional health was very good or excellent for . % of men but only . % of women (p < . ). women have looked more for support from family ( . % versus . %, p < . ), general media ( . % versus . %, p < . ), friends ( . % versus . %, p < . ), provincial/federal health authorities ( . % versus . %, p < . ), professional ( . % versus . %, p < . ), colleagues ( . % versus . %, p < . ). looking for support from the government (financial support, financial relief, resources) was not different between women and men. over the last weeks, women were more bothered by the following problems, more than half of the days or nearly every day: trouble falling/staying asleep or sleeping too much ( . % versus . %, p < . ), feeling tired or having little energy ( . % versus . %, p < . ), feeling nervous ( . % versus . %, p < . ), trouble relaxing ( . % versus . %, p < . ), excessive worrying ( . % versus . %, p < . ) or constant worrying ( . % versus . %, p < . ). when looking to the covid- outbreak impact among individuals under and over years, the income substantially decreased for less elderly ( . % versus . %, p < . ). the alcohol consumption increased more for the younger ( % versus . %, p < . ). the quality of sleep and food decreased more for the younger ( . % versus . %, p < . ; . % versus . %, p < . , respectively). the quantity of intake increased more for the younger ( % versus . %, p = . ). the younger accessed more mental health services for anxiety ( . % versus . %, p < . ), stress ( . % versus . %, p < . ) and depression ( . % versus . %, p < . ). nevertheless, the current mental/emotional health was very good or excellent for . % of elderly but only . % of younger (p < . ). . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint since march, elderly have looked more for support from family ( . % versus . %, p < . ), friends ( . % versus . %, p < . ), general media ( . % versus . %, p < . ), provincial/federal health authorities ( . % versus . %, p = . ), professional ( . % versus . %, p < . ) or community/volunteer organization ( . % versus . %, p < . ). looking for support from colleagues was less frequent among the elderly ( . % versus . %, p < . ). over the last weeks, the younger were bothered more by the following problems, more than half of the days or nearly every day: trouble falling/staying asleep or sleeping too much ( . % versus . %, p < . ), feeling tired or having little energy ( . % versus . %, p < . ), feeling nervous ( . % versus . %, p < . ), trouble relaxing ( . % versus %, p < . ), excessive worrying ( . % versus . %, p < . ) or constant worrying ( . % versus . %, p < . ). association between being tested and demographic, risk exposure, pre-existing medical conditions and covid-related symptoms we compared the demographic, exposure and clinical characteristics of the participants who have been tested to those who have not. participants below the median age were most frequently tested (p < . ). there was no difference between men and women. participants living in the montreal area were more likely to be tested than those living outside of montreal ( . % versus . %, p < . ). participants living in a house or duplex were less likely to be tested than those living in apartment or condominium ( . % versus . %, p = . ). this relationship is still significant when adjusted for living in montreal or outside. participants coming back from international travel were most frequently tested ( . % versus . %, p = . ). medical workers and people having contact with a covid- positive individual were most frequently tested ( . % versus . %, p < . and . % versus . %, p < . , respectively). participants having at least one pre-existing medical condition (as defined above) were more frequently tested (p = . ). in particular, individuals having a preexisting condition such as asthma (p < . ), copd (p < . ), chronic bronchitis (p < . ), nonalcoholic fatty liver disease (nafld) (p < . ) were more frequently tested (supplementary table ) . a multiple logistic regression analyzis showed that place of residence, dweling, risk exposure (medical worker, contact with a covid- positive patient, international travel), having at least one pre-existing condition were independent factors associated with the outcome ( table ) . all the covid-related symptoms were more frequent among tested participants (supplementary table ) . taking into account socio-demographic, medical and exposure factors (place of residence, dweling, medical worker, contact with a covid- positive patient, international travel, pre-existing condition) as confounding factors and covid-related symptoms as explanatory variables, we performed a gpltr analyzis for identifying the combinations of symptoms leading to the most homogeneous sub-groups with respect to being tested. the procedure with the bic criterion led to a final tree having five leaves built with three selected covid-related symptoms: dyspnea, dry cough and fever ( figure a) . . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint we identified: (i) a leaf with a very low rate for being tested ( . %, / ) with none of the selected covid-related symptoms; (ii) a leaf with the highest rate . % ( / ) of tested individuals having both dyspnea and dry cough; (iii) three leaves with at least one of the symptoms with a rate of being tested: dyspnea ( . %, / ), fever ( . %, / ), dry cough ( . %, / ). table displays odd-ratio estimates and p-values for the confounding variables and terminal leaves corresponding to the optimal gpltr tree for being tested. association between being covid- positive and demographic, risk exposure, medical pre-existing conditions and covid-related symptoms participants below the median age were most frequently positive (p < . ). there were more women among positives ( . % versus . %, p = . ) but it was no longer significant after multiple testing adjustment. there was no difference between geographical area of residence or international travelers. medical workers (p < . ) and people having contact with a covid- positive individual (p < . ) were most frequent among positives (supplementary table ). participants having at least one medical pre-existing condition (as defined above) were less frequently positive ( . % versus . % p = . ) but it was no longer significant after multiple testing adjustment. other variables such as blood group, treatments, pre-existing conditions, vaccination (influenza and bcg), smoking, bmi, presence in the household of children or pets were not significantly associated with positive status. a multiple logistic regression analyzis showed that being a medical worker or having contact with a covid- patient were the only independent factors associated with the outcome (table ) . patients with loss of taste and smell, fever, dyspnea, headache, pain, fatigue, shivering, loss of appetite, dry cough and nausea symptoms were more frequent among positive individuals. wet cough and other symptoms were not significantly associated (see supplementary table ) . when estimating the probability of being positive given that the person has experienced a particular symptom (see statistical section), we showed ( figure , left panel) that symptoms with the highest probabilities are ageusia, anosmia, loss of appetite, headache, fatigue. in contrast, ear, nose and throat (ent) symptoms (running nose, sore throat, hoarseness, sinus pain) and wet cough showed the lowest probabilities. taking into account exposure status (contact with covid- infected patient, medical worker) as confounding factors and covid-related symptoms as explanatory variables, we performed a gpltr analyzis for identifying the combinations of symptoms leading to the most homogeneous sub-groups with respect to being positive. our procedure with the bic criterion led to a tree with four leaves built with three different covid-related symptoms selected: anosmia, headache and fever. we identified: (i) a leaf with a very low rate of being positive ( . %, / ) with no anosmia and no fever; (ii) a leaf with a low rate ( . %, / ) of being positive with fever but without anosmia; (iii) a leaf with a moderate rate ( . %, / ) of being positive with anosmia but no headache; (iv) a leaf with a very high positive rate with both anosmia and headache ( . %, / ). results from the bagging . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint procedure associated with the tree-based model provided a ranking of the variables based on depth deviance importance scores (ddis). anosmia, fever and headache selected in the optimal gpltr tree showed high importance scores (figure , right panel). table displays odd-ratio estimates and p-values for the confounding variables and terminal leaves corresponding to the optimal gpltr tree for positivity. among the participants tested, the menni et al. predictive model was available for individuals. the model led to an auc of . % (supplementary figure ) . the sensitivity was of . % and the specificity was of . %. we report the results of an online survey of population-based cohort participants whose main objective was to analyze the characteristics and consequences of the first pandemic wave of covid- spring outbreak in quebec, canada. we also report the exposure risk factors and covid-related symptoms associated with the status of having been tested for sars-cov- and having been declared positive. as seen from our analyzis, the demographic characteristics of the respondents are broadly representative of the middle-aged and older population of quebec. montrealers, individuals living in an apartment/condominium, having a pre-existing medical condition and having risk exposure (medical worker, contact with a covid- patient, international travel) were more frequently tested. as expected, medical workers and individuals with known or suspected contact with a covid-positive individual were the most tested. these later findings are in accordance with public health notices giving priority to health care workers and individuals in contact with people tested positive for sars-cov- , whether they had symptoms or not. results from the extended tree-based model analyzis, adjusted on exposure factors, show that the combination of dyspnea, dry cough and fever are highly associated with being tested. these results are consistent with the case definition chosen by the public health authorities in early spring. the fact that anosmia is not selected reflects its paucity in the general population ( . % as compared to . % to % for the other three symptoms) and that it has been added later in the official list of the main symptoms. among the covid-related symptoms associated with testing, ear, nose and throat (ent) symptoms (running nose, sore throat, hoarseness, sinus pain) and wet cough were not related to a positive test in univariate analyzis. results from the extended tree-based model analyzis, adjusted on exposure factors, show that a combination of anosmia, fever and headache are the most discriminant factors for a positive test in our series. individuals with both anosmia and headache had the highest chance (almost two third) of being positive while those with anosmia alone had almost one-fourth chance of being positive. individuals without anosmia and fever had less than two percent chance of being positive. these results underline the importance of neurological symptoms such as anosmia and headache, as compared to ent and gastro-intestinal symptoms. results obtained from the bagging procedure confirm the importance of the selected symptoms and suggest that the final tree-based model is sufficiently reliable. they also show the importance of fatigue and loss of appetite that are, with anosmia, the main factors of the menni et al. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint predictive model. in our series, the operating characteristics of the menni et al. predictive model are close to those published with a weak sensitivity and a high specificity. however, it is difficult to disentangle the effect of the testing criteria applied in our population from those of the menni et al. algorithm since the positive cases are only those being tested. it is worth noting that among the positive individuals, five did not meet the four criteria chosen by the public health authorities, two of them reported few symptoms such as fatigue, shivering without fever and/or loss of appetite and three individuals did not experience covid-related symptoms. interestingly, all these five patients were tested for having a contact with people being tested positive for sars-cov- . this highlights that a non-negligible fraction of infected people could be asymptomatic or pauci-symptomatic, even in this age group. it underlines the importance of contact tracing as an essential component of the toolbox for containing the covid- outbreak. interestingly, we observe some discrepancies between being tested and being positive among the studied factors. some of them are linked to both outcomes such as being a medical worker, having a contact with a covid- patient and fever. anosmia increases the discriminative power for being positive as compared to being tested, reflecting its value for positivity. in contrast, dyspnea, that was the main factor for being tested, has a lower discriminative power for positivity. some factors associated with testing were not related to a positive test such as international travel, pre-existing conditions and ent symptoms. while the first covid- cases were linked to international travelers, the public health measure (e.g. quarantine, border closure) mitigated this risk. the lack of relevance for the ent symptoms should lead to withdraw these symptoms from the list of covidrelated symptoms. for the pre-existing conditions, this discrepancy reflects the testing policies that have focused on group of patients that might be of high risk for severe disease if exposed to the virus. it is worth to note that this over-representation of people having a pre-existing condition led to an inverse relationship with a positive test that is however no longer significant after multiple testing adjustment. such spurious association could be related to an ascertainment bias caused by testing primarily individuals reporting specific conditions and thought to be positive. as reported by the participants, the economic consequences in this early stage of the pandemic seem still moderate but is more important for younger participants. however, the real economic impact of the pandemic may appear in the coming months. the alcohol and food consumption slightly increased during the lockdown, especially among women and younger participants. the current emotional health is considered good or excellent for the majority of the participants, but lower for women. as feared, one third of the participants have experienced a decreased access to health services with surgery or medical procedures canceled or deferred for more than ten percent of them. however, it is interesting to note that virtual consultations were widely used. one of the main strengths of this study is its embedding within the cartagene cohort. it provides a rich body of information collected before the pandemic that is representative of the middle-aged and older population, which seems to be the most commonly affected group. thus, it offers a unique opportunity to appreciate the . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint impact of covid- infection and public health measures in the quebec population. in particular, we highlight the selection process for testing at the population level. we show that the most exposed people (medical worker and people having a contact with a covid- positive patient) were more widely tested than the rest of the population. in this later group, only the individuals having all the covid-related symptoms criteria had a high probability of being tested. this emphasizes the need of increasing the accessibility of testing for the general population who meet the testing criteria through easy to access point-of-care or drive-thru testing centers. there are however some limitations to this study. firstly, we experienced a low response rate that might be explained by the online survey in a population that was previously used to paper surveys and by the short time allowed to respond. nevertheless, our series is broadly representative of the entire cohort. secondly, it relies on self-reported data, which could be subjected to biases in respondents' recall and to potential effect from mainstream media coverage. thirdly, when analyzing the factors related to a positive test, there is an ascertainment bias caused by testing primarily individuals reporting specific exposures or symptoms. this may blur some relationship between factors and a positive outcome. this highlights the interest of seroepidemiological studies at the population level. fourthly, our population is limited to middle and older adults and has less than one percent of individuals living in senior's house that were severely affected by the covid- outbreak in the province. finally, this study is a first step toward a follow-up study intended to understand the course of the pandemic and its consequences in the population. it will also allow us to compare the public health policies between provinces and countries. moreover, it will be enriched with a serological study in order to analyze more thoroughly the non-tested symptomatic and asymptomatic cases. to our best knowledge, this is one of the first report about the consequences of covid- outbreak at the population level. we have shown some discrepancies between the symptoms and risk factors associated with being tested and being positive. in particular, the anosmia is a major discriminant symptom for positivity whereas ent symptoms should be withdrawn from the list of covid-related symptoms. it also emphasizes the need of increasing the accessibility of testing for the general population. the authors declare that they have no competing interests. author's contributions rj: conceptualization, data curation, formal analyzis, investigation, methodology, writing -original draft. nn: conceptualization, resources, writing -original draf. scb: writing -original draft. cl: resources. tm: data curation, software. yp: data curation, software. pb: conceptualization, formal analyzis, methodology, project administration, supervision, validation, writing -original draft. ethics approval and consent to participate this project has been approved by the research ethics board of the chu sainte-justine on th may under the reference mp- - - , . all participants have given their consent. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted september , . is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint additional file - fig s . tif figure s : number of tested participants and cumulative number of tested participants over time. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted september , . . https://doi.org/ . / . . . doi: medrxiv preprint situation of the coronavirus (covid- ) in québec public health agency of canada presenting characteristics, comorbidities, and outcomes among patients hospitalized with covid- in the new york city area features of uk patients in hospital with covid- using the isaric who clinical characterisation protocol: prospective observational cohort study clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study. the lancet covid- : a retrospective cohort study with focus on the over- s and hospital-onset disease ethnic and socioeconomic differences in sars-cov- infection: prospective cohort study using uk biobank serocov-pop): a population-based study. the lancet real-time tracking of self-reported symptoms to predict potential covid- cohort profile of the cartagene study: quebec's population-based biobank for public health and personalized genomics the canadian partnership for tomorrow project: a pan-canadian platform for research on chronic disease prevention questionnaire study on coronavirus and covid- définition de cas de covid- -québec controlling the false discovery rate: a practical and powerful approach to multiple testing a novel tree-based procedure for deciphering the genomic spectrum of clinical disease entities r: a language and environment for statistical computing we would like to thank all the cartagene participants for their generous investments in health research. we would also like to thank the ramq and the commission d'accèsà l'information (cai) for their support in obtaining the data. not applicable. the data that support the findings of this study are available from cartagene but restrictions apply to the availability of these data. data are available directly from cartagene (http://cartagene.qc.ca; access@cartagene.qc.ca; + - - ). key: cord- -xhpv y authors: land, kevin j.; boeras, debrah i.; chen, xiang-sheng; ramsay, andrew r.; peeling, rosanna w. title: reassured diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date: - - journal: nat microbiol doi: . /s - - - sha: doc_id: cord_uid: xhpv y lack of access to quality diagnostics remains a major contributor to health burden in resource-limited settings. it has been more than years since assured (affordable, sensitive, specific, user-friendly, rapid, equipment-free, delivered) was coined to describe the ideal test to meet the needs of the developing world. since its initial publication, technological innovations have led to the development of diagnostics that address the assured criteria, but challenges remain. from this perspective, we assess factors contributing to the success and failure of assured diagnostics, lessons learnt in the implementation of assured tests over the past decade, and highlight additional conditions that should be considered in addressing point-of-care needs. with rapid advances in digital technology and mobile health (m-health), future diagnostics should incorporate these elements to give us reassured diagnostic systems that can inform disease control strategies in real-time, strengthen the efficiency of health care systems and improve patient outcomes. or in sequence. in case of discrepancies, a third test is used as a tiebreaker. an example of this approach is for hiv case detection. specificity. diagnostics should have low false positive rates. the ideal scenario is where the sensitivity and specificity achieved from the diagnostics used at the poc approach those of laboratory-based assays wherever possible. however, a lower specificity can be tolerated if the harm of overtreatment is much less critical than missing the diagnosis of an infection. screening syphilis during pregnancy is an example of this approach, as missing maternal syphilis can lead to stillbirths, preterm birth and congenital syphilis in a third of pregnant women compared to the harm of overtreatment with a single dose of penicillin . user friendliness. tests should be easy to perform in - steps and require minimal user training with no prior knowledge of diagnostic testing. typically, results should be available in - minutes after sample collection and enable patient management and treatment during the same visit. the benefits of a rapid test versus a more accurate test that requires patients to return for results have been previously demonstrated . robustness refers to the ability of the test to withstand the supply chain (temperature, humidity, time delays, mechanical stresses) without requiring additional (and often costly) transport and storage conditions (for example, refrigeration). ideally the test does not require any special equipment or can be operated in small portable devices that use solar or battery power. deliverable to end-users. delivery refers to the organizational structures and relationships established with the purpose of coordinating and steering the logistics of selecting, procuring, shipping, storing, distributing and delivering a new health technology to ensure it reaches the end-users in resource-constrained settings . compared to when assured was proposed, access to laboratories in resource-limited settings has improved dramatically both in numbers and in quality , , especially in areas such as hiv and malaria testing, cd counting and tb. however, there remains a critical need for a wider range of diagnostics that can be performed at the poc. from this perspective, we undertake a review of the assured benchmark over the last years, assess the factors contributing to the success and failure of the assured diagnostics over the past decade, identify areas that have remained difficult to address as well as lessons learned from implementation in resourcelimited settings, and highlight additional conditions that should be considered in addressing poc needs. since , several diagnostic tests that satisfy (or nearly satisfy) the assured criteria have been developed to identify major human pathogens. this includes tests for hiv, malaria, syphilis and tb ( table ) . the hiv rapid test is the first test to fulfil the assured criteria, followed closely by the malaria and syphilis rapid tests and, recently, a near-poc test for tb. much of this development was the result of advocacy by donors such as the bill & melinda gates hiv rdts. early detection of hiv infection has been a critical component of hiv control programmes worldwide since the early days of the epidemic. since most infected individuals do not show specific symptoms and the period of viraemia is short, screening for hiv antibodies in blood as a marker of exposure has been the most cost-effective means of identifying infected individuals. the who developed a process and criteria for validating the performance of hiv antibody detection assays more than a decade ago and showed that hiv rdts using finger-pricked whole-blood specimens has acceptable performance compared to laboratory-based immunoassays , . many donors -for example, global fund and implementation partners, including the who, unaids and pepfar -have helped affected countries with the procurement and introduction of rapid hiv tests and enable early detection and prevent onward transmission. as a result of funding from donors, increased accessibility of rdts, and the 'architecture' provided by national hiv/ aids control programmes, hiv tests successfully reached as many as million children and adults in low-and middle-income countries in (ref. ) . two major challenges remain: training and quality assurance. with thousands of poc testing sites across a country, even the most well-organized control programmes would find it difficult to provide adequate training on an ongoing basis. this problem is most acute in health facilities where there is high turnover of staff. the us centres for disease control and prevention (cdc) has developed a convenient means of external quality assurance by working with countries to generate thermally stable proficiency panels that can be shipped to every poc testing site to ensure competence of testing personnel. however, a study in south africa found that only % of hiv rdts were performed correctly . although not every error will result in an incorrect diagnosis, the alarming reality is that with million tests being performed annually worldwide, assuming a % accuracy rate, as many as . million incorrect results per year could potentially be generated. ongoing quality assurance efforts include developing key policy and quality documents for the implementation of hiv-related poc testing . for example, as poc technologies for hiv viral load and early infant diagnosis were being developed, there was tremendous emphasis on quality, given the complexity of the test and lessons learned from hiv rdts. malaria is estimated to be the cause of at least a million deaths a year worldwide, most of which are in sub-saharan africa. while microscopic identification of parasites in blood smears has been the traditional means of diagnosing malaria in patients presenting with fever, microscopy requires equipment, a source of electricity and trained laboratory technicians. malaria rdts were developed as many rural communities lack these resources, and to date there are over brands of malaria rdts made by approximately companies , which vary widely in performance, manufacturing quality and price. the who has set up a pre-qualification programme with the cdc and the foundation for innovative new diagnostics to evaluate these tests to inform test selection and procurement for national malaria control programmes . in countries that permit the sale of malaria rdts and medicines over the counter, the quality of these commodities cannot be guaranteed. the price of most rdt brands is between us$ . and us$ . per test , , and as with all diagnostics, it is important to caution that price pressure will ultimately affect quality. as with hiv, with the support of donors, selection of high-quality rdts and the architecture provided by national malaria control programmes, malaria rdts have reached millions of patients every year. this promising trend, coupled with the effectiveness of bednets for preventing transmission, has led to the call for malaria elimination in many parts of the world . however, challenges remain for the future of malaria poc testing and the global elimination of malaria. first, highly accurate tests are required for all malaria species affecting humans, but these panspecific tests are usually about % more expensive than rdts that only detect plasmodium falciparum. most p. falciparum rdts detect a malarial antigen, histidine-rich protein (hrp) , and the discovery of parasites that have a deletion in this gene has raised concerns about false negative results and ongoing transmission. also, the problems of providing adequate training and quality assurance of malaria tests and testing at remote poc sites are similar to those described for hiv rdts , . in the near future, as countries progress towards malaria elimination, funding for rdts may become an issue. as the intensity of transmission decreases due to lower parasite density in infected individuals, more sensitive tests will be needed, which can only be achieved with costlier amplification steps or with ultrasensitive platforms for antigen detection. also, decreasing numbers of cases mean that malaria tests are no longer cost-effective, and thus it is more difficult to justify funding in light of multiple competing priorities for limited health budgets. syphilis. syphilis, caused by the spirochete treponema pallidum, has a long latent period during which patients have no symptoms, but can remain infectious. syphilis in pregnancy can lead to adverse outcomes of stillbirths and miscarriage, and babies born with congenital syphilis in the developing world only have a % chance of survival during the first years of life , . despite the availability of simple diagnostic tests for antenatal screening and the effectiveness of treatment with a single dose of long-acting penicillin, syphilis is re-emerging as a global public health problem . it is estimated that , babies die each year as a result of syphilis-associated stillbirths and congenital syphilis, largely because of lack of access to antenatal screening , . rdts exist for detecting syphilis and are reported to have acceptable performance , and operational characteristics. the introduction of rdts was also acceptable to patients and health care providers and was shown to contribute to the improvement of antenatal care in low-resource settings . despite all this, syphilis rdts have not had the same success as hiv and malaria rdts. the main reasons for this are the lack of advocacy and political will to translate the evidence to national policy, lack of funding to make the tests affordable to those in need and the lack of a national control programmes to provide the architecture needed to coordinate all the different aspects of testing. ensuring adequate training for health care workers and supplies of commodities were cited as key implementation barriers in africa , . dual hiv and syphilis rdt testing in countries was prioritized by the who for the elimination of mother-to-child transmission (mtct) of hiv and syphilis by , , but a recent review showed that while prevention of mother to child transmission (pmtct) programmes for hiv have resulted in a dramatic decrease in the number of hiv-positive infants in sub-saharan africa, the rate of syphilis screening of pregnant women in the same countries has remained at unacceptably low levels of approximately % (ref. ). this is due largely to disparity in funding and lack of political will despite the global fund allowing countries to purchase syphilis rdts with hiv rdts since (ref. ). countries need to harness the architecture provided by hiv pmtct programmes to screen women for both infections using a single drop of blood in a single visit to a health care facility. dual rapid hiv-syphilis rdts with acceptable performance are now available and the who, as well as many countries, has adopted these hiv and/or syphilis rdts into their national guidelines , . tuberculosis. tb causes . million deaths a year, % of which occur in low-and middle-income countries. ending the tb epidemic by is among the health targets of the sustainable development goals . the tb lipoarabinomannan (lam) antigen test provides poc screening for active tb in hiv positive patients. this novel rapid test detects lam in urine samples, providing results in just minutes, enabling earlier treatment for patients . the lam test does not assess tb drug susceptibility, but multidrug-resistant tb is a threat to global health security with an estimated , new cases a year showing resistance to rifampicin (rif) -the most effective first-line drug . nucleic acid tests (nats) for tb are available and provide highly sensitive and specific means of diagnosis. the recent development of a sample-in-answerout automated testing device that allows for simultaneous detection of mycobacterium tuberculosis (mtb) and rif resistance in h min has improved case detection and could decrease transmission, though nats still require patients to make a return visit for test results and treatment. this test system is available in - modules, allowing for flexibility in throughput. the mtb/rif near-poc assay can improve time to diagnosis and treatment and increase the efficiency of the health system if introduced appropriately - , and as of june , two-thirds of high-burden mtb countries and half of countries with a high multidrug-resistant mtb had adopted this assay into their national tb programme guidelines. a wider adoption of such high-performing assays would allow countries to increase their case detection rates and potentially reach the milestones of the end tb strategy . although national tb programmes provide a robust architecture for the implementation of new technologies, challenges associated with the near-poc nat assay remain as barriers -affordability (molecular assays are device-based and costly, even with subsidy), expertise (more technically demanding than lateral flow rdts) and sustainability , in addition to power and per-test time. we expect that addressing these barriers would improve patient outcomes, but a true poc test is still needed to overcome remaining challenges such as sample preparation and demands on human resources . while culture has been a long-standing microbiological gold-standard and is highly specific, it is also the most technically demanding, costly and slowest of diagnostic options, requiring patients to return for another clinic visit to obtain their test results and treatment if necessary. thus, it does not conform well to the development of assured diagnostics. successful poc tests achieve high sensitivity, which is needed as screening tools to ensure that all true and suspect cases are brought to the attention of control programmes and appropriately managed. in particular, antibody-based detection tests, such as those for hiv and hepatitis c virus, are highly sensitive as antibodies are present in large quantities in blood, and blood samples can be collected with a finger prick and put directly into the test without any prior processing. also, antibody detection can be rapid and easy to perform with minimal training required (table ) . however, the choice of the antibody target affects a test's effectiveness -unless the diagnostic target is specific to the intended infection, there is the potential for false positive results due to cross-reactivity, which is the case with dengue and zika immunoassays , . therefore, antibody detection assays should be interpreted within the appropriate epidemiological context and findings from physical examination. the other major disadvantage of antibody-based tests is that antibodies are usually a marker of exposure to a pathogen and cannot be used to distinguish between those with active and past infection, which is the case of the rk tests for visceral leishmaniasis (vl) . a presumptive diagnosis of active vl can only be made using a combination of a positive rk test and more than weeks of fever and splenomegaly. the same is true of most syphilis rdts, which detect long-lived antibodies to treponemal antigens and thus do not diagnose active syphilis. antibodies to a non-treponemal antigen, which appears with infection and declines in the months after successful treatment, are used in a flocculation assay called the rapid plasma reagin assay, which can yield a result in minutes but requires electricity to operate, a centrifuge for processing serum from whole blood, a shaker and cardiolipin as an antigen. a combination treponemal and non-treponemal rapid test has been developed in an immunochromatographic test in a lateral flow format with acceptable performance characteristics . antigen detection poc tests, such as those for chlamydia and gonorrhoea, suffer from three major drawbacks (table ) . first, the specimen used for sexually transmitted infections are usually from urethral, cervical or vaginal swabs that require multiple steps to solubilize the bacteria and free antigen before reaction with the capture antibody. this sometimes requires a heating step and adds to the complexity and cost of the poc test. urine is the preferred specimen in men with such infections, and current poc tests require a urine centrifugation step to concentrate the bacteria before processing and reaction. another common drawback of antigen detection tests is the potential for false positive results due to cross-reactivity with antigens from closely related bacterial or viral species. this is especially true if polyclonal antibodies are used as capture antibodies. finally, a common disadvantage of current antigen detection poc assays is low sensitivity, often requiring to bacteria for the rdt to become positive. malaria rdts are an exception to these drawbacks in that the parasites are present in large quantities in blood and no pre-processing or concentration steps are required. for most antigen detection poc tests, the low sensitivity may be due to low concentration of target antigens, inefficiency of extraction or limited optimization of reagents, which has hampered chlamydia and gonorrhoea tests , . however, gift et al. showed that rapid chlamydia tests with a sensitivity of % can lead to more infected patients being treated compared to nats, which require patients to return for their test results . they called this the rapid test paradox, which was also recently seen with a p assay for early infant diagnosis of hiv, where a sensitivity of % can still lead to a higher 'diagnostic yield' than nats performed on dried blood spots sent from remote antenatal clinics . nats offer a more sensitive and specific alternative to antigen detection assays as nucleic acid targets can be selected from a genome sequence with high specificity, and the amplification process to increase sensitivity can be fairly rapid (table ) . for example, the near-poc tb diagnostic involves primer-based amplification of mtb dna specifically, including regions associated with rif drug resistance. thus, nat tests are generally highly sensitive and more specific than antigen-or antibody-based tests, and may help inform on drug susceptibilities. while instruments are available for highthroughput screening of patients and subsidies can bring test costs down to us$ , the equipment (capable of four tests at a time) costs more than us$ , , which may be prohibitive in high-incidence regions. thus, a truly poc diagnostic based on nats without needing any equipment is still a promise and not a reality as yet , . of all the criteria originally accepted, the requirement of equipment-free is perhaps the only one which is not as critical as originally defined. a wide range of near-poc nats have been developed for use outside of laboratory settings and most of these assays are automated, requiring only - minutes of hands-on time and minimal training. these near-poc devices come in sealed units with internal self-calibration making it easier to ensure quality of testing and most are also equipped with data transmission capabilities, which make these platforms very attractive in the context of disease surveillance and epidemic preparedness. most of these near-poc devices have a broad menu of diagnostic targets which makes the capital cost of purchasing the device less of an issue. reagents are pre-measured and dried ready for hydration with the introduction of the specimen. however, near-poc nat cartridges are expensive to manufacture and not affordable to most developing countries without subsidies. rapid advances in miniaturization, material science, electronics and data transmission in recent years have made minimal instrumentation a reality for new diagnostics, including the use of smart phones, which are widely available, custom developed and low cost. the use of a dongle to connect a smart phone to a microfluidic disc to detect hiv and syphilis antibodies in finger-pricked blood allows the phone to power the reaction, interpret the results and transmit the data to a central database. this smart phone-based poc assay is currently undergoing clinical trials . use of a smart phone to power nats is in development and will play an important role in future poc applications , . in particular, there has been considerable interest shown in utilizing mobile phones as readers and connectivity for rdts using rfid (radio frequency identification) to prevent errors in subjective interpretation and transcription [ ] [ ] [ ] [ ] . while phone-based diagnostics are attractive as an option, regulatory approval and rapid updates of phone software that can affect test performance are important challenges. defining and quantifying risks and benefits. while successes need to be celebrated, significant challenges remain. first, as no diagnostic is perfect, countries continue to struggle with defining acceptable risks of false positive or negative results when a novel diagnostic technology may provide incremental clinical benefits. in the developing world where over % of the population reside in rural areas, and the sustainable development goals urge countries to provide universal health coverage and leave no one behind, the trade-off between accuracy (sensitive and specific) and accessibility (user friendly, rapid and deliverable) becomes paramount . while it impossible to give absolute values across different tests, both sensitivity and specificity remain critical. in selecting an ideal test, the positive and negative predictive values, which are dependent on the prevalence of the disease as well as the characteristics of the diagnostic test, should be taken into account, but few studies have been performed to determine quantitatively what tradeoffs are acceptable. an analysis for syphilis screening compared the use of a laboratory-based immunoassay with treponemal rdts in tanzania . it showed that a test that has % sensitivity but can only be used in sophisticated laboratories can realistically only be accessed by - % of the population, while a rapid lateral flowbased antibody test that has only % sensitivity, but can be used at all levels of the health care system effectively gives a correct diagnosis to as many as % of the population, highlighting that tests should not be evaluated purely on technical performance, but rather on diagnostic performance and clinical impact. training and quality assurance. assuring the quality of tests and testing is the biggest challenge when testing is decentralized at poc. there are many rapid tests from various manufacturers available, and test quality may impact accurate and inconsistent diagnosis across different sites, with studies showing that high rates of errors were observed even in performance of simple rdts for hiv and malaria , . quality of testing requires proficiency panels be sent to all the poc testing sites by a national reference laboratory. including positive and negative controls with each box of tests will allow all tests to be approved once they arrive at their destination and before first use. recently, nine african countries developed a national system for assuring the quality of poc testing for hiv , . with data connectivity from each testing site, quality assurance results can be linked to test results at each poc testing site at a centralized database to trigger alerts for corrective action. supply chain software can also be linked through these connectivity solutions, avoiding stock-outs. demonstrating the value of a novel diagnostic technology. the value of a diagnostic goes beyond the technology, as each test needs to be matched to its 'testing environment' , which includes population characteristics, prevalence of target diseases, comorbidities/coinfections and health system characteristics. national programmes should take advantage of the rapid turnaround time of assured tests to streamline patient pathways and increase the efficiency of the health care system. the roll-out of poc diagnostics requires the use of implementation science to ensure success , taking into account the cultural, behavioural, socioeconomic and health systems contexts. this includes a careful assessment of acceptability and feasibility linked to possible increased stresses on the health system/provider when testing is introduced into settings where thus far no or limited testing was performed. studies using the genexpert mtb/rif tb test showed that new diagnostic tests would not have the expected impact on outcomes if test introduction is not accompanied by changes in patient pathways or practices , . these studies highlight the importance of programmatic monitoring of the impact of novel technologies beyond studies that are usually conducted under controlled conditions. likewise, same-day testing and treatment using a syphilis rdt strengthened health systems in the amazon forest and rural china when policy makers were involved and testing was introduced within the appropriate social and cultural contexts , . for example, in peru, women normally need to present six times to the largest maternal hospital in lima for their prenatal syphilis screening to be completed and treatment provided, but the introduction of the rapid syphilis test streamlined testing and treatment to one visit, reducing patient out-of-pocket expenses and increasing the efficiency of a busy health care facility . there are few detailed analyses which have been conducted to accurately determine the economic impact of many of the available tests, including the diagnostic cost versus the overall economic impact. while these benefits are intuitively important, they are often difficult to quantify . it would, therefore, be extremely useful to have economic analysis tools for each of the major diseases or conditions, so that developers have an understanding of cost implications and what cost structures would be acceptable to health service implementers. as an example, it may be necessary to accept cost trade-offs when addressing global health threats (for example, zika, ebola, and so on), where speed of intervention is critical. this having been stated, low-cost diagnostic tests remain critical in resource-limited settings. in the past two decades, the biggest drivers of diagnostic development were well-resourced diseases such as hiv, malaria and tb. in recent years, the increasing frequency and severity of global health emergencies caused by infectious diseases of epidemic potential, such as severe acute respiratory syndrome (sars) coronavirus, middle east respiratory syndrome coronavirus (mers) co-v, ebola and zika virus, have made the global community realize the need to accelerate assured test development, validation, manufacturing and deployment. there is a need for innovation in rapid detection technologies that are assured but allow multiplex detection of a panel of pathogens such as major causes of respiratory illness, haemorrhagic fevers or enteric infections in a single specimen. these tests should not only identify the cause of outbreak but also be used to process multiple specimens with high throughput throughout the outbreak. another major driver of test development is the need for cheaper, better and faster tests that can be used at poc to reduce inappropriate antimicrobial use. an estimated , people die from untreatable conditions due to antimicrobial resistance (amr) every year worldwide , and if amr continues to spread, by , million people may die from resistant infections annually at an economic cost estimated at $ trillion. at the primary care level, a simple rapid test that can be used to distinguish bacterial from nonbacterial causes of fever, respiratory and enteric infections would allow health care providers to reduce antibiotic use and preserve them for future generations. the o'neill report also pointed out that a test that can identify a pathogen and its antibiotic susceptibility at the poc would allow the safe use of first-line drugs or drug combinations with savings to the health care system. to stimulate interest in innovation in diagnostic tests that can be used at poc, several countries have set up challenge prizes. in , the united kingdom announced the longitude prize of £ million, which seeks an affordable, accurate, fast and easy-to-use test for bacterial infections that will allow health professionals worldwide to administer the right antibiotics at the right time. the challenge is currently ongoing, with final submission by . more information available at: https://longitudeprize.org. in september , the us department of health and human services announced a challenge prize competition in which up to $ million will be awarded for one or more novel and innovative poc diagnostics that would have clinical and public health value in combating the development and spread of antibiotic resistant bacteria. more information is available at: https://dpcpsi.nih.gov/amrchallenge. these prizes may catalyse new technologies, but there are still no guarantees to the sustainability of these tests in resource-limited countries given that cost is a critical factor woven into every step needed to bring about and sustain testing. donors and funders of diagnostics, such as the the bill & melinda gates foundation, global fund, unitaid and aid agencies from national governments such as pepfar and dfid, play a critical role in incentivizing diagnostic innovation and addressing market dynamics. technology advances to support innovation. technology , markets and medical devices have matured to enable connected diagnostics to become a useful tool for epidemiology, patient care and tracking, research, and amr and outbreak surveillance. the ability to digitize data from laboratory and poc platforms, including lateral flow rdt results, can standardize the interpretation of results and allows data to be linked to proficiency testing to ensure testing quality, reducing interpretation and transcription errors. remote monitoring of poc instrument functionality and utilization through connectivity allows programmes to optimize instrument placement, algorithm adoption and supply management. alerts can be built into the system to raise alarm at unusual trends such as outbreaks. the application of mobile devices and related technologies to health care is improving patients' access to health information and treatment, offering possibilities to diagnose, track and assess the impact of infectious disease interventions across the world , . smart devices can also be used to automatically add data to a central database and allow systems to assess likelihood of a diagnosis or predict disease outbreaks through machine learning, providing a route to smart diagnostics that incorporates historical or epidemiologic data to make diagnoses more accurate. finally, new engineering fields such as the internet of things (iot), industry . and printed electronics [ ] [ ] [ ] [ ] promise to add significantly to the technologies that can be chosen and incorporated into new diagnostic devices. many of these technologies are aimed at high-volume and low-cost distributable manufacturing, thus fitting in well with the goal of poc diagnostics. new detectors and light sources also suggest that incorporating these into tests could allow for more accurate result reading and the possibility of multiplexing. while it is clear that the original assured criteria remain relevant, opportunities exist to improve future diagnostics by incorporating new technological elements to provide real-time quality control for testing and treatment and overcoming the difficulties in specimen collection and/or processing , which currently limits scaling-up of diagnostics in resource-limited areas. we therefore propose two additional criteria of r (real-time connectivity) and e (ease of specimen collection and environmental friendliness) into the original assured, to create a new acronym of reassured (table ) . to use testing to effectively survey or treat patients, it is critical to obtain and analyse results at the poc . however, one of the main challenges to poc testing is ensuring that results are rapidly provided to the patient once testing has been completed ; this is formidable challenge when testing is decentralized at hundreds or thousands of different sites by health care workers who are not consistently skilled in reading test results, leading to risk that incorrect data is being recorded and/or transmitted. one solution would be to allow the analysis of test results at a centralized level for consistent diagnosis and epidemiological surveillance. many manufacturers are now embedding connectivity into poc and near-poc instruments (for example, the alere pima poc cd device ). other manufacturers have developed innovative connectivity solutions that can use mobile phones to read the results from lateral flow assays and provide electronic result exchange, while a third option would be to include connectivity directly onto the test . ideally, connectivity should not only include collection and transmission of test data, but also analysis to provide feedback for immediate patient treatment or for surveillance. with the addition of barcodes, two-dimensional codes or electronic storage into tests, a number of other data points can be collected, including manufacturing information (for example, lot numbers), dates, expiry dates, stock availability and possibly even environmental conditions such as temperature and humidity under which the tests have been manufactured, transported, stored and used. for instrumented tests, maintenance and other machine data can be collected. thus, connectivity solutions can increase quality assurance for poc tests and would allow for centralized and real-time decision-making, even across tiered laboratory systems and during outbreak investigations and global health emergencies. moving forward, it is critically important to make provisions for poor or non-existent internet availability to support sustainability standards and that systems are developed with compatibility so that they can be linked into central databases. ease of specimen collection. specimen collection and processing may need further in-depth development. first, it is ideal to have noninvasive specimen collection given that more tests become available as self or home tests. second, samples come in many different formats (blood, urine, sputum, stool, swab, breath, and so on) and require different preparation depending on the test to be performed. this may include concentrating the sample (or possibly titration), purification, lysing of cells, target amplification, and so on. while most of these processes can be easily performed in the laboratory, there remain few solutions for collecting and performing these tasks at the poc . oral tests for hiv and hepatitis c virus are good examples of advances in non-invasive sampling, although the collection device is more expensive than blood collection via disposable capillary tubes. related, given that rapid lateral flow antigen detection tests often have lower sensitivity, extra processing steps such as heating or other forms of extraction are required when using specimens other than blood. environmental friendliness. advances in technology have made the assured requirement for equipment somewhat less daunting. however, in light of more diagnostic tests now being performed in both urban and rural areas, there could be more future effort devoted to the environmental impact of these tests. the cumulative effect of many tens of thousands of tests performed at remote sites away from laboratory infrastructure may pose health and environmental risks and put a strain on limited resources. some examples include the plastics used in current rapid tests that cannot be recycled and give out toxic fumes when burned, and testing cartridges that may even contain harmful chemicals and need to be disposed of properly. recyclable materials should be used, when possible, for the housing, substrate matrix materials, and reagents used in tests. paper, an obvious choice of substrate material that has many inherent advantages over standard plastic materials, will see increased usage, not only in lateral flow formats but other paper based formats as well such as in micro paperbased analytical devices (μ pads) [ ] [ ] [ ] . and recently, cell-free synthetic gene networks for in vitro applications at poc, have been achieved by freeze-drying cell-free systems onto paper, which increases stability at room temperature and can be easily transported and stored, and simply re-activated by adding water . other factors also need to be considered, such as disposal of test reagents, clinical samples and materials used for active components such as electronic tracks and electrodes. the assured criteria have been a valuable framework for developing devices and methods to detect major human diseases in challenging poc contexts. however, over the last decade, new technologies, not envisaged or available at the time of the first assured criteria definition, have given rise to the possibility of including new considerations into the next generation of devices and tests. we propose the acronym reassured for the design of future diagnostic tests to address important priorities such as global health emergencies and amr. an ideal test would be one that combines the best of both existing diagnostic worlds (instrumented laboratory based tests with lateral flow tests) and technologies currently being developed (fig. ) , which would provide an important extension to diagnostic laboratory systems and fulfil the sustainable development goals of 'no one left behind' in terms of effective health care service delivery. such tests can only be created by forming strong collaborative partnerships across many disciplinary boundaries, and we look toward a future when data connectivity linking cost-effective assured diagnostics to laboratory systems will form the backbone of health care systems and provide real-time data for evidence-based disease control and prevention strategies, more efficient health systems and improved patient outcomes. diagnostics for the developing world mapping the landscape of diagnostics for sexually transmitted infections: key findings and recommandations the costs of accessible quality assured syphilis diagnostics: informing quality systems for rapid syphilis tests in a tanzanian setting reducing the burden of sexually transmitted infections in resource-limited 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diagnosis, treatment and control? metaanalysis of the performance of a combined treponemal and nontreponemal rapid diagnostic test for syphilis and yaws systematic reviews of point-of-care tests for the diagnosis of urogenital chlamydia trachomatis infections performance and operational characteristics of point-of-care tests for the diagnosis of urogenital gonococcal infections the rapid test paradox: when fewer cases detected lead to more cases treated: a decision analysis of tests for chlamydia trachomatis sex point-of-care p infant testing for hiv may increase patient identification despite low sensitivity emerging technologies in point-of-care molecular diagnostics for resource-limited settings a simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings expert review of molecular diagnostics portable devices and mobile instruments for infectious diseases point-of-care testing a smartphone 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and control: a call worth making bringing mhealth connected infectious disease diagnostics to the field integrating electronics and microfluidics on paper from smartphones to diagnostics : low cost electronics for programmable digital microfluidics and sensing a flexible future for paper-based electronics biosensors: sense and sensibility rapid diagnostic tests for neurosyphilis compounding diagnostic delays: a qualitative study of point-of-care testing in south africa data connectivity: a critical tool for external quality assessment functional screen printed radio frequency identification tags on flexible substrates, facilitating low-cost and integrated point-of-care diagnostics a low cost point-of-care viscous sample preparation device for molecular diagnosis in the developing world; an example of microfluidic origami sensing approaches on paper-based devices: a review diagnostics for the developing world: microfluidic paper-based analytical devices recent developments in paper-based microfluidic devices paper-based synthetic gene networks printed microfluidic channels the authors declare no competing interests. reprints and permissions information is available at www.nature.com/reprints.correspondence should be addressed to x.-s.c. or r.w.p.publisher's note: springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. key: cord- -ktet wl authors: lim, jong-min; do, eunju; park, dong-chan; jung, go-woon; cho, hyung-rae; lee, seo-young; shin, jae wook; baek, kyung min; choi, jae-suk title: ingestion of exopolymers from aureobasidium pullulans reduces the duration of cold and flu symptoms: a randomized, placebo-controlled intervention study date: - - journal: evid based complement alternat med doi: . / / sha: doc_id: cord_uid: ktet wl aim: the objective of the study was to assess the efficacy of exopolymers from aureobasidium pullulans (eap) on the incidence of colds and flu in healthy adults. methods: we conducted a randomized, double-blind, placebo-controlled study at the onset of the influenza season. a total of subjects ( – years of age) were recruited from the general population. the subjects were instructed to take one capsule per day of either eap or a placebo for a period of weeks. the duration of cold and flu symptoms, a primary variable in assessing effectiveness, and serum cytokine levels as well as wbc counts as secondary variables were also evaluated. results: eap was associated with a statistically significant decrease in the duration of cold and flu symptoms, a primary variable in assessing effectiveness. although cold and flu symptom levels were not significantly different at a significance level of %, the cold and flu symptom levels of the eap group were less severe compared to the placebo group. no statistically significant changes of serum cytokine levels as well as wbc counts were observed. conclusion: the results showed that eap is a useful pharmaceutical and functional food material for preventing and treating colds and flu. the immune system has evolved to protect multicellular organisms, including humans, from pathogens. immunostimulatory effects are regulatory actions that counteract reduced immune responses caused by immunodeficiency diseases, viral infections, malnutrition, tumors, and aging. two strategies have been developed to stimulate the immune system. one method is to increase antigen-specific or nonspecific immune responses, and the other method involves the use of appropriate immunosupplements for antigen administration [ ] . respiratory viruses are among the most infectious pathogens in humans, and many differences occur in the kinds of pathogens, their antigenicities, and their worldwide infection patterns. recently, respiratory diseases such as middle east respiratory syndrome, severe acute respiratory syndrome, and the flu caused by novel swine-origin influenza a strains have emerged and begun to spread rapidly [ ] [ ] [ ] . as the associated respiratory viruses show very strong tendencies to spread, there is a growing interest in foods that promote immune functions as well as a global monitoring system for influenza [ ] . the results of several researches have revealed a positive correlation between food nutrition and the control of human immune functions, and various foods have been recognized as functional foods that can improve immune functions. these food materials may be derived from vegetables [ ] , evidence-based complementary and alternative medicine seafood [ ] , mushrooms [ ] , microbes such as lactic acid bacteria [ ] , chitosan [ ] , and peptides [ ] . - , / , -glucan is derived from yeast cell walls and modulates many in vivo and in vitro activities [ , ] . its main immunopharmacological activities [ ] [ ] [ ] are associated with antitumor effects [ ] , increased host resistance to viral, bacterial, and parasitic infections [ ] , and adjuvant effects [ ] . proximate composition of extracellular polysaccharides of aureobasidium pullulans is carbohydrate . %, sugar . %, crude protein . %, and moisture . %. namely, above % of the proximate composition is polysaccharides and there is a small amount of protein and fat (personal comm. dr. dong-chan park). it has been reported that the extracellular polysaccharides isolated from aureobasidium pullulans are pullulan (poly-- , -maltotriose-based exopolysaccharide, eps) [ ] , aubasidan ( - , -d-glucan with - , -branches to - , side chains) [ ] , and -glucan ( - , / , -d-glucan) [ ] . however, the physiological activity of polysaccharides produced by aureobasidium pullulans has been mainly studied for - , / , -d-glucan [ ] . exopolymers purified from aureobasidium pullulans sm- (eap; its solubility is about % in water), the test food material used in this study, containing % - , / , -glucan [ ] , are used in foods and have shown potent immunomodulatory activities in a mouse model [ ] . in addition, eap showed no adverse events in clinical studies designed to evaluate its effectiveness on bone metabolism improvement [ , ] and on atopic dermatitis [ ] . therefore, -glucan is considered safe for human ingestion. many reports have described the immunomodulatory activities of -glucan against immune-related diseases [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] , but only a few reports have described its effects against colds and flu. for this reason, a clinical study is now being performed to evaluate the efficacy and safety of -glucan from aureobasidium pullulans against colds and flu in patients. in this study, we selected adult subjects who provided written, informed consent to participate, who satisfied our selection criteria, and who did not meet exclusion criteria. we randomly administered eap or a placebo, where subjects took a daily dosage of mg for weeks. we evaluated immunological improvements of the test food by observing functional changes in the immune system before and after administering the test food materials in the eap and placebo groups. we also observed the duration and total levels of cold and flu symptoms during the test period. the eap and placebo products used in this clinical research study were packaged inside boxes provided by glucan co., ltd. (busan, korea) and were supplied and distributed by aribio co., ltd. (seongnam-si, gyeonggi-do, korea). some eap samples were deposited in the herbarium of silla university (busan, korea; encoded as eap choi ). sixty-five capsules were provided to each subject, taking into consideration an -week dosage ( days, capsules), a visitation window of days ( capsules), and storage products ( capsules). the test food was manufactured as maroon-colored hard capsules, and each capsule of test food contained mg of eap and . mg of microcrystalline cellulose, whereas the placebo food contained . mg of microcrystalline cellulose. the test food was supplied to a testing agency in sealed white plastic bottles, each containing capsules intended for person. the test foods used in this study were identical in appearance and description and would be difficult to distinguish with the naked eye. the experiment was conducted in doubleblind format for the subjects and researchers by attaching identical labels to the test foods. the main ingredients, generic names, and lot number were not recorded on the test food labels to avoid exposing the differences between the test groups. subjects took eap hard capsule once daily for weeks on an empty stomach, with a sufficient amount of water. the subjects were healthy adults who did not have any disease that required proactive treatment. the number of subjects assigned to each group was ( overall). in consideration of a potential % dropout rate, the number of subjects in each group would decrease to , the minimum number of subjects for an effectiveness analysis ( figure ). subjects included in this study had to meet the following criteria: adults between and years of age; individuals with a white blood cell (wbc) count of - × / l; individuals who could be monitored throughout the test period; individuals who listened to a thorough explanation of the study's purpose and contents and voluntarily signed an informed consent form to participate in the experiment. subjects for whom the following criteria were applicable were excluded from the experiment: individuals with a body mass index (bmi) under or over ; individuals who exceeded the normal maximum alanine transaminase and aspartate transaminase levels by -fold; females who were pregnant or were breast-feeding; females of childbearing age who did not agree to use contraceptives via medically proven methods (e.g., condoms, lubricant, and femidom) during the test period; individuals with a fasting plasma dextrose concentration over mg/dl; individuals with high blood pressure (systolic blood pressure of mm hg or diastolic blood pressure of mm hg); individuals continuously using medicine that could affect the effectiveness assessment (hyperlipidemia medicine, steroid medicines, hormone medicines, immunosuppressants, and antibiotics); individuals who require continuous treatment for psychiatric disorders such as anorexia, depression, and manic depression; individuals with systemic diseases such as immunity-related diseases, serious hepatic and renal insufficiencies, malignant tumors, pulmonary disease, collagenosis, multiple sclerosis, allergic skin conditions, and other autoimmune diseases; individuals with a medical history of drugs and clinically significant allergic reactions; individuals with a history of gastrointestinal disorders that could affect the absorption of the test foods or a history of gastrointestinal surgery (excluding a simple appendectomy or hernia operation); individuals who consumed medicine or herbal medicines within a month of participation in the experiment which could affect immunity; individuals who participated in a different human study or clinical test and took experimental products within months of participation in this experiment (excluding human studies with cosmetics); and individuals whom the researchers otherwise determined might have difficulty completing the experiment. dosages of the experimental products were temporarily suspended at instances where it was appropriate to stop the experiment for the welfare of the subjects. events that may have occurred. in the following cases, administration of the test foods was temporarily suspended: (a) a temporary interruption on the occurrence of an adverse reaction or for the treatment of an adverse reaction; (b) when showing adverse events related to the safety of the test foods; and (c) in case of showing acute reactions (allergies and hypersensitivity) to the test foods. however, in the case of a temporary interruption for the occurrence of an adverse reaction or for the treatment of an adverse reaction, if there was no problem in its compliance, the study was continued. cases that were processed as dropouts included those in which test foods were allocated and the subject or a legal representative withdrew consent from participation in the experiment, cases where results for a final inspection could not be obtained, cases where subjects did not adhere to the test protocol resulting in a significant effect on the test results, cases where there was an interruption in contact with the subject (i.e., when the subject could not be traced), cases where the subject failed to make visits, subjects for whom a disease was discovered which went unnoticed during the screening inspection, cases where compliance with usage of the test food fell below %, as assessed with the usage log, cases in which, without the direction of the researcher, the subject used a medicine or product while they were taking the test food which could affect the research results or interpretation of data, cases in which the subject had an average weekly drinking quantity as ethanol of g/week throughout the test period, or cases where the lead researcher determined that the research proceedings were inappropriate or that there could be a significant effect on the safety of the subjects or the experiment results. subjects stopped taking test foods and were processed as dropouts for the following reasons, in which it was not possible to continue the human study: cases in which a serious adverse event occurred with the subject, cases in which an adverse event made participation in the experiment impossible, cases in which the researcher determined that the usage and observation of the test foods would be impertinent, or cases in which clinical tests were not possible due to the death of a subject or emergence of a disease. subjects who took the test foods and later dropped out of the study, where a portion or the entire estimate value of the final assessment (visit ) was omitted, were included in the itt group's analysis data. missing values were processed after a dropout occurred using missing value processing method for effective assessments. the results of all subjects who dropped out were excluded from assessment of the per protocol (pp) group ( figure and table ). . . . drinking, diet, and exercise among the subjects. during the experiment, subjects maintained regular levels of drinking, diet, and exercise which were similar to levels prior to participation in the experiment. to verify this, on the day of base evaluations, we examined the dietary contents evidence-based complementary and alternative medicine for contiguous days prior to the visitation day and the weekly exercise types and times prior to the visitation day. the number of alcoholic drinks and the amount of ethanol consumed during the week prior to the visitation day were also examined. subjects kept a daily record of whether they consumed the test foods and recorded contiguous days of their diets, including saturday or sunday. exercise, alcoholic drinks, and test food consumption were recorded in a chart provided by the testing agency, a comparison was made against these quantities prior to participation in the experiment, and observations were made as to whether there were any changes that could have significantyl affected the experiment results. subjects were assigned to the eap group (the group taking eap) and the placebo group (the group taking the placebo) based on a randomized list produced with a random sampling table generated using microsoft excel on microsoft windows ( figure ). the exclusion criteria used to select subjects during the screening visit (visit ) were verified, and individuals who met selection criteria and had met no exclusion criteria were selected as subjects for this study. food materials were allocated to the subjects during visit . the subjects selected for the experiment were issued a subject number in the order of visits made during visit and were provided with the test foods, which were randomly allocated. the foods used in the human test were provided only to the participating subjects, based on the process described in the human test protocol ( table ) the visitation dates allowed for the set base visitation days + additional days. those who were selected as test subjects received the test foods within days from the base evaluation date (selection inspection date) and began taking the test foods by the next morning. demographic data including the initials, age, gender, birthdate, weight, and height of the subjects and basic information such as medical history, medicinal intake history, combined treatment, concomitant drugs, smoking, drinking, and exercise habits were recorded in detail. the contents during the last years were recorded in the medical histories, and contents during the last weeks were recorded in the medicinal intake history. the types of exercise and the exercise times were examined for week prior to the time of the visitation day. diet and exercise were compared during the base evaluation period and experimental period and observed to determine whether any important changes occurred which could affect the test results. the number and quantity of alcoholic drinks consumed during the week preceding the visitation day were examined, and that information was converted into the number of grams of ethanol consumed and recorded. levels. blood pressure, body temperature, and pulse were measured and recorded as vital signs. obesity levels were measured using a body fat analyzer (inbody . , biospace, korea), and the bmi (kg/m ), percent evidence-based complementary and alternative medicine my daily life was very uncomfortable due to symptoms, and proactive treatment was needed. in the case of severe discomfort, i may stop working or studying or be admitted to the hospital body fat (%), waist-hip ratio, and visceral fat area (cm ) were recorded. hematological examination of wbcs, red blood cells, hemoglobin levels, hematocrits, and platelets was performed using an automated analyzer (sysmex xp- ; sysmex, kobe, japan). the levels of blood urea nitrogen, creatinine, uric acid, total bilirubin, albumin, total protein, alkaline phosphatase, glucose, alanine transaminase, aspartate transaminase, gamma-glutamyl transferase, triglyceride, total cholesterol, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol were measured using a clinical chemistry analyzer (dimension xpand plus; siemens, munich, germany). all urine samples were stored in the dark at ∘ c and were analyzed within two hours of collection. the ph, specific gravity, and protein and glucose levels were measured using a semiautomated analyzer (uriscan pro ii; yd diagnostics, seoul, korea). pregnancy testing was performed using a kit detecting human chorionic gonadotropin. serum concentration of cytokines was analyzed by using hmaglxsa ( plex) multiplex elisa kit (r&d systems, minneapolis, mn). cytokine levels were determined using luminex (luminex, austin, tx, usa) and the data were reported as median fluorescent intensities. comparisons. if immune functions improve, the disease duration and symptom levels should decrease due to increased resistance to viral diseases such as colds and flu. accordingly, we examined the duration and levels of cold and flu symptoms after consuming the test food products as a functional index of immunological improvements. for the survey following the administration of test foods, a form was provided in which subjects made a daily record of their health conditions, with a daily record of their test food dosages. nine symptoms were monitored to inspect the health conditions of the subjects in the survey: fever, chills, runny nose, nasal congestion, coughing, sneezing, sore throat, headache, and gastrointestinal symptoms (nausea, vomiting, diarrhea, and abdominal pain). subjects marked i for "symptoms exist" and × for "no symptoms." to record the symptom levels, subjects used a -step scoring point system, where they marked ( ) for no symptoms, ( ) for minor symptoms, ( ) for moderate symptoms, and ( ) for serious symptoms [ ] and marked whether they took early leave or were absent from work or school due to symptoms. table shows a detailed explanation of the criteria used for reporting symptom levels. to assess the effectiveness of the experimental food products, subjects kept daily records in their dosage logs of cold and flu symptom durations and symptom levels during the testing period. compliance with ingesting test foods was evaluated based on the food-usage logs. during the final visit, the number of remaining foods collected was compared with the usage log records. in cases where there were differences between the recorded and actual amounts of food taken, compliance was verified when the differences were small. primary effectiveness assessment variables included the duration and total score of symptom levels for cold and influenza. secondary effectiveness assessment variables included serum il- , il- , il- , il- , tnf-, and inf-levels, as well as wbc counts and differential blood counts. evidence-based complementary and alternative medicine on significance comparisons between the eap and placebo groups. the methodologies described below were followed for detailed analysis. analysis sets obtained from the test subjects were composed largely of an itt analysis group and a pp analysis group. the itt group comprised the primary data set used for effectiveness assessments, and the pp group was additionally analyzed to assess the effectiveness. subjects in the itt group included those who had taken the test food materials and whose assessment variables were measured at least once during visit . subjects in the pp group included those in the itt group who completed the test according to the study protocol. it has been predicted that fewer subjects will contract viral diseases such as cold and flu if their immune functions are enhanced and that the duration and levels of symptoms will decrease if one of the diseases is contracted. the activation state of principal cells related to immunity can be determined by measuring changes in the serum contents of cytokine il- , il- , il- , il- , tnf-, and inf-. to assess the effectiveness of the test food materials, the significance of the mean difference (visits - ) was tested for each variable included in the effectiveness test. in other words, a statistical comparison was made between the average variation before and after food ingestions in the eap and placebo groups. to this end, normality was tested for the evaluation data. the parametric method of a twosample t-test was chosen if normality was satisfied, whereas the nonparametric method of a wilcoxon's rank-sum test was chosen if normality was not satisfied. in addition, the above significance tests were performed on mean differences between the eap and placebo groups between each visit after test food ingestions. to analyze the prevalence of cold symptoms, subjects recorded the duration and levels of symptoms when they contracted a cold or the flu prior to ingesting the test food. during visit , subjects recorded the duration and total symptom scores of cold and influenza symptoms during the test period. accordingly, it was not meaningful to compare the mean difference between visits, considering that the rating scales used in visits and were different. in other words, we confirmed homogeneity between the test groups in visit and evaluated the effectiveness by comparing the results between test groups in visit . forward (locf) method (a single-imputation method) for data missing in the final effectiveness assessment. typically, the locf method is easy to use in clinical trials, despite the restricting assumption where missing data are treated as a constant. the locf method is commonly used because it provides conservative results. however, there are no commonly recommended methodologies for processing missing values [ ] . in this study, the statistical analytic data collected was comprised of only the baseline assessment prior to the ingestion of test food materials and the final assessment after ingestion of test food materials. the missing values during the final assessment were not replaced by the base assessment values but were substituted by the average of each group and assessed. in this study, we screened individuals who voluntarily agreed to participate in this human study, and subjects who met the selection criteria and did not meet any exclusionary criteria were enrolled. among the subjects, were assigned to the eap group and were assigned to the placebo group ( figure ). four instances were verified in which subjects violated the study protocol while consuming the test foods. these subjects were processed as dropouts. among the subjects who were selected, individuals from the eap group dropped out due to violations in the visitation schedule and shortfalls in compliance, and individuals from the placebo group dropped out due to withdrawal of informed consent and shortfalls in compliance. the remaining subjects adhered to the test protocol and completed the test. the current states of dropouts are separated according to the test group ( figure ) . compliance with ingesting test food materials was assessed in visit . the contents recorded in the daily record filled out by the subjects as well as the quantity of remaining products returned during the final visit were confirmed and assessed. compliance was calculated using the following formula: compliance (%) = (number of food materials ingested/number of food materials that should have been ingested) × , where the number of food materials ingested = number of food materials provided − number of food materials returned. subjects whose compliance was below % were set as dropouts, and there were dropouts in this study due to compliance shortfalls. the compliance of test food material ingestion was . ± . % in the eap group and . ± . % in the placebo group. a significant difference in compliance between the test groups was not observed (table ) . a homogeneity test was conducted between test groups for the following: measurement values prior to food material ingestion regarding demographic information of the subjects including age, gender, medical history, treatment history, medication history, and concomitant medication and measurement values before and after ingestion of food materials regarding items that could affect the test results based on changes in lifestyle habits during the test period including regular exercise, smoking, and drinking. the results of a preliminary investigation on the age, gender, medical history, treatment history, medication history, concomitant medication, exercise, smoking, and drinking among the subjects are summarized in tables and . no significant differences were found between the test groups regarding any of the items examined. missing values were replaced with averages and used in the itt group data analysis. (a) (b) figure : foundational statistics and comparisons of cold symptom durations (days; (a)) and levels (b) between test groups: eap group (black columns) and placebo group (gray columns). variables in the itt group. the results of a -test performed to evaluate significant differences between groups before and after ingesting the test food materials verified that the duration of cold symptoms ( value = . ) and cold symptom levels ( value = . ) at visit were not significant at a significance level of %. statistical analysis also showed that no difference occurred between test groups prior to the ingestion of food materials. during visit , the duration of cold symptoms in the experiment group ( . ± . days) was lower than that of the placebo group ( . ± . days). the difference between the test groups was statistically significant ( value = . ). the eap group also had a lower score for cold symptom levels than the placebo group ( . ± . versus . ± . , resp.). this difference was significant at a level of % ( value = . ) but not % (figure ). were verified with respect to the mean difference of each measured item between the visitation times to assess the effectiveness of the test food materials on the blood test results. the results were not significantly different between the eap and placebo groups (table ) at a significance level of %. for wbc, basophil, and lymphocyte counts that wilcoxon's rank-sum test was used to analyze variables that did not follow normality. missing values were replaced with averages and used in the itt group data analysis. did not follow normality, a nonparametric wilcoxon's ranksum test was conducted. the results were not significantly different between the eap and placebo groups (table ) at a significance level of %. to assess the effectiveness of the test food materials, a -test was conducted to evaluate significance differences in the mean cytokine concentrations between visits - . the results were not significantly different between the eap and placebo groups (table ) at a significance level of %. il- , il- , il- , and tnf-values did not satisfy normality; a nonparametric statistics wilcoxon's ranksum test was conducted, revealing no significant differences in any of the items at a significance level of % (table ) . adverse events were observed in individuals from the placebo group and in individual from the eap group. in the placebo group, nausea and pruritus were confirmed in subject e , asthenopia and rash in subject e , and a sore throat in subject e . no other adverse events were observed aside from these. in the eap group, headache was confirmed in subject e , but no other adverse events were confirmed aside from this. all these adverse events subsided within a few days. in the case of subject e , who ingested the test food materials, the headache was completely alleviated after days, and the subject was judged as having no cause-and-effect relationship with ingesting the test food materials (data not shown). while the sgot or sgpt exceeds normal upper limit by fold, the finding is not considered to represent an abnormal phenomenon. however, the -gtp value was found to be abnormally high during visit for subject e , but examination of the results showed that the abnormal values were not related to the ingestion of test food materials. instead, the results were due to excessive drinking, where the subject consumed alcoholic drinks frequently ( days/week) and a high quantity of ethanol (average = g/week) (data not shown). with the occurrence of adverse events and abnormal changes in clinical test results, no items were found to correlate with the use of test food materials or were suspected to have a correlation. thus, the test foods were found to be safe in the context of this study. the various biological activities of -glucan were verified through in vitro testing, animal testing, and clinical trials [ ] . recently, the effectiveness of -glucan on respiratory diseases has been studied in rodent [ ] and human [ ] [ ] [ ] because their prevalence has increased rapidly. eap, exopolymers purified from aureobasidium pullulans sm- , containing % - , / , -glucan [ ] , are used in test foods and have shown potent immunomodulatory activities in a mouse model [ ] . however, this study is the first to evaluate the use of eap against respiratory diseases. to assess the ability of eap to improve human immunological responses and to alleviate cold or flu symptoms, adults aged - years with a white blood cell count of - x / l were screened. individuals were enrolled as subjects who satisfied the selection criteria and did not fall under any exclusion criteria (data not shown). in an aspect of subject's respiratory morbidity, none of the subjects had a respiratory disease at the time of enrollment. within weeks prior to the screening date of the subjects, there were subjects with light respiratory disease. after confirming no symptoms at the enrolment, the subjects were proceeded to obtain informed consent. the subjects (administrated with the test foods for a period of weeks) were randomly assigned to either eap or a placebo group. blood tests and surveys of cold or flu symptoms were conducted before and after ingesting test food materials, and the duration and symptom level of colds or flu, as well as the results of the blood test and cytokine analysis, were compared. the eap and placebo groups were composed of individuals that exhibited homogeneity and showed no statistically significant differences in their compliance of ingesting test foods or in gender, age, compliance, regular exercise, smoking, drinking, medical history, medicinal history, or concomitant drug administration. clinical data have shown that immunity-promoting functions can prevent acute respiratory infections from cold or influenza viruses and reduce the frequency of contracting colds or flu, symptom levels, and symptom durations based on effectiveness criteria [ ] . in this study, statistical analysis of the duration and level of cold symptoms, a primary variable for assessing effectiveness, showed that there were no differences in assessment values between the eap and placebo groups before ingesting test food materials. however, the duration of cold and flu symptoms after ingesting test food materials was significantly lower in the eap group than in the placebo group at a % significance level. the eap group also showed lower levels of cold and flu symptoms, which were statistically different at the % (but not %) significance level than placebo group. it is predicted that individuals whose immune functions are enhanced will contract fewer viral diseases such as colds and flu, with reduced durations and levels of symptoms. the activation state of primary cells related to immunity can be determined by measuring the serum levels of the cytokines il- , il- , il- , il- , tnf-, and inf- [ ] . according to the "guideline for safety and efficacy assessments of functional food on immune function improvement" from the ministry of food and drug safety of korea, changes in cytokine levels, wbc counts, t cell counts, and nk cell activity in the peripheral blood should be measured when determining the functionality of immunity reinforcement in humans [ ] . in this study, secondary variables including serum cytokines (il- , il- , il- , il- , tnf-, and inf-) and wbcs (neutrophil, eosinophil, basophil, lymphocyte, and monocyte) for assessing effectiveness did not exhibit statistically significant differences before and after ingestion of test food materials at a significance level of %. these results are consistent with those of choi et al. ( ) [ ] , where the daily intake level of eap (polycan tm ) or placebo food materials was set at mg, and changes in serum cytokines were studied (with the intention of observing effectiveness in immunity improvements of eap), but no statistically significant changes were found. although eap has shown potent immunomodulatory activities in a mouse model [ ] , no immunity improvement of eap on the human was observed in this study. the cytokine is a factor that needs to change suddenly according to the individual health condition and then return to the normal range [ ] . on the normal range of blood cytokine concentration, its individual variation is very large. thus, a large number of subjects are required to measure the normal range of cytokine concentrations [ ] . indeed, in a study of normal korean cytokine levels, subjects were studied [ ] , and in a study of normal american cytokine levels, subjects were examined [ ] to estimate the normal range of blood cytokine concentration. serval studies have shown that no changes in blood cytokine levels have been observed following ingestion of multivitamin and mineral supplement [ ] , probiotic supplement [ ] , fish oil [ ] , and cordyceps militaris [ ] , which are known to help improve immunity. this may be because the cytokine level increased during the test period and then returned to normal, or the number of subjects was small, indicating that the individual deviation range was not statistically significant. in this study, the total number of subjects was : in the test group and in the control group, respectively. therefore, the results of this study may not statistically overcome the individual variation range of the subject's cytokine level due to the small number of subjects. further research is needed on extensive clinical studies with clear statistical numberings to confirm the effects of eap on plasma cytokines. no significant adverse events occurred during the period of test food material intake, and adverse events (excluding colds) were observed in individuals from the placebo group (nausea, pruritus, asthenopia, rash, and sore throat) and in individual from the experiment group (headache). all these adverse events subsided within just a few days and were determined to have no cause-and-effect relationship with the ingestion of test food materials. changes in blood test values were also observed in the eap group with an increase in sgpt, tg, and -gtp values, but this was difficult to determine as being clinically abnormal. in addition, in an aspect of the respiratory morbidity, the subjects who suffered from cold during the test period appeared and then fully cured after the treatment, and no respiratory morbidity was shown in all subjects. therefore, eap was verified to be harmless to the human body. collectively, our data revealed that eap was associated with a statistically significant decrease in the duration of cold and flu symptoms, a primary variable in assessing effectiveness. although cold symptom levels were not different at a significance level of %, the cold and flu symptom levels of the eap group were less severe compared to the placebo group. no statistically significant changes were observed in the serum cytokine concentrations, wbc, and differential blood counts (secondary variables for assessing effectiveness). therefore, our data showed that eap is a useful medicine and functional food material for preventing and treating colds and flu. the data used to support the findings of this study are available from the corresponding author upon request. the authors declare that there are no conflicts of interest. human infection with mers coronavirus after exposure to infected camels from sars to avian influenza preparedness in hong kong whole-genome characterization of a novel human influenza a(h n ) virus variant, brazil epidemiological characterization of respiratory viruses detected from acute respiratory patients in seoul a review on immunostimulatory plants bioactive compounds from marine processing byproducts-a review mushroom immunomodulators: unique molecules with unlimited applications probiotic immunomodulation in health and disease application of chitin and chitosan derivatives in the pharmaceutical field bioactive peptides: production and functionality clinical and physiological perspectives of -glucans: the past, present and future functional food for immune regulation-beta-glucan a week randomized, double-blind human trial to compare the efficacy and safety of aureobasidium pullulans cultured solution and placebo on improvement of immune in subjects immunomodulatory activities of oat -glucan in vitro and in vivo immunomodulatory effects of aureobasidium pullulans sm- exopolymers on the cyclophosphamide-treated mice effect of glucan on natural killer (nk) cells: further comparison between nk cell and bone marrow effector cell activities purification of solubleglucan with immune-enhancing activity from the cell wall of yeast glucan as an adjuvant for a murine babesia microti immunization trial characterization and enzymatic hydrolysis of hydrothermally treated - , - , -glucan from aureobasidium pullulans an aubasidan-like -glucan produced by aureobasidium pullulans in thailand the structure of the carbohydrate moiety of an acidic polysaccharide produced by aureobasidium sp. k- production of ß , / , glucan by aureobasidium pullulanssm safety and efficacy of polycalcium for improving biomarkers of bone metabolism: a -week open-label clinical study randomized, doubleblind, placebo-controlled trial of the effects of polycan, ß-glucan originating from aureobasidium pullulans, on bone biomarkers in healthy women a clinical study for the efficacy and safety of ß-glucan from aureobasidium pullulans in mild to moderate atopic dermatitis patients a placebo-controlled trial of korean red ginseng extract for preventing influenza-like illness in healthy adults korea food and drug administration (kfda, guidelines for clinical trial statistics sample size calculations with dropouts in clinical trials Β-glucan derived from aureobasidium pullulans is effective for the prevention of influenza in mice immunomodulatory effect of pleuran ( -glucan from pleurotus ostreatus) in children with recurrent respiratory tract infections preventive effect of pleuran ( -glucan from pleurotus ostreatus) in children with recurrent respiratory tract infections -open-label prospective study placebo-driven clinical trials of yeast-derived ß-( , ) glucan in children with chronic respiratory problems efficacy of cold-fx in the prevention of respiratory symptoms in community-dwelling adults: a randomized, doubleblinded, placebo controlled trial guidelines for functional evaluation of health functional foods, 'can help improve immune function conceptual and methodological issues relevant to cytokine and inflammatory marker measurements in clinical research serum cytokine profiles in healthy young and elderly population assessed using multiplexed bead-based immunoassays baseline levels and temporal stability of multiplexed serum cytokine concentrations in healthy subjects the effects of a multivitamin/mineral supplement on micronutrient status, antioxidant capacity and cytokine production in healthy older adults consuming a fortified diet probiotic supplement consumption alters cytokine production from peripheral blood mononuclear cells: a preliminary study using healthy individuals proand anti-inflammatory cytokines in healthy volunteers fed various doses of fish oil for year regulation of human cytokines by cordyceps militaris this research was performed with the support of the industry core technology development project (no. ), ministry of trade, industry, and energy, republic of korea. jong-min lim and eunju do contributed equally to this work. key: cord- -beb oy authors: charpentier, charlotte; ichou, houria; damond, florence; bouvet, elisabeth; chaix, marie-laure; ferré, valentine; delaugerre, constance; mahjoub, nadia; larrouy, lucile; le hingrat, quentin; visseaux, benoit; mackiewicz, vincent; descamps, diane; fidouh-houhou, nadhira title: performance evaluation of two sars-cov- igg/igm rapid tests (covid-presto and ng-test) and one igg automated immunoassay (abbott) date: - - journal: j clin virol doi: . /j.jcv. . sha: doc_id: cord_uid: beb oy the aim of this study was to assess the analytical performances, sensitivity and specificity, of two rapid tests (covid- presto® test rapid covid- igg/igm and ng-test® igm-igg covid- ) and one automated immunoassay (abbott sars-cov- igg) for detecting anti- sars-cov- antibodies. this study was performed with: (i) a positive panel constituted of sars-cov- specimens collected from patients with a positive sars-cov- rt-pcr, and (ii) a negative panel of serum samples, all collected before november , including samples with a cross-reactivity panel. sensitivity of covid-presto® test for igm and igg was . % and . %, respectively. sensitivity of ng-test® for igm and igg was . % and . %, respectively. sensitivity of abbott igg assay was . % showing an excellent agreement with the two rapid tests (κ = . and κ = . for ngtest ® and covid-presto® test, respectively). an excellent agreement was also observed between the two rapid tests (κ = . ). specificity for igm was % and . % for covid-presto® test and ng-test®, respectively. specificity for igg was . %, . % and . % for covid-presto®, ngtest ®, and abbott, respectively. most of the false positive results observed with ng-test® resulted from samples containing malarial antibodies. in conclusion, performances of these rapid tests are very good and comparable to those obtained with automated immunoassay, except for igm specificity with the ng-test®. thus, isolated igm should be cautiously interpreted due to the possible false-positive reactions with this test. finally, before their large use, the rapid tests must be reliably evaluated with adequate and large panel including early seroconversion and possible cross-reactive samples sars-cov- antibodies. this study was performed with: (i) a positive panel constituted of sars-cov- specimens collected from patients with a positive sars-cov- rt-pcr, , in particular patients presenting strong covid- suspicions with negative pcr. serological tests also make it possible to catch up later with undiagnosed people at time of active infection, since antibodies have been found in almost all people who have been in contact with sars-cov- within a variable period depending on the severity of the infection [ , ] . furthermore, studies showed that the kinetics of appearance of igm and igg were relatively close [ ] . two types of tests are available to detect anti-sars-cov- antibodies: rapid lateral flow tests and automated immunoassays. several studies have assessed analytical performances of the automated immunoassays [ ] [ ] [ ] [ ] . on the other hand, although a very large number of rapid tests have been developed, few of them have been reliably evaluated with a suitable serum panel. however, this is very important to have data about the efficacy of these rapid tests to reliably detect anti-sars-cov- antibodies, since their increasing use in the world. the aim of this study was to assess the analytical performances (sensitivity and specificity) and agreement of two rapid tests and one automated immunoassay for detecting antibodies against sars-cov- . in addition, we assessed five samples containing autoantibodies (four rheumatoid factor and one systemic lupus erythematosus). we also assessed the serum of health-care workers who presented clinical symptoms during the epidemic period for whom sars-cov- rt-pcr was negative or not carried out. we evaluated two lateral flow tests: covid-presto ® test rapid covid- igg/igm (aaz, boulogne-billancourt, france) and ng-test ® igm-igg covid- (ng biotech, guipry, france) according to the manufacturer's instructions. five and ten microliters of serum for covid-presto ® test and ng-test ® , respectively, were added and results were read and interpreted minutes after depositing serum. abbott sars-cov- igg kit (chemiluminescent microparticle immunoassay) (abbott, il, usa) was performed according to the manufacturer's instructions. the assay cut-off is an index of . and the assigned grey zone is comprised between . and . . all statistical analyses were performed using excel. to assess sensitivity, rt-pcr results were chosen as gold standard. cohen kappa statistics and absolute agreement were calculated to evaluate the agreement between the different tests. all participants were not opposed to the collection of their data. sensitivity of covid-presto ® test was assessed on samples collected between day and day after onset of symptoms and sensitivity of the ng-test ® was assessed on a subgroup of samples among the samples tested with covid-presto ® test, collected between days and after onset of symptoms ( table ) . sensitivity of covid-presto ® test for igm was % (n= / ), % (n= / ) and % (n= / ) for samples collected between days and , between days and , and after days after onset of symptoms, respectively. sensitivity of covid-presto ® test for igg was % (n= / ), % (n= / ) and % (n= / ) for samples collected between days and , between days and , and after days after onset of symptoms, respectively. when combining igm and igg, sensitivity of covid-presto ® test was % (n= / ), % (n= / ) and % (n= / ) for samples collected between days and , between days and , and after days after onset of symptoms, respectively. sensitivity of ng-test ® for igm was % (n= / ), % (n= / ) and % (n= / ) for samples collected between days and after, between days and , and after days after j o u r n a l p r e -p r o o f onset of symptoms, respectively. sensitivity of ng-test ® test for igg was % (n= / ), % (n= / ) and % (n= / ) for samples collected between days and , between days and , and after days after onset of symptoms, respectively. when combining igm and igg, sensitivity of ng-test ® test was % (n= / ), % (n= / ) and % (n= / ) for samples collected between days and , between days and , and after days after onset of symptoms, respectively. among the serum samples of this pcr positive panel tested by the two rapid tests, were compared with abbott sars-cov- igg automated immunoassay. sensitivity of abbott igg test was % (n= / ), % (n= / ) and % (n= / ) for samples collected between days and , between days and , and after days after onset of symptoms, respectively. agreement between abbott assay and rapid tests (igm/igg combined) was of . % (n= / ). in one case, the two rapid tests detected igg that were not detected by abbott (index= . ), this sample was collected between days and after symptoms onset. for the second case, igg were detected in the greyzone of abbott (index= . ) but not by ng-test ® . this latter sample was collected between days and after symptoms onset and igm were positive with the two rapid tests. specificity of covid-presto ® test was assessed on samples described in the methods section. specificity of ng-test ® and abbott assay was assessed on a subgroup of samples among the samples tested with covid-presto ® test ( table ) . npv was . %, . % and . % for covid-presto ® , ng-test ® and abbott, respectively. in the present study, we evaluated two different lateral flow tests (covid-presto ® and ng-test ® ) and compared their performances to that of the automated abbott immunoassay using the same samples panel. sensitivity has been assessed using a panel of serum samples of covid- -infected patients (confirmed with a positive pcr), serum was collected between day and day after symptoms onset. sensitivity for igm, among the samples collected before day after symptoms onset, was % and % for covid-presto ® test and ng-test ® , respectively. in the recent study of nicol et al., they found sensitivity of ng-test for igm of . % for the samples collected before day after symptoms onset and of . % among all samples [ ] . the excellent sensitivity of covid-presto ® test observed in our study confirmed the findings of the prazuck et al. study showing % of sensitivity in samples collected more than days after symptoms [ ] . among some samples collected before day after symptoms onset, a simultaneous detection of igm and igg antibodies has been detected. these findings are in line with the antibodies kinetics described for igm and igg also using lateral flow rapids, as previously described with other techniques [ ] . in the present study for covid-presto ® test, it allowed to increase the sensitivity from % when only igm are taken into account to % when both igm and igg are taken into account, highlighting the important added value to interpret the rapid tests by combining igm and igg antibodies. sensitivity for igg in samples collected later than days after symptoms onset was excellent with the different tests being equal to . %, . % and % for covid-presto ® , ng-test ® , and abbott, respectively. thus, both rapid tests showed an excellent sensitivity for igg with a very good agreement with abbott. a previous study assessing abbott test performance j o u r n a l p r e -p r o o f showed sensitivity of % for igg for samples collected after days after symptoms onset and of % for samples collected between and days after symptoms onset [ ] . in this latter study, results sensitivity for igg were similar using ng-test ® [ ] . in another study, igg sensitivity of abbott test was . % for patients hospitalized days after symptoms onset and . % for patients non-hospitalized days after symptoms onset. a limitation of our study could be that most of the patients of the positive panel presented severe infections, since % of them were hospitalized in infectious disease unit or in intensive care. interestingly, among the out-patients, samples were collected for of them days after symptoms onset, showing positive igm and/or igg in seven cases with covid-presto ® test. insufficient quantity of serum for these patients was available to also test with ng-test ® and abbott. previous studies have reported that the kinetics and intensity of immune response could differ depending on the disease severity [ , ] , thus it will be needed to also evaluate rapid tests in mild and pauci-symptomatic patients. another limitation is the difference in the number of tested samples for the early panel (serum samples collected before days after symptoms onset) between the two rapid tests that which can bias the comparison between these tests for this group. a limitation is that we make this evaluation from serum samples and not from capillary blood specimens. regarding specificity evaluation, a crucial point for rapid tests, we used a large panel with pre-endemic samples including representatives of different profiles that can generate possible cross-reactivity. in our study, we showed an excellent specificity, above % in all cases and equal to % for igm with covid-presto ® test. the excellent specificity of covid-presto ® test was also observed in the study of prazuck et al. [ ] . in our study, the only issue regarding specificity is for igm with ng-test ® , since specificity is only of . %. however, this low specificity is mainly due to cross-reactivity with sera containing reactivity malarial antibodies. in the study of nicol et al. igm specificity with ng-test ® was . % [ ] , higher j o u r n a l p r e -p r o o f than in our study, however their negative panel contained no serum with malaria antibodies. regarding automated immunoassay, we showed a very good specificity of . % for igg with abbott, confirming previous results of . %, . % and % [ ] . serum samples containing malarial antibodies are absent or underrepresented in the negative panel of the other studies, although they are known to generate possible cross reactivity. this is very important to include it in the negative panel, since this is a differential diagnosis in patients returning from malaria endemic region with flu-like symptoms. overall, in our study, we observed a very good ppv and npv for both rapid tests. in conclusion, analytical performances for detection of anti-sars-cov- igg antibodies by two lateral flow rapid tests are very good and quite comparable to those obtained with automated immunoassay. however, serological tests should be used after day following symptoms onset. before this, rt-pcr is the gold standard test for covid- diagnosis. the interpretation by combining igm and igg increased sensitivity of rapid tests. the presence of isolated igm should be cautiously interpreted due to the possible false-positive reactions. finally, the rapid tests must be reliably evaluated with adequate and large panels including early seroconversion and possible cross-reactive samples, before their large use and particular interest in low-resource settings. antibody responses to sars-cov- in patients with covid- different longitudinal patterns of nucleic acid and serology testing results based on disease severity of covid- patients interpreting diagnostic tests for sars-cov- inmicovid- laboratory team, performance evaluation of abbott architect sars-cov- igg immunoassay in comparison with indirect immunofluorescence and virus microneutralization test assessment of sars-cov- serological tests for the diagnosis of covid- through the evaluation of three immunoassays: two automated immunoassays (euroimmun and abbott) and one rapid lateral flow immunoassay (ng biotech) immunoassays in comparison with microneutralisation clinical evaluation of serological igg antibody response on the abbott architect sars-cov- infection evaluation of performance of two sars-cov- rapid whole-blood finger-stick igm-igg combined antibody tests saint-louis core (covid research) group, evaluation of covid- igg/igm rapid test from orient gene biotech key: cord- -ru iw py authors: peeling, rosanna w; wedderburn, catherine j; garcia, patricia j; boeras, debrah; fongwen, noah; nkengasong, john; sall, amadou; tanuri, amilcar; heymann, david l title: serology testing in the covid- pandemic response date: - - journal: lancet infect dis doi: . /s - ( ) -x sha: doc_id: cord_uid: ru iw py the collapse of global cooperation and a failure of international solidarity have led to many low-income and middle-income countries being denied access to molecular diagnostics in the covid- pandemic response. yet the scarcity of knowledge on the dynamics of the immune response to infection has led to hesitation on recommending the use of rapid immunodiagnostic tests, even though rapid serology tests are commercially available and scalable. on the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. the who r&d blue print expert group identified eight priorities for research and development, of which the highest is to mobilise research on rapid point-of-care diagnostics for use at the community level. this research should inform control programmes of the required performance and utility of rapid serology tests, which, when applied specifically for appropriate public health measures to then be put in place, can make a huge difference. the covid- pandemic, now only a few months old, , has brought into sharp focus inequalities within and among countries. john nkengasong, director of the africa centres for disease control and prevention, reported that "the collapse of global cooperation and a failure of international solidarity have shoved africa out of the diagnostics market". sadly, the same is true of many other low-income and middle-income countries (lmics) outside africa. why are diagnostics important? in any epidemic response, diagnostic testing plays a crucial role and this pandemic is no exception. because early clinical presentations of infected patients are non-specific, testing is needed to confirm the diagnosis of covid- in symptomatic patients, as soon as possible, so that these patients can be appropriately isolated and clinically managed. , , diagnostic testing is also needed for individuals who have come into contact with someone with confirmed covid- . some testing strategies examine only contacts who have symptoms or develop illness of any kind during the -day period after contact. other strategies examine all contacts when identified, regardless of whether they have any symptoms. studies have shown that a large number of infected individuals might have no symptoms at all, and there is concern that these individuals are still able to shed the virus and transmit infection through saliva droplets as they speak. [ ] [ ] [ ] [ ] [ ] [ ] tracking all contacts of confirmed cases and testing them for severe acute respiratory syndrome coronavirus (sars-cov- ) is key to successful pandemic control. diagnostics are also needed to support rapid serosurveys that establish whether and to what extent sars-cov- has circulated in a community, and sur veillance systems, such as that for influenza-like illness, that monitor disease trends over time. diagnostics can also be used to identify atrisk populations and assess the effectiveness of control strategies. tedros adhanom ghebreyesus, director-general of who, urged countries to implement a comprehensive package of measures to find, isolate, test, and treat every case, and trace every contact. goodwill between countries has already been shown through the publishing of the sars-cov- genetic sequence and shared laboratory protocols to detect the virus. however, as these molecular assays require sophisticated labora tory facilities, countries with insufficient infrastructure quickly accumulate a backlog of testing. the rapid spread of covid- around the world has led to a global shortage of reagents and supplies needed for testing. point-of-care molecular assays for sars-cov- detection are now available to enable community-based testing for covid- in lmics. unfortunately, the production of these test cartridges takes time and, again, global demand has outstripped supply, leaving lmics struggling for access. in march, , who urged member states to "test, test, test". widespread testing can help countries to map the true extent of the outbreak, including identifying hot spots and at-risk populations, and monitor the rate at which the epidemic is spreading. however, most lmics find that molecular testing, including point-of-care testing, is neither scalable nor affordable on a large scale. relying solely on centralised testing puts countries at risk of having nothing to use. what diagnostic alternatives are available to support decentralised testing that would allow countries to mount an adequate response to the pandemic? rapid antigen detection tests that are simple to do at point of care and can give results in less than min would be viable alternatives to molecular testing for confirming covid- cases, enabling appropriate case management, and guiding public health measures, such as quarantine or self-isolation. however, although scaling up rapid antigen testing offers an effective means of triaging symptomatic individuals in community settings, early evaluations of rapid antigen detection tests show personal view suboptimal sensitivity for these tests to be recommended for clinical diagnosis or triage. rapid antibody detection lateral flow tests are also simple to use, generally requiring a few drops of whole blood from a finger prick placed onto the test strip with no processing needed. these tests take - min to do with minimal training and can be done at the point of care as most do not require any equipment. rapid antibody testing is an attractive option for scaling up testing but only if these tests show satisfactory performance for a clearly specified use. the detection of sars-cov- infection and immune response has been described in relation to different diagnostic tests. in this section, we summarise the evidence from studies to date. studies have shown that sars-cov- rna can be detected - days before onset of symptoms and can remain detectable up to - days after the onset of symptoms, particularly in patients who remain symptomatic for an extended period. , , sars-cov- rna can be detected for longer in respiratory samples from patients with severe disease than in samples from patients with mild illness. viral rna concentrations peak within the first days after onset of symptoms and decrease slowly with rising antibody concentrations. , , however, rna clearance is not always associated with rising antibody concentrations, particularly in patients who were critically ill. , an important question for the potential for spread of covid- is whether individuals who are rna-positive are shedding infectious virus. a small study in nine patients found that viral replication stopped - days after onset of symptoms but patients remained rna-positive for - weeks after this point. hence, there remains some uncertainty as to whether a patient who is rna-positive is shedding live virus or not. maturation of the immune response typically takes days with variations in the dynamics of the antibody response depending on disease severity and other factors still to be discovered. in most studies of laboratoryconfirmed covid- cases, igm antibodies start to be detectable around - days after onset of symptoms and rise rapidly. , - igg antibody concentrations follow the igm response closely. seroconversion is typically within the first weeks with the mean time for seroconversion being - days after onset of symptoms for total antibody, - days for igm, and - days for igg. , , , antibodies against the receptor-binding domain of the spike protein and the nucleocapsid protein have been associated with neutralising activity. , , neutralising anti bodies to these domains can be detected approximately days after onset of symptoms and rise steeply over the next weeks. , several studies showed that patients can remain rna-positive despite high concentrations of igm and igg antibodies against the nucleocapsid protein and the receptor-binding domain of the spike protein. whether the presence of neutralising antibodies translates into protective immunity in patients with covid- is unclear. some researchers speculate that antibodies can enhance infectivity as higher antibody concentrations have been observed in patients with severe disease than in those with mild disease. , in one study (n= ), a greater proportion of patients with high igg concentrations had severe disease than did those with low igg concentrations ( % vs %, p= · ). the role of antibody response in the pathogenesis of covid- remains unclear pending further studies. who and the pan american health organization have stated that they do not currently recommend the use of immunodiagnostic tests except in research settings, , because of scarce information on test performance and appropriate use when immunity to covid- is not well under stood. however, many countries are struggling to scale up testing to implement the key strategies of diagnosing all symptomatic patients and tracing all contacts. delays in confirming covid- cases allow continued transmission within communities and can result in failure to contain the pandemic despite other mea sures such as physical distancing and travel restrictions. countries are assessing all available testing options to address their range of needs. in settings where challenges with molecular testing exist or access to laboratories is scarce, rapid serology tests offer a needed additional option. a rapid serology test with good performance character istics is extremely important to avoid missing true cases of covid- and imposing unnecessary quaran tine for people with false-positive results due to cross-reactivity with seasonal coronaviruses. studies have shown more anti body cross-reactivity between the nucleo capsid proteins of sars-cov- and common corona viruses than between their spike proteins. , tests that use the spike protein or fragments of the spike protein as targets might have the least amount of cross-reactivity with common coronaviruses, on the basis of sequence analysis. clear articulation of the benefits and limitations of serology tests will hopefully incentivise manufacturers to improve performance. when is serology testing recommended? where there is little or no access to molecular testing, rapid serology tests provide a means to quickly triage personal view suspected cases of covid- , provided the test is highly specific for the disease. a positive result for igm in symptomatic patients fulfilling the covid- case definition is strongly suggestive of sars-cov- infection. this approach is probably most effective in individuals - days after symptom onset. in peru, public health facilities for molecular testing are sparse and only beds in intensive care units exist for a population of million. the ministry of health has set up a hotline and website for individuals who have symptoms to be interviewed by a health professional for possible follow-up, prioritising the visits according to age, risk factors, and severity of symptoms. a testing team visits the individual at home to do the rapid anti body test. individuals who are igm and igg positive and have mild symptoms are quarantined, whereas people who need critical care are referred to hospital. all contacts are also tested with the rapid serology test. anyone who tests negative in the antibody test has a swab collected for molecular testing. as of may , , people had been triaged in peru with testing positive, of whom were found to be positive by use of a rapid test. this approach has allowed a large number of sympto matic individuals and contacts to be rapidly tested in the community, relieving the backlog, reducing waiting time for molecular testing, and preventing the health-care system from being overwhelmed. experience in china has also shown that, in symptomatic patients, the use of igm tests or total antibody tests can increase the sensitivity of covid- case detection. further research should explore the performance and utility of rapid antigen-igm and antigen-igg combo tests and the timing of testing. in individuals who test negative for igg, research should also explore, if resources allow, the value of doing a follow-up antibody test - days later to document a definitive diagnosis through seroconversion. studies have shown that a large number of infected individuals could have only mild symptoms or no symptoms at all, but they can still transmit infection, with as much as % of infections being transmitted by presymptomatic individuals. , , experience from singapore shows that tracking down all contacts of people with confirmed covid- , testing them for evidence of infection, regardless of symptoms, and putting those contacts who test positive into isolation is an urgent priority for interrupting the chain of transmission and containing the epidemic. [ ] [ ] [ ] this approach is particularly important in the early stages when there are only sporadic or clusters of cases, or for countries coming down from the peak to continue to reduce the extent of infection in the community. only individuals who test negative should have a throat swab collected for molecular testing, which will reduce the strain on laboratories doing these tests. in countries that have set up syndromic surveillance, such as surveillance for influenza-like illness or severe acute respiratory infections, and where blood or throat swabs are routinely collected at these sentinel sites, collected samples can be tested for covid- with molecular, antigen, or serology tests, either alone or in combination. if any of these samples are positive, it means covid- has been circulating in the community. where serial samples are available, it might be possible to date when covid- established itself in a community or country. in general, antibody tests can be used to establish the true extent of an outbreak, map its geographical distribution, and identify hotspots and populations that are particularly at risk. this information can in turn be used to inform public health measures and control strategies. in this case, researchers need to stick to the same serology test and test sentinel populations repeatedly, avoiding the variation in sensitivity between different rapid tests. the use of serology tests for population surveys is not recommended in low prevalence settings as this approach will probably result in more false-positive than truepositive results, even if a test with high specificity is used. for example, if the prevalence of infection is % in the general population, a test with % specificity will identify two false-positive results for every true positive result. these results could lead to a false sense of security regarding the extent of immunity in the population and premature easing of public health measures on the basis of misleading disease estimates. patients at an early stage in the disease course, or asympto matic or paucisymptomatic patients, might have low antibody concentrations that could give falsenegative results. patients' disease stage and severity are important points to consider, along with the population being tested. the estimated level of risk can be considered before using a serology test, because of the changing falsepositive rate or low positive predictive value across different populations. among the groups with the highest risk of the disease are symptomatic patients with clinical presentation of covid- , patients with other respiratory symptoms, contacts of confirmed cases, and health-care workers in settings with little personal protective equipment. we suggest countries consider risk levels before using serology tests and creating public health guidance. scaling up testing, particularly at the community level, allows for better estimates of risks, which in turn allows more effective public health measures to be put into place than would be otherwise. in a pandemic, countries must strive to maintain a robust health-care workforce. key workers who develop personal view symptoms should be prioritised for molecular testing and receive care if infected. on recovery, should a serology test be used to decide when they can safely return to work? this strategy is based on the assumption that antibodies confer protective immunity. although antibodies against the receptor-binding domain of the spike protein and the nucleocapsid protein have been correlated with neutralising activity, , , the development and duration of immunity has not yet been established. , although it is tempting to speculate that serology tests based on the detection of neutralising antibodies can be used as markers of protective immunity, and people who test positive can get a so-called immunity passport to return to work, studies have shown that a significant proportion of patients remain rna-positive despite high concen trations of antibodies against the receptor-binding domain of the spike protein and the nucleocapsid protein. , , , , wang and colleagues found that elevated serum igm concentrations are correlated with poor outcomes in patients with covid- pneumonia, and tan and colleagues found that high concentrations of igg antibodies were correlated with severe disease outcomes. hence a substantial igm or igg response is not necessarily a surrogate marker of protective immunity. to date, insufficient evidence exists to recommend the use of serology testing for health-care workers to return to work. a negative molecular test remains the safest option to establish whether health-care workers can work again safely. a policy brief by the world bank suggested that serology testing could potentially have a high net benefit if it can allow dilution of restrictions for essential workers to return to work and revive essential segments of the economy. the type of tests that can be used for immunity passports remains unclear. a better understanding of the interaction between infection and immune response dynamics is needed before these passports can be considered. hospital beds are often in short supply. the recommended criteria for hospital discharge are two negative molecular tests over several days. however, molecular testing is often scarce or unavailable. can serology tests be used for discharging recovered patients when molecular testing is not available? as patients can remain positive for viral rna despite rising concentrations of antibodies against the nucleocapsid protein and receptor-binding domain of the spike protein, which are correlated with neutralising activities, antibody tests cannot be used in the place of molecular tests to confirm that the patient is virus-free or at least no longer shedding live virus. the events over the past few months have taught us that this pandemic is caused by an extraordinary pathogen that requires extraordinary measures to combat its spread and end the pandemic. the latest finding that as much as % of covid- transmission happens before index cases become symptomatic means that a great deal still needs to be learnt about this novel pathogen and its spread through a population. the paucity of knowledge on the dynamics of the immune response to infection has led to much hesitation on recommending the use of rapid immuno diagnostic tests, particularly serology tests. on the basis of our current knowledge and understanding of viral infectivity and host response, we urge countries with restricted capacity for molecular testing to embark on research into the use of serology tests in triaging symptomatic patients in community settings, testing contacts of confirmed cases, and in situational analysis and surveillance. rapid and scalable tests are needed to deal with this pandemic. rapid serology tests, applied in the right situation for appropriate public health measures to be put into place, can make a huge difference. on feb , , leading health experts from around the world identified eight research and development priorities at the who r&d blue print meeting in geneva, switzerland, of which the top priority was to "mobilize research on rapid point of care diagnostics for use at the community level". in line with this decision, research on the use of rapid serology tests to inform control programmes of their required performance and utility is an urgent priority in the covid- pandemic response. rwp wrote the first draft of the manuscript. all authors contributed to the manuscript conception and supported manuscript revisions. we declare no competing interests. who. molecular assays to diagnose covid- : summary table of available protocols director-general's opening remarks at the media briefing on covid- find evaluation update: sars-cov- immunoassays interpreting diagnostic tests for sars-cov- temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study diagnostic value and dynamic variance of serum antibody in coronavirus disease viral load dynamics and disease severity in patients infected with sars-cov- in zhejiang province, china evidence summary for covid- viral load over course of infection antibody responses to sars-cov- in patients of novel coronavirus disease serology characteristics of sars-cov- infection since exposure and post symptoms onset profiling early humoral response to diagnose novel coronavirus disease (covid- ) viral kinetics and antibody responses in patients with covid- antibody responses to sars-cov- in patients with covid- neutralizing antibody responses to sars-cov- in a covid- recovered patient cohort and their implications evaluation of nucleocapsid and spike protein-based enzyme-linked immunosorbent assays for detecting antibodies against sars-cov- profile of igg and igm antibodies against severe acute respiratory syndrome coronavirus (sars-cov- ) immune phenotyping based on neutrophil-to-lymphocyte ratio and igg predicts disease severity and outcome for patients with covid- advice on the use of point-of-care immunodiagnostic tests for covid- advice on the use of point-ofcare immunodiagnostic tests for covid- developing antibody tests for sars-cov- covid- in peru investigation of three clusters of covid- in singapore: implications for surveillance and response measures connecting clusters of covid- : an epidemiological and serological investigation interrupting transmission of covid- : lessons from containment efforts in singapore covid- immunity passports and vaccination certificates: scientific, equitable, and legal challenges what policy makers need to know about covid- protective immunity elevated serum igm levels indicate poor outcome in patients with coronavirus disease pneumonia: a retrospective case-control study how-two-tests-can-help-contain-covid- -and-revive-the-economy.pdf?sequence= &isallowed=y world experts and funders set priorities for covid- research we thank sergio carmona and jilian sacks of the foundation for innovative new diagnostics for helpful discussions. key: cord- - blsjicu authors: missel, malene; bernild, camilla; dagyaran, ilkay; christensen, signe westh; berg, selina kikkenborg title: a stoic and altruistic orientation towards their work: a qualitative study of healthcare professionals’ experiences of awaiting a covid- test result date: - - journal: bmc health serv res doi: . /s - - - sha: doc_id: cord_uid: blsjicu background: extensive measures to reduce person-to-person transmission of covid- are required to control the current outbreak. special attention is directed at healthcare professionals as reducing the risk of infection in healthcare is essential. the purpose of this study was to explore healthcare professionals’ experiences of awaiting a test result for a potential covid- infection. methods: qualitative interviews with healthcare professionals were performed, underpinned by a phenomenological hermeneutical analytical framework. results: the participating healthcare professionals’ experiences of awaiting a covid- test result were found to be associated with a stoic and altruistic orientation towards their work. these healthcare professionals presented a strong professional identity overriding most concerns about their own health. the result of the coronavirus test was a decisive parameter for whether healthcare professionals could return to work. the healthcare professionals were aware that their family and friends were having a hard time knowing that the covid- infection risk was part of their jobs. this concern did not, however, cause the healthcare professionals to falter in their belief that they were doing the right thing by focusing on their core area. the threat to own health ran through the minds of the healthcare professionals occasionally, which makes access to testing particularly important. conclusion: the participating healthcare professionals had a strong professional identity. however, a discrepancy between an altruistic role as a healthcare professional and the expectations that come from the community was illuminated. a mental health coronavirus hotline for healthcare professionals is suggested. the covid- pandemic puts healthcare professionals (hcp) under pressure both physical and psychological [ ] . the challenges include increased workload created by the outbreak but also fears of contagion for themselves, their families and patients. particularly psychological health outcomes and distress are highlighted in current research regarding the initial stage of the covid- outbreak in terms of anxiety, depression and post-traumatic symptoms [ ] [ ] [ ] [ ] [ ] . across these studies hcps working during the epidemic report frequent concerns regarding their own health. based on our knowledge, little information is however available regarding the impact on hcps awaiting a test result for potential covid- infection or interventions for supporting them during this waiting time. therefore, this study aim to shed light on hcps' experiences of awaiting a test result for a potential covid- infection through individual interviews. this qualitative investigation will thus highlight what is at stake for hcps while in quarantine and awaiting a response as to whether they are infected with the coronavirus. the study offers an in-depth understanding of the meaning of the waiting for the test result for covid- infection from the hcps' perspective and should be of interest to a broad readership and add knowledge to the growing covid- evidence base and in developing supportive inetrventions targeted hcps in such a pandemic. while hcps, e.g. nurses, physisians, porters and healthcare workers, are caring for some of the most vulnerable groups of people both in hospital but also in primary care, they are currently also facing an unprecedented disease caused by the outbreak of a previously unknown virus [ ] . this new coronavirus that can cause covid- disease [ ] puts hcps in a position where they must avoid exposing themselves to infection but also avoid transmitting the infection to the vulnerable patients and citizens to whom they have a caring responsibility. because an infected hcp is a potential vehicle for virus dissemination, research suggests that reducing the risk of infection amongst hcps is essential [ ] . spread of virus has been reported during the ebola outbreak resulting in a compromised healthcare system [ ] as well as during the severe acute respiratory syndrome (sars) [ ] and the middle east respiratory syndrome (mers) epidemics [ ] . experiences from these previous outbreaks highlight fear among hcps in transmitting the disease and the importance of screening for the virus. on th january , the world health organization declared the chinese outbreak of covid- to be a public health emergency of international concern. the emergency committee stated that the spread of covid- may, among other preventive efforts, be interrupted by early detection and isolation [ , ] . general hygiene precautions are crucial in order to minimize the risk of contamination [ ] . hcps have always played an important role in infection prevention, infection control, isolation, containment and public health, which for nurses initially was advocated for by florence nightingale [ ] . there are studies that define the pathophysiological characteristics of covid- however, the mechanism of spread is uncertain. current knowledge is derived from similar coronaviruses, which are transmitted from human-to-human through respiratory infection [ ] . typically, respiratory viruses are most contagious when a patient is symptomatic. however, increasing evidence suggests that human-to-human transmission may be occurring during the asymptomatic incubation period of covid- [ , ] . the disease is reported to be very contagious, and measures to reduce person-to-person transmission of covid- are therefore required to control the outbreak [ ] [ ] [ ] . special attention and efforts to prevent or reduce transmission is applied in susceptible populations including hcps in order to reduce transmission to patients or other vulnerable groups of people in the community [ ] [ ] [ ] . hcps are thus among those groups of people who are being rapidly tested for coronavirus in denmark. considering the severity of infection and illness [ ] , the test result might be of great importance for the healthcare system but also for the individual hcp. a sudden decrease in the number of hcps because of quarantining or isolation due to covid- infection would potentially overload the healthcare system and the capacity to treat either patients with coronavirus or patients with other serious conditions would be challenged [ ] . for the individual hcp, it might furthermore be a threat to their own health. as far as we are aware, no research has so far focused on how hcps might perceive this test situation. therefore, the purpose of this study is to explore hcps' experiences of awaiting a test result for a potential covid- infection. such knowledge from the hcps' perspective are expected to increase the awareness of potential needed support while awaiting a crucial test result from a contagious and rare virus. furthermore, the study will help hospital managers to establish strategies to ensure the best possible working conditions for hcps during the pandemic. this study used a phenomenological hermeneutical methodology inspired by ricoeur's narrative philosophy [ ] . in this study phenomenology was apllied as an epistemological stance for exploring first-person accounts of what it is like to wait for a test result for potential covid- infection. pre-reflexive experiences from the participant's lifeworld is the starting point, while hermeneutics was focused on interpreting the surplus meaning contained in this lifeworld. as human beings we leave traces when we express ourselves, and these traces are formed by the meanings and traditions to which we belong. often, it is impossible to directly understand individual's experiences because the sense in the traces is hidden. therefore, reflection on an individual's lived experiences takes place via the narratives expressed by the individuals [ , ] . the threefold mimesis is central in ricoeur's narrative philosophy and can be seen as an epistemological approach for understanding the participants' lived experiences [ ] , which, in this study, has inspired the research process as a three-fold process [ ] : mimesis i (prefiguration): the life lived before it is formulated as spoken or written narrative (data collection); mimesis ii (configuration): the language stage, formulating a narrative (from speech to text); and mimesis iii (refiguration): the comprehension stage, when the text is interpreted (analysis and interpretation) [ ] [ ] [ ] . participants in this study were recruited from a population of hcps who had been tested for coronavirus but who did not necessarily care for covid- patients. if they had symptoms of covid- infection, hcps in denmark were offered testing for the virus. we used a convenience sampling strategy [ ] by encouraging tested hcps to approach the research team by e-mail if they were willing to attend an interview. the interviews were conducted by telephone based on ethical accountability for not contributing to the spread of the virus and they were scheduled in the gap between test and its result. the result of the test was during the study period given to a tested person within h. the society of denmark was on lockdown due to the threat of coronavirus on march th . coronavirus was in this period still relatively new in denmark, and - patients were hospitalized and patients died due to covid- during week three of the epidemic. fifteen hcps agreed to participate in the study and were interviewed in march and april . thereafter data saturation was achieved, making further interviewing unnecessary [ ] . we included hcps with different professional backgrounds and different responsibilities from both primary care and hospitals. the characteristics of the participants are shown in table . data were collected through individual interviews. human events are characterized by unreflecting preunderstanding, which ricoeur calls prefiguration (mimesis ) [ , ] . with the aim of gathering the participants' indepth narrative accounts of their experiences of awaiting a covid- test results, open questions were used. each interview began with a broad opening question, such as; "could you please tell me what led you to being tested for a potential covid- infection and your experiences while awaiting the test result?" table lists the interview questions. the interviews lastet on average min (range - min). the interviews were separately conducted by three experienced qualitative researchers who all had a professional background as registret nurses, and interviews were audio-recorded and transcribed into pages. the participants' stories were thus transcribed into a textual configuration of their unarticulated experiences (from prefiguration to configuration) [ , ] . according to ricoeur, people's narratives contain surplus meaning and hermeneutics is concerned with interpreting this surplus meaning (from configuration to refiguration). the study was undertaken in accordance with the guidelines of the danish ethical research committee and was approved by the danish data protection agency (p- - ). the investigation conforms with the principles outlined in the declaration of helsinki [ ] . the participants received written information about the purpose of the study and their right to withdraw at any time. written informed consent was obtained from each of the participants before the interview. data were anonymized by means of identification codes. the participants were informed that interview data would be treated confidentially. according to ricoeur, interpretation is the central methodology in phenomenological research. interpretation involves a process consisting of naive interpretation, structural analysis, and comprehensive understanding [ ] . naive interpretation is superficial interpretation, whereby the narratives are read and re-read to see what the texts mean to the researchers, giving an overall view of the narratives. structural analysis deals with patterns in the text that can explain what it is saying. explaining what the text expresses means moving from what the text says to what it is talking about. during the structural process, we analyzed and structured the narratives based on units of meaning, extracting meaning or themes that recurred in the narratives. the units of meaning were condensed such that the essential meaning was expressed. these units of meaning were then further condensed and gathered into themes [ , ] . the comprehensive understanding continues with a discussion of the themes that were identified in the structural analysis, the purpose being to reach a new understanding of the possible dimensions of the participants' experiences while awaiting a covid- test result. the deeper interpretation of the narratives is a process of understanding in which theoretical perspectives are drawn on to help clarify and comprehend phenomena in the participants' experiences [ , ] . see fig. . throughout the study methodological rigor was attained by using the qualitative concepts of relevance, validity, and reflexivity, as described by malterud [ ] . this study is one of only a few qualitative studies exploring the lived experiences of hcps during the covid- pandemic and to our knowledge this is the first qualitative study exploring hcps' experiences of awaiting a test result for a potential covid- infection. the qualitative interview method was selected in order to gain insight into these individuals' perspectives in order to understand the meaning of the investigated phenomena, i.e. the transition from experience to meaning [ ] . the relevance of the study and the chosen methodology thus seems appropriate. several strategies were employed to demonstrate internal validity, including collecting indepth data, prolonged involvement with the data and use of the participants' own words to formulate and illustrate themes. the participants are quoted in order to ensure transparency and substantiate the findings of the study. ricoeur's steps in the analytical process are clearly set out and have been stringently followed. the process from prefiguration through configuration to refiguration reflects the shift from lived life to narrative accounts of lived life to the final interpretation, which provides an insight into the individual hcps' concrete experiences and into universal phenomena of life for hcps awaiting a test result. thus other researchers are able to judge and validate the extracted themes. reflexivity was ensured by discussions between the authors, both during the data collection phase and in the analysis. the fact that all interviewers were registered nurses meant that a certain agreement but also equality between participant and interviewer was present. this meant that the conversation was relatively easy and straightforward. in order, however, to prevent blind spots in relation to the research purpose, the interviewers were particularly aware of their role as researchers and qualitative interviewers and tried to bridle preunderstandings from their background as hcps and adapting a curious stance. the comprehensive understanding illuminated the meaning of the participants' experiences of awaiting a covid- test result as a stoic and altruistic orientation towards their work. these hcps presented a strong professional identity overriding most concerns about their own health. the result of the coronavirus test was a decisive parameter for whether healthcare professionals could return to work. experiences related to the test situation as well as the strong sense of professional identity will be described in more detail in the following. what led the participants to the test for coronavirus were their experiences of mild to moderate symptoms, which aroused suspicion of possible infection. they described the importance of protecting patients, vulnerable citizens and colleagues from the risk of infection and therefore stayed away from work until they were certain that they were not contributing to the spread of the virus. this distance from work, however, had an impact on participants who described a dilemma in terms of both feeling responsible and hypochondriac at the same time. as hcps they already knew the usual workload and therefore described feelings of failing colleagues by not taking part in the work, "we are busy in healthcare, so if there is one who is sick, then the others just have to run faster" (participant k). thus, the test result was extremely important in terms of whether one could return to work and help one's colleagues. the participants, furthermore, talked of particular responsibilities in being prepared to care for and treat patients with covid- . they watched what is going on in the rest of the world in other healthcare settings where the epidemic of covid- exceeded the healthcare systems' resources. they were very concerned about their colleagues in other countries but at the same time had an altruistic view that they themselves must also be prepared. in this context, coronavirus tests are also particularly important for the participating hcps. they did, however, describe an ambivalence around the test response; if you are tested positive, then hopefully you will form some kind of immunity and thus be able to go to work after a period of quarantine without being infected again. if, on the other hand, you are tested negative, you can return to your job immediately, "i hope i don't have corona, but on the other hand, then you have had it …" (participant c). participants describe concerns and fears that many hcps will be infected at the same time, and that there will be no one to take care of the ill patients or vulnerable citizens. therefore, it was necessary to have the hcps tested so that an overview of the workforce can be maintained as hcps cannot easily be replaced. the way to being tested could, however, be quite obscure for some of the participants. for participating hcps working in the hospital, access to testing is easy and straightforward. they noticed symptoms, they discussed it with their boss, and they got tested. however, working in primary care posed major problems in figuring out access to being tested. those hcps narrated experiences of not being taken seriously, which produced a kind of powerlessness, "all of us who work in healthcare, we are there to make a difference, but you just feel that we sometimes are banging our head against the wall [experiencing lack of understanding] … it gives a sense of powerlessness" (participant e). they furthermore described frustrations of wasting precious time waiting to get to the test; time that could have been spent usefully in continuing their work. the particular commitment to caring for vulnerable and ill people was evident when participating hcps were just waiting to be tested. even though being tested for coronavirus when experiencing symptoms was strongly preferred by the participants in this study, the test situation, however, reminded and confronted them with the seriousness of the pandemic. they described their experiences of coming into the interimistic tents outside the hospital and meeting with test staff in protective equipment. the participants, being hcps, were prepared for this scenario but are anyway confronted with feelings of being part of a surreal experience or a science fiction movie but also that this new virus was real, "it is a peculiar experience to meet another person who is covered from head to toe. you suddenly feel very dangerous" (participant f). they also, however, told of a professional set-up and that being tested provided certainty, tranquility and direction. the participating hcps in this study presented a strong sense of professional identity and were highly oriented towards their work. they talked about how they were preparing for battle against the coronavirus despite the risk of being infected themselves. the frontline hcps with the critical task of caring for covid- patients told how for a long time and with no evidence of even having the disease, they had isolated themselves at home, "i already decided days ago that we should stop sleeping in the same room and avoid physical contact completely. i have also written on my wife's and my behalf to family and friends that we will not be able to see anybody for a while" (participant b). they were tremendously aware of their specific role and duty and that nobody could stand-in for them and explained it as just being a part of their job and with a fatalistic attitude. these participants expressed a paramount need to know if they were contagious. common to the participants was that, by virtue of their profession, they had important professional knowledge about drop infections, hygiene, symptoms and pathways of infection, all of which gave them a readiness to act. they narrated how they were extremely aware of not transmitting the infection to others, as well as how to take distance and hygiene measures when they noticed symptoms of potential covid- . these measures seemed to be integrated as an almost natural act in the participants' lives with them not questioning the necessity of doing so, "i've locked myself inside a room now and told the others in the family to stay away. and if i'm going to the toilet ..., our apartment is quite small ... but then i just shout that now i go to the toilet. and then i have hand sanitizer and cleansers and wipe it all off afterwards" (participant c). the situation thus appears to have been tackled with stoic calm by the participants as they awaited answers as to whether their possible symptoms are related to covid- . despite their professional knowledge, participants also told of chaotic and conflicting information from the healthcare system expressed as an information flow that had become incomprehensible and overwhelming. this resulted in uncertainty and difficulty in keeping up with guidelines. the participants' social network was marked by the possible threat of covid- from the hcps who were just doing their job in healthcare. the participating hcps were highly aware that their family and friends were having a hard time knowing that the covid- infection risk was a necessary condition of their job, while they at the same time are forced to keep a distance. this concern did not, however, cause participants to falter in their belief that they were doing the right thing by focusing on their core area, which was caring for ill and vulnerable people. the threat to their own health ran though the minds of the participants once in a while, "that people who take care of their work and do what they can to make others survive can end up getting infected with covid- themselves, i think that's a little hard, but that's just how it is" (participant g). the participating hcps express a need to share such thoughts with somebody and ask for some kind of follow-up or a hcp corona hotline, e.g. after being tested for the virus, "when you are nervous and scared, it would be helpful if you could go to one specific place where knowledge and expertise about corona was gathered -a mental health corona hotline" (participant d). being oriented towards their job was described as a natural part of the participating hcps approach to life. they had a strong passion for and pride in their work and in this epidemic context showed solidarity across professional boundaries. they did question if they may be too uncritical but explained it with the fact that they are in a time when it is necessary to do as one is told. the participants, however, described how they have experienced the community tribute e.g. public applause for them as on the edge of hypocrisy. they rejected more applause from society and express how genuine societal recognition would be more resources in hospitals to solve problems and to give the hcps a tolerable everyday life and a decent salary. awaiting a covid- test result for the participating hcps was associated with a stoic and altruistic orientation towards their work in which the result of the test was crucial. this study illuminated how hcp prepare and get ready for battle against covid- in a devoted and solidarity-based way. this war metaphor as a response to the pandemic might illuminate the hcps' stoic and altruistic work identity. seeing the coronavirus as an enemy that should be defeated and as a part of one's job require hcps who approach their work with a stoic calm and an altruistic attitude. a similar commitment to supporting their health system and communities has been reported during the ebola epidemic [ ] . the participants in our study presented a strong professional identity and their attention was directed to caring and protecting patients and vulnerable citizens while also preventing the spread of infection among colleagues. being stoic in their approach to work does not mean that hcp are cold and distant, it is rather an attitude of remaining calm and carrying on and may also involve having a certain degree of self-control and maintaining a sense of conscious self-awareness [ ] . the altruistic attitude or behavior of the participants was characterized by the fact that the individual sought to promote the well-being of others without thought for their own interests and needs. according to hume, altruism is a character trait of humans that normally extends to strangers only in a weakened form and it is rare to meet with one in whom the affections of altruism do not over-balance the selfish [ ] . altruism was, however, a strong moral part of the participants' professional identity which seems to be based on the inner logic of the hcp discipline. understanding of the roles altruism might play in the social and medical response to an epidemic and the stories about the nature of hcps' moral obligations has been discussed and implies the willingness to take personal risks in the line of duty [ ] . a professional identity can be defined as a social identity that relates to people's understanding and presentation of themselves as professionals [ ] . it is seen as the identity a person has developed through learning and practicing a given profession and thus can fulfill a particular employment function designed and integrated into a given work and professional culture. according to goffman, identities are not created individually, but rather the individual gains his or her professional identity through the attribution of certain characteristics that have the character of normative expectations [ ] . in addition to performing the expected functions associated with a specific field, the individual thus supports and supplements his or her position by simultaneously playing the normatively expected role associated with that group [ ] . to follow goffman [ ] , the stoic and altruistic orientation towards their work presented by hcp in the present study might also point to these hcp acting in accordance with a specific role within a given social context, such as healthcare. society's normative expectations of hcp may influence their perception of their own professional identity. our study, however, illuminates a discrepancy between an altruistic role as hcps and the normative expectations that come from the community that pays tribute to them, and then an experience of working conditions and salaries that do not indicate recognition. altruism has been reported to be declining in the face of economic and pragmatic motivation [ ] which might threaten healthcare practice during an epidemic such as covid- . another threat to our study participants' stoic and altruistic orientation towards their work was also experiences of receiving chaotic, conflicting and an overwhelming information flow resulting in difficulties in keeping up with best practice guidelines. research from the a/h n influenza pandemic have demonstrated how perceived sufficiency of information was associated with reduced degree of worry and how hcps less frequently felt unprotected [ , ] . these points highlight that hospital managers should try to provide and direct information for hcps according to what is needed during the different and specific phases of a pandemic based on the affected hcps' perspectives in order to offer favourable working conditions in times of extreme distress. being tested for coronavirus for the hcps in our study was significant in order to maintain their professional identity and continue working. they did, however, also describe experiences of uncertainty and fear for own health and expressed a need to share such thoughts with somebody. a threat to the mental health of hcps during epidemics has been reported [ , , ] , and interventions to promote mental well-being in hcps exposed to covid- are suggested to be immediately implemented [ ] . a hotline for patients during the current covid- outbreak has been established in some places, e.g. in new york where citizens are guided to assess their own symptoms at home and can discuss any psychological impact from the disease [ ] . similar initiatives directed at hcps are needed. recomandations from a recent systematic review also suggest to establish a forum for medical personnel to voice their concerns as well as a psychological assistance hotline comprised of volunteers who have received relevant psychological training to be able to provide telephonic guidance to personnel to help effectively tackle mental health problems [ ] . telephone interviews in this study were unavoidable due to the risk of virus transmission between participants and interviewers. such interviews do, however, have some disadvantages. they are more impersonal in that it is not possible to have eye contact, and as an interviewer, it is difficult to show that you are interested and included in what is being said. in addition, breaks are generally less acceptable [ ] . despite this, we found that participants were willing to participate in the study and appreciated talking about their experiences. the sample included in this study consisted of more female hcps (n = ) and most were nurses (n = ) which might be an uneven distribution of participants. women, however dominate the nursing profession, and nurses are the largest professional group in healthcare [ , ] and the sample thus represents the general healthcare workforce. what is worth noting is that this study was conducted during the first phase of the pandemic. this means that the stoic and altruistic orientation as well as the war metaphor that we have found and described may change over time as the pandemic progresses and hpcs may experience burnout. the perspectives of hcps awaiting a test result for coronavirus provide an important contribution to the growing body of literature about covid- . these hcps had a strong professional identity with their attention directed towards caring and protecting patients and vulnerable citizens while also preventing the spread of infection among colleagues. a discrepancy between an altruistic role as a hcp and the normative expectations that come from the community was also illuminated. the clinical implications of this study is thus, that as a stoic and altruistic attitude dominated hcps' identity, access to testing for covid- for these professionals is crucial. furthermore, a mental health corona hotline for hcps should be established. abbreviations hcp: healthcare professionals mental health care for medical staff and affiliated healthcare workers during the covid- pandemic timely mental health care for the novel coronavirus outbreak is urgently needed prevalence of depression, anxiety, and insomnia among healthcare workers during the covid- pandemic: a systematic review and meta-analysis the psychological impact of epidemic and pandemic outbreaks on healthcare workers: rapid review of the evidence the psychosocial impact of flu influenza pandemics on healthcare workers and lessons learnt for the covid- emergency: a rapid review updated understanding of the outbreak of novel coronavirus ( -ncov) in wuhan world health organization declares global emergency: a review of the novel coronavirus (covid- ) covid- diagnosis and management: a comprehensive review the health impact of the - ebola outbreak uniformed service nurses' experiences with the severe acute respiratory syndrome outbreak and response in taiwan working experiences of nurses during the middle east respiratory syndrome outbreak world health organization. novel coronavirus ( -ncov), situation report- . covid- : emerging compassion, courage and resilience in the face of misinformation and adversity transmission of -n-cov infection from an asymptomatic contact in germany early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak a rapid advice guideline for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (standard version) retningslinjer for håndtering af covid- i sundhedsvaesenet (guidelines for managing covid- i the healthcare system). copenhagen; severe acute respiratory syndrome coronavirus (sars-cov- ) and coronavirus disease- (covid- ): the epidemic and the challenges ricoeur's narrative philosophy: a source of inspiration in critical hermeneutic health research en hermeneutisk brobygger. tekster af paul ricoeur nursing research: generating and assessing evidence for nursing practice declaration of helsinki discource and the surplus of meaning qualitative methods in medical research we and the nurses are now working with one voice": how community leaders and health committee members describe their role in sierra leone's ebola response the therapy of desire. in: theory and practice in hellenistic ethics altruism in hume's treatise diminishing returns? risk and the duty to care in the sars epidemic bankmedarbejderen-splittet mellem varnaes og scrooge (bank employees -split between varnaes and scrooge) two studies in the sociology of interaction. united states: martino fine books professional nursing values: a concept analysis general hospital staff worries, perceived sufficiency of information and associated psychological distress during the a/h n influenza pandemic psychological impact of the pandemic (h n ) on general hospital workers in kobe health professionals facing the coronavirus disease (covid- ) pandemic: what are the mental health risks? a phone call away: new york's hotline and public health in the rapidly changing covid- pandemic factors affecting the psychological well-being of health care workers during an epidemic: a thematic review sundhedsvaesen og sundhedspolitik (healthcare and healthcare politics) closing the gap in indigenous health inequity -is it making a difference? publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations the research team wishes to thank all those people who collaborated and participated in this study by sharing their experiences. without them, this study would not have been possible. we also thank anne alexandrine Øhlers, camilla rotvig jensen, christina jensen, mette skriver and miriam bianca besser biyai for their help in relation with the transcription of the interviews. all authors conceived and contributed to the design and conduct of the study. skb, cb and mm conducted the collection of data material and led the analysis together with swc and id. all authors were involved in the analysis and the writing of the manuscript. all authors contributed to the preparation of this manuscript and read and approved the manuscript. this work was supported by the novo nordisk foundation (grant number nnf sa ), and centre for cardiac, vascular, pulmonary and infectious diseases, rigshospitalet, copenhagen university hospital, denmark.availability of data and materials all authors have full control of all primary raw data (interview transcripts) and allow the journal to review our data if requested. all raw data are written in danish. data are stored in a locked file cabinet in a locked room at the copenhagen university hospital as requested by the danish data protection agency. the data material used in this study are available from the corresponding author on reasonale request which will not conflict with the anonymity and confidentiality of the data.ethics approval and consent to participate registration and permission was received from the authorities in the danish data protection agency under the capital region of denmark: (p- - ) and the study were undertaken in accordance with the guidelines of the danish ethics research committee. the participants received verbal and written information about the study prior to the study. written consent was obtained from the participants. given the qualitative nature of the study, the local ethics committee in the capital region of denmark ruled that no formal ethical approval was required in this particular case. not applicable. the authors have no conflicts of competing interest to declare.author details clinical nurse specialist at the department of cardiothoracic surgery, centre for cardiac, vascular, pulmonary and infectious diseases, rigshospitalet, key: cord- -e idc authors: atchison, christina; pristerà, philippa; cooper, emily; papageorgiou, vasiliki; redd, rozlyn; piggin, maria; flower, barnaby; fontana, gianluca; satkunarajah, sutha; ashrafian, hutan; lawrence-jones, anna; naar, lenny; chigwende, jennifer; gibbard, steve; riley, steven; darzi, ara; elliott, paul; ashby, deborah; barclay, wendy; cooke, graham s; ward, helen title: usability and acceptability of home-based self-testing for sars-cov- antibodies for population surveillance date: - - journal: clin infect dis doi: . /cid/ciaa sha: doc_id: cord_uid: e idc background: this study assesses acceptability and usability of home-based self-testing for sars-cov- antibodies using lateral flow immunoassays (lfia). methods: we carried out public involvement and pilot testing in volunteers to improve usability. feedback was obtained through online discussions, questionnaires, observations and interviews of people who tried the test at home. this informed the design of a nationally representative survey of adults in england using two lfias (lfia and lfia ) which were sent to , and , participants, respectively, who provided further feedback. results: public involvement and pilot testing showed high levels of acceptability, but limitations with the usability of kits. most people reported completing the test; however, they identified difficulties with practical aspects of the kit, particularly the lancet and pipette, a need for clearer instructions and more guidance on interpretation of results. in the national study, . % ( , / , ) of lfia and . % ( , / , ) of lfia respondents attempted the test and . % and . % of respondents completed it, respectively. most found the instructions easy to understand, but some reported difficulties using the pipette (lfia : . %) and applying the blood drop to the cassette (lfia : . %). most respondents obtained a valid result (lfia : . %; lfia : . %). overall there was substantial concordance between participant and clinician interpreted results (kappa: lfia . ; lfia . ). conclusion: impactful public involvement is feasible in a rapid response setting. home self-testing with lfias can be used with a high degree of acceptability and usability by adults, making them a good option for use in seroprevalence surveys. lateral flow immunoassays (lfia) offer a rapid point-of-care (poc) approach to novel coronavirus (sars-cov- ) antibody testing. while lfias may not currently be accurate enough for individual-level clinical decisions ( , ) , they are valuable as a public health tool. on a population level, by conducting seroprevalence surveys through widespread random sampling of the general public, and by adjusting for the sensitivity and specificity characteristics of the lfia used, it is possible to estimate the levels of past infection with sars-cov- in the community ( ) . however, testing hundreds of thousands of people would be impractical if it required a blood sample to be drawn followed by processing in a laboratory. one solution is to use self-sampling and selftesting in the home with participants reporting results to the researchers. however, there is limited understanding of public acceptability and usability of these lfias in the home setting, as most are currently designed as poc tests performed by healthcare professionals. self-sampling and self-testing are widely used in healthcare for monitoring, for example in diabetes management ( ) , and for diagnostics, for example for hiv ( , ) . there are many advantages in terms of uptake, cost, patient activation and scale ( , ) , but also potential disadvantages in relation to validity, usability and practicality which should be explored ( , ) . usability research on hiv selftesting has generally found good acceptability, the devices easy to use and high validity in interpretation of self-reported test results ( ) ( ) ( ) . however, these hiv test kits were designed for selfsampling and self-testing and went through several iterations before designs were appropriate for home use and therefore the same levels of acceptability and usability for home-based self-testing for sars-cov- antibody using lfias cannot be assumed. as part of the real-time assessment of community transmission (react) programme ( ), we evaluated the acceptability and usability of lfias for use in large seroprevalence surveys of sars-cov- antibody in the community. a c c e p t e d m a n u s c r i p t we evaluated two lfias with different usability characteristics from five lfias being validated in parallel in our laboratory-based study ( ). both lfias required a blood sample from a finger-prick and produced a self-read test result after or minutes. lfia (guangzhou wondfo biotech co ltd) was a cassette-based system containing a "control" indicator line and a "test" indicator line (for detection of combined igm and igg antibodies). lfia (fortress orient gene biotech co ltd) was a cassette-based system containing a "control" indicator line and separate indicator lines for igm and igg ( figure ). in early may we carried out rapid, iterative public involvement and a pilot usability study including an online forum with four discussion groups (n= ), a study of lfia test use with volunteers (n= ) and a broader public sample (n= ), and a nested observation and interview study (n= ). further details on the methods, including how we recruited participants from our existing involvement networks, are available online (supplement, s ). the test kits dispatched in the pilot study included one test cassette, one button-activated g lancet and a ml plastic pipette, alongside an instruction booklet also containing a weblink to an instructional video. based on findings from the pilot study, for the larger population-based usability study, the lancet and pipette were replaced with two pressure-activated g (larger) lancets and a smaller ml plastic pipette, respectively. the design and language in the instructional booklet and video were changed and an alcohol wipe was also included in the kit. a c c e p t e d m a n u s c r i p t in late may we carried out a larger population-based usability study of a representative sample of the adult population (aged years and over) in england. we used addresses from the postal address file to draw a random sample of , households in england to which study invitation letters were sent. we allowed up to four adults aged and over in the household to register for the study. self-testing lfia kits were then posted to each registered individual. on completion of the test, participants recorded their interpretation of the result as part of an online survey, with the option of uploading a photograph of the test result. reminder letters were sent to participants who had not completed the online survey or uploaded a photograph within days of test kits being dispatched. metrics to evaluate usability and acceptability were based on the hiv self-testing literature ( , , ) and were measured as the percentage of participants responding to specific closed questions in the online survey. the questionnaire used is available as an online supplement (supplement, s ). the main outcome was usability of the lfia kits. this was defined as a participant's ability to complete the antibody test, and how easy or difficult it was to understand the instructions and complete each step in the process. acceptability was measured in terms of people consenting to and using the provided self-test, and the proportion who reported they would be willing to repeat a self-administered finger-prick antibody test in the future. analyses were conducted in stata (version . , statacorp, texas, usa). data obtained from the questionnaires on acceptability and usability were summarised by counts and descriptive statistics, and comparisons were made between lfia and lfia using pearson's chisquared test. multivariate regression was used to identify sociodemographic factors independently associated with the proportion of participants conducting the test that achieved a valid result. variables that appeared to be associated (p< . ) in the unadjusted analyses were considered in the adjusted analyses. adjusted odds ratios (aor) and % confidence intervals (ci) were estimated. associations with a p-value < . in the adjusted analyses were considered statistically significant. agreement between participant-interpreted and clinician-interpreted result for test outcomes (negative, igg positive, invalid, unable to read) was assessed using the fleiss kappa statistic. a c c e p t e d m a n u s c r i p t ( ). therefore, we used the same operational definition of positivity for lfia . participants were informed in the instructions to consider igm results as negative. the study obtained research ethics approval from the south central-berkshire b research ethics committee (iras id: ). overall, members of the public contributed feedback during the involvement and pilot. this led to changes in the design and language used in the instructional video and booklet, the type and number of lancets and the size of pipette in the lfia kits (further details available online, supplement s ). for the national study, , household invitation letters were sent, and , individuals registered for the study from , households. due to the maximum number of kits we had available for the study, , participants were selected at random from those who registered. thus, , lfia kits were distributed, with , individual user surveys completed ( . % response rate), and , lfia kits were distributed, with , individual user surveys completed ( . % response rate). most commonly, two adults participated per household (table ). baseline characteristics of study participants are shown in table . the median age of participants across lfia and lfia was . years (range to ). there were some differences between lfia and lfia participants by ethnicity, region and household size. acceptability of self-testing was high ( a c c e p t e d m a n u s c r i p t as in the pilot, most respondents were willing to perform another finger-prick antibody test in the future (lfia : . %; lfia : . %). only a minority preferred to do the antibody test in a clinical care or community setting than at home. as with the pilot study, respondents with children showed a high willingness to perform the antibody test on them, and this proportion increased with the age of the children (table ) . in the pilot study most people ( . %, / ) who attempted the test managed to complete it. however, significant usability issues were identified, including challenges with the lancet to obtain a blood drop and the pipette to transfer the blood to the sample well. the problems with the lancet led to some participants using alternative objects to draw blood, including pins and sewing needles, while others opened the lancet casing to access the blade. some people reported minor problems putting buffer into the buffer well. this led to the inclusion of two lancets and changes to the instructions for the national study. in the national study, almost all participants who attempted the antibody test reported completing it ( . % for lfia and . % for lfia ) ( table ) . reasons for not completing the test are shown in the table. of lfia participants who reported damaging the test, the majority reported either accidentally removing the entire lid off the buffer bottle and spilling the solution all over the test cassette or putting the blood and buffer in the wrong well. for lfia , few participants damaged the test and they all reported putting the blood and buffer in the wrong well. about one in four participants asked someone to help them to administer the test. most found the instructions easy to understand (figures ), but as in the pilot, participants reported some difficulties in performing the test. for lfia , difficulties with using the pipette were reported by . % ( , / , ) of participants. in addition, . % ( / , ) had difficulties applying the blood to a c c e p t e d m a n u s c r i p t the sample well ( figure ). therefore, for lfia the instructions were changed to omit the use of the pipette and instead directly transfer blood from the finger-prick site to the sample well. however, participants still found creating a blood drop from the finger-prick site ( . %; / , ) and then applying the blood to the well ( . %; / , ) difficult. lfia was deployed after lfia because there was a delay in arrival of lfia from the supplier. this differential timing in dispatch of the kits had the unexpected benefit of allowing us to make iterative changes to the instructions. overall, . % of lfia and . % of lfia participants reported an invalid result (table ). there was some variation in the proportion of participant-reported invalid results using lfia by age and gender. the higher the number of participants registered for the study in the same household, the lower the odds of the participant reporting an invalid result. no sociodemographic factors were associated with a participant-reported invalid result using lfia (table ). after adjusting for sociodemographic differences between lfia and lfia participants, there was no difference between lfia and lfia in terms of being able to read the result ( . % vs. . %; aor . ( % ci: . - . ); p . ). but a lower percentage of invalid test results were reported by lfia participants ( . % vs. . %; aor . ( % ci: . - . ); p < . ). table shows concordance between participant and clinician interpreted results in the national study. for lfia , there was substantial agreement overall (kappa . ( % ci: . - . ); p< . ), however there were important differences: while there was . % agreement for results reported as negative, and . % agreement for invalid results, a clinician confirmed only . % of participantreported positives. visible reasons (from the photograph) were insufficient blood volume to cover the bottom of the sample well, or insufficient movement of the blood and buffer solution across the result window. in addition, the clinician was able to interpret the results of all but four out of a c c e p t e d m a n u s c r i p t ( . %) tests from the photographs of results participants reported as "unable to read". the four results unreadable by the clinician were because blood had leaked out of the sample well and obscured the result window. of participant-reported unable to read results, . % were clinicianinterpreted as invalid (for all these tests, the control and "test" lines were both absent). table ). the clinician could not interpret the results from photographs reported as readable results by participants, reasons included blurred photographs and shadowing obscuring the indicator lines. overall, we found that self-testing with the two lfia kit designs used in this study was highly acceptable among adults living in england. high acceptability of in home self-testing is in keeping with self-sampling and self-testing studies in diabetes management ( ), and hiv diagnostics ( , ) . the majority of participants who attempted the test successfully completed it despite some continued difficulties with using the pipette (lfia ), creating a drop of blood from the finger-prick site (lfia ) and applying the blood to the sample well (lfia and lfia ). based on these findings, we proportion of invalid tests for lfia could reflect the better designed buffer bottle (which was a significant issue for lfia ), better performance characteristics of lfia over lfia (e.g. easier movement of the blood and buffer solution across the result window), or improved ability to get sufficient blood in the sample well using the direct blood transfer technique over using a pipette. participants' ability to obtain a valid test result using lfia varied marginally by age and gender and increased with the number of participants registered for the study in the same household. the latter observation is not surprising as observing another household member performing the test is likely to improve the performance of others in the same household. no sociodemographic differences in obtaining a valid result were found for lfia . of note, about one in four participants reported that they had help administering the test, irrespective of lfia used. this could put individuals living alone at a disadvantage in terms of usability. however, comparing those that had help to those that did not, we found no difference in ability to complete the test ( . % vs. . %; p . ) or reported invalid results ( . % vs. . %; p . ). overall, there was good agreement between self-reported results and those reported by a clinician. therefore, our findings broadly support self-reporting of home-based test results using lfias. but the public and individual health impact of misinterpreting a test result that is negative but read as positive is a concern as an individual could falsely conclude that they have antibodies for sars-cov- and may change their behaviour as a result. to mitigate against this, and given the scientific our study is original because focusing on the acceptability and usability of lfias for self-testing for sars-cov- antibody in a home-based setting has not been done at such scale in the general population. it provides an attractive solution for conducting large seroprevalence surveys. the study has, however, some limitations. study participants may not be representative of the general adult population of england. however, we had data on the england population profile ( census data ( )), as well as the study registration profile and survey completion profile of the study participants which gave us an indication of response bias. our sample was broadly similar to the england population profile. in addition, the usability study was conducted in parallel with our laboratorybased study of performance characteristics of lfias. as such, we did not know the accuracy of the lfias chosen for the usability study at the time, or whether either would perform well enough in the laboratory to be considered for the large national seroprevalence study planned as part of the react programme ( ). however, given that the majority of commercially available lfias have a similar cassette-based design and test result read out to lfia or lfia we were confident that our results would be generalisable and applicable to whichever lfia was finally selected. findings from our laboratory-based study, including the performance characteristics of lfia and lfia are forthcoming ( ). overall, our study has demonstrated that home-based self-testing lfias for use in large communitybased seroprevalence surveys of sars-cov- antibody are both acceptable and feasible. although this study identified a few usability issues, these have now been addressed. lfia , fortress orient gene, has been selected for a large national seroprevalence study as part of the react programme. this decision was based on criteria including the usability and acceptability determined in this study, a c c e p t e d m a n u s c r i p t years where asked whether they would carry out the test on children of that age living in their households. denominator is th e number of participants who reported having children of that age living in their household. m a n u s c r i p t antibody testing for covid- : a report from the national covid scientific advisory panel evaluation of nine commercial sars-cov- immunoassays prevalence of sars-cov- in spain (ene-covid): a nationwide, population-based seroepidemiological study self-monitoring of blood glucose in type diabetes: recent studies acceptability, feasibility, and individual preferences of blood-based hiv self-testing in a population-based sample of adolescents in kisangani, democratic republic of the congo reliability of hiv rapid diagnostic tests for self-testing compared with testing by health-care workers: a systematic review and meta-analysis interferences and limitations in blood glucose self-testing: an overview of the current knowledge usability assessment of seven hiv self-test devices conducted with lay-users in we thank key collaborators on this work --ipsos mori: stephen finlay, john kennedy, duncan key: cord- - gd f m authors: deak, eszter; marlowe, elizabeth m. title: right-sizing technology in the era of consumer-driven health care date: - - journal: clinical microbiology newsletter doi: . /j.clinmicnews. . . sha: doc_id: cord_uid: gd f m abstract technology for modern clinical and public health microbiology laboratories has evolved at an impressive rate over the last two decades. contemporary diagnostics can rapidly provide powerful data that can impact patient lives and support infectious disease outbreak investigations. at the same time, dramatic changes to health care delivery are putting new pressures on a system that is now focusing on patient-centric, value-driven, convenient care. for laboratories, balancing all these demands in a cost-contained environment remains a challenge. this article explores the current and future directions of diagnostics in our dynamic health care environment. the affordable care act (aca) in the united states was enacted by president obama in march . the goal of the aca was to improve the quality of and access to health care by transforming insurance coverage and lowering health care costs. we have seen shifts in health care plans (i.e., account-based health plans) that have the consumers of the health care opting for lower monthly premiums with higher deductibles. these deductibles are often paid for by personal health savings accounts, thus pushing the costs of health care onto the individual consumer. couple this with an unprecedented boom in technology, which in some cases can offer on-demand diagnostics within the time of an office visit, and the result is consumer-driven health care, particularly for those who can afford it. despite recent administrative changes in washington and the uncertainty of "repeal and replace" in the republican agenda for the current aca, the trend toward consumer-driven health care, with an emphasis on pre-budgeted spending, is likely to continue. for consumers of a product who will continue to pay more of the bill, the bright side of this trend is a movement to value-based care delivery from the perspective of the affluent consumer. valuebased care is defined as safe, appropriate, and effective care at a reasonable cost, which is predicated on evidence-based medicine and proven outcomes. patients are looking for more pricing transparency and more options for efficient care delivery (i.e., telemedicine, retail care providers, and mobile health solutions). health care providers are trying to better understand consumer wants and needs, measure performance, and improve the patient experience; this is a distinct change from the historical fee-for-service system that did little to incentivize providers to produce value. from the laboratory's perspective, there continue to be operational challenges to lead these changes. emerging and re-emerging pathogens demand rapid responses at an unprecedented level. the skilled workforce continues to shrink, while the work demands go up. there are legislative influences on testing. at the same time, reimbursement and budgets are contracting. yet still, at the end of the day, the laboratory is expected to produce quality results for improved patient care. initiatives like antibiotic stewardship are helping to drive better outcomes with laboratory results, but many of these programs are dependent on post-analytical variables for the optimal impact on patient care to be realized [ , ] . another key laboratory issue is the breath and scope of the technology that is now available. today, we have molecular point-ofcare (mpoc) devices that can provide a rapid diagnostic answer within minutes in a clinic, multiplex pcr sample-to-answer devices that can screen for > analytes in a single specimen in about an hour, high-volume automation that can enhance throughput and efficiency in the clinical microbiology laboratory with digital imaging, and next-generation sequencing (ngs) that can reveal a treasure trove of information in a single test. combined, the changes in health care and technology have left many laboratories asking how to "right-size technology" for routine care while transforming practice. ultimately, change will depend on the goals that are driving the conversion and utilization of the technology into daily laboratory practice. factors may include syndrome-specific diagnostic needs, ease of use, the need for rapid results, improved sensitivity and specificity, operational needs (such as staffing and expertise), laboratory design (such as centralized versus decentralized models), cost, consumer demand, and the potential for improved patient outcomes. the laboratory must weigh all these factors while trying to make a business case to improve service despite the fact that there are few or no outcome data available to support the use of new technology. technology comes at a cost that is often shifted to the consumer, the patient. while consumer choice can help push innovation, one also has to wonder to what extent the market will allow the significant increases in testing costs that can come with technology. for example, in the case of acute gastroenteritis which is typically a self-limiting infection with the majority of specimens coming from an outpatient setting, traditionally a stool culture would be ordered that would cost a patient less than $ . the newer multiplex stool pcr panels can result in a charge that can cost a patient over $ , . will patients be willing to bear paying this increased cost for such a diagnostic test long term? while one can agree that there is improved turnaround time, sensitivity and pathogen coverage in a sophisticated multiplex diagnostic assay, it must be used in conjunction with diagnostic algorithms that prevent needless additional downstream testing as well as excess costs. clearly, there is a need for diagnostic stewardship alongside antibiotic stewardship to improve quality and the prudent use of health care dollars. this article explores the impact of technology on the clinical and public health microbiology laboratory in the age of consumer-driven health care. testing considerations "right-sizing technology" means that the right test is offered at the right time for the right patient with maximal operational efficiency and cost-effectiveness. the outcome of right-sizing is to provide results with the potential to inform therapeutic and infection control decisions for improved care and, ultimately, reduced downstream costs. the diagnostic testing needs of a medical institution such as kaiser permanente in northern california, which is comprised of hospitals and over medical offices spread out over a wide geographical area with over . million members and serviced by a central laboratory, are significantly different than those of a -bed county hospital with an on-site laboratory. advances in technology have provided flexibility in diagnostic testing to address the differing needs of health care systems and the laboratories that serve them. for any given analyte, there are a number of highly sensitive and specific tests available from which to choose. considerations that go into the selection of a test or instrument platform for implementation include perceived turnaround time needs for improved patient care, sample volume requirements, number of tests expected, suitability for the intended laboratory based on available expertise and desired workflow, as well as cost. in the past decade, manufacturers have targeted their research toward development of more sensitive and specific mpoc diagnostic infectious disease platforms and tests. such mpoc tests have evolved for more practical use at the bedside. manufacturers have appreciably simplified tests by removing the need for sample manipulation and handling. instrumentation has become more automated and/or involves fully integrated systems that are portable or significantly smaller and more modular. instruments have also incorporated mechanisms for recording and transmitting results. all the while, tests have become faster while demonstrating improved sensitivity and specificity [ ] . these modifications in technology have enabled molecular testing to migrate from large central laboratories. most poc tests are still moderately complex, which is defined by the clinical laboratory improvement amendments of (clia) as one requiring basic laboratory knowledge and training for personnel performing the test. users of these tests must adhere to clia regulatory requirements, which includes quality assurance, along with appropriate documentation, validation of analytical performance, proficiency testing, and ongoing competency training. clia director oversight is still required [ ]. increasingly, diagnostic molecular tests are being designed and submitted for clia-waived status. clia-waived tests are defined by the food and drug administration (fda) as being "so simple and accurate as to render the likelihood of erroneous results negligible; or pose no reasonable risk of harm to the patient if the test is performed incorrectly" [ , ] . based on this definition, non-laboratorians can perform the test without clia director oversight if they are following the manufacturer's instructions [ ]. the first clia-waived mpoc test to receive fda approval was the alere i influenza a&b in . to better ensure quality results are being reported, some of the new mpoc tests have incorporated internal electronic and reagent quality control (qc) and have built in a shut-down mechanism in the event of failed qc. since the waived testing program began in , the number of approved clia-waived diagnostics has increased from to over , with more than analytes approved for infectious disease testing [ ] . there are over , laboratories in the united states that now hold a certificate of waiver, which enables them to perform any clia-waived test [ ]. however, just because anyone can perform the test does not mean they should. there must be an understanding of test limitations by all testing personnel. few non-laboratorians realize that the central laboratory filters out many inappropriate specimens, and nonlaboratorians require extensive training to understand the testing complexities of even waived tests. laboratories frequently receive incorrectly collected specimens and are asked to test them because there is a lack of appreciation of why these specimens would not be tested. for example, clostridium difficile testing is not performed on a formed stool specimen or for patients less than year old due to the confounding issues of potential colonization, and as in a central laboratory, pre-analytical knowledge and conditions would need to exist to prevent misuse of testing. one question is whether we would be needlessly treating people in these cases if left to the facility performing the waived testing. also, testing a specimen type that is not included in the intended use of an fda cleared test will result in an off-label use of an assay. application of diagnostics in medicine is a balancing act between what we can do, what we need, and what we can afford. diagnostics will continue to evolve. it will become faster, cheaper, and easier to perform, but technology comes at a price, and implementing new technologies with faster turnaround times nearer the patient requires careful thought about placement within the flow of the patients. moving a rapid molecular test closer to the patient has the potential to have an immediate impact on therapeutic decisions. a prospective cohort study examined the potential cost benefit of near-patient mpoc testing for chlamydia trachomatis (ct) and neisseria gonorrhoeae (ng) in a clinic based on reduction of contact attempts [ ] . as part of the study, , patients who had ct/ng nucleic acid amplification tests (naat) also completed a questionnaire to ascertain the maximum time patients were willing to wait after consultation for ct/ng test results and thus the potential for immediate treatment of individuals testing positive while preventing unnecessary treatment of patients who tested negative. the study determined that of the , patients, . % were unwilling to wait even minutes for the results of an mpoc test. based on the results from a questionnaire, of patients who tested positive by a naat, use of a -minute mpoc test would have resulted in immediate treatment of . % of the individuals, whereas a -minute test would have influenced the immediate treatment time of only . % of these positive patients. of , patients who tested negative for ct/ng by naat, use of a -minute mpoc test would have prevented . % of empirical treatments, while a -minute mpoc test would have prevented . % of the empirical treatments. another study looked at the impact of the -minute xpert ct/ng test when sample collection was performed on arrival of the patient, with the intention being that the patients receive their results and treatment as needed during the appointment [ ] . actual wait times were evaluated. only . % of the patients received their results before leaving the clinic with the -minute xpert test. it was determined that a test turnaround time greater than minutes would likely not be effective, given that it took minutes from the time of sample collection to the clinical consultation. for such mpoc tests to affect patient management, results will need to be available at the time of consultation to maintain patient flow. there are limited studies examining the clinical impact of mpoc tests for other infectious diseases [ ] . the infectious disease society of america's practice guidelines for group a streptococcus (gas) currently recommends two-tiered testing for pediatric patients [ ] . it is recommended that rapid antigen detection tests (radts) be performed on throat swabs due to the rapid turnaround time of the test (< minutes). however, due to the low sensitivity, bacterial cultures are recommended for confirmatory testing of negative radts. clia-waived mpoc gas diagnostic tests with turnaround times comparable to those of the radts are becoming more readily available. these pcr tests do not detect group c or group g streptococci. however, they have been shown to have improved sensitivity for detection of gas, even compared to culture [ , ] . additional studies are needed to assess the clinical value of these tests and the potential for detection of low-level colonization. in a retrospective study, blaschke et al. [ ] examined visits to u.s. emergency departments (eds) using data from the national hospital ambulatory medical care survey. they found that rapid influenza diagnostic tests (ridt) were performed during . million visits and that % of influenza diagnoses were made in association with ridt. test results did suggest that some influence on physician behavior occurred, as patients diagnosed with influenza had fewer ancillary tests ordered ( % versus % of visits), fewer antibiotic prescriptions ( % versus %), and increased antiviral use ( % versus %) when the diagnosis was made in association with ridt. thus, diagnosis of influenza made in conjunction with ridt resulted in fewer tests and antibiotic prescriptions and more frequent use of antivirals. early influenza virus antigen-based poc tests lacked sensitivity [ , ] . the newer mpoc tests are significantly more reliable and have the potential for improved outcomes in the poc environment [ ] . however, as more mpoc options become available, it will be important for laboratories to continue to assess their performance, as not all mpoc tests may demonstrate the same sensitivity and specificity [ ] . a recently published open-label, randomized, controlled trial looking at the routine use of mpoc testing of respiratory viruses in adults presenting to hospital with acute respiratory illness enrolled patients ( assigned to poc testing and to routine care). the authors found that routine use of mpoc for respiratory viruses did not reduce antibiotic usage. however, many patients in the study were already started on antibiotics before the mpoc results were available. mpoc was also associated with a reduced length of stay and improved antiviral use [ ] . the clinical laboratory and diagnostic effectiveness (clade) study was a prospective observational cohort study undertaken to assess the impact of a highly sensitive ( %) -minute cliawaived mpoc influenza test on patient management in the emergency department (ed) and associated economic benefit [ ] . the study indicated that % of the ed physicians changed their management of patients, primarily of patients who tested influenza virus negative. the influenza test results impacted decisions about hospital admissions and discharges, ordering of additional medical procedures, and laboratory tests, as well as antimicrobial and antiviral usage. this model, applied to , ed visits, revealed a cost savings of nearly $ , [ ] . the study reiterated that getting the right information to the right people at the right time has the ability to impact clinical care. community pharmacies have also become effective players in infectious disease management through provision of vaccinations and are increasingly offering poc tests. over % of the laboratories with a certificate of waiver are in pharmacies [ ] . a physician-pharmacist collaborative practice agreement (cpa) can be set up to delegate prescriptive authority to pharmacists for treatment of infectious diseases based on clia-waived poc test results. the use of this model has been shown to be effective for influenza virus and gas [ , ] . in a pilot study conducted at pharmacies in states using the cpa model, pharmacists performed a clia-waived poc influenza test to screen individuals presenting with influenza-like symptoms [ ] . pharmacists provided oseltamivir to all individuals who tested positive for influenza virus by the poc test within an hour of the initial encounter. meanwhile, individuals who tested negative for influenza virus did not receive inappropriate antiviral therapy. in a similar pilot study, pharmacists performed a clia-waived poc gas diagnostic test to screen individuals coming into the pharmacies with symptoms of pharyngitis [ ] . about million physician office visits are due to acute pharyngitis every year. rates of antimicrobial use as high as % have been reported in the literature to treat pharyngitis, although gas has been shown to be associated with only % to % of pharyngitis cases. of the individuals screened in the study, about % tested positive for gas and were thus treated with an antimicrobial consistent with prevalence studies. this study indicates a significant potential of poc tests in pharmacies to decrease inappropriate antibiotic usage in the outpatient setting, although it must be emphasized that moving testing from a central laboratory to a medical unit or more accessible location does not guarantee improved outcomes without systematic changes in management. additionally, when poc testing is performed by clinical staff, errors can arise from a lack of understanding of the importance of qc and quality assurance [ ] . the american academy of microbiology recently convened a colloquium of industry thought leaders and subject matter experts to evaluate the role of "near-patient testing," as well as the impact of this diagnostic "paradigm shift" for microbiology [ ] . the report from this colloquium was recently published, with thoughtful recommendations. these recommendations were divided into three categories: (i) implementation, (ii) oversight, and (iii) evaluation. key recommendations included (i) rethinking patient flow in the clinical setting to optimize poc utilization, (ii) retaining proper oversight by the microbiology laboratory, and (iii) the need for better outcome data which includes health economics data [ , ] . syndromic testing has gained popularity in recent years. these multiplex tests detect most common and some uncommon pathogens associated with a syndrome based on similar signs and symptoms. in , the luminex xtag respiratory viral panel was the first multiplex molecular panel to receive fda clearance in the united states. since then, a number of large syndromic multiplex panels have been fda cleared for use in clinical diagnostics. multiplex panels currently exist for gastroenteritis (gastrointestinal [gi]), bloodstream infections, and meningitis/encephalitis. although some instrument platforms still require offline extraction, many platforms have evolved into sample-to-result assays requiring less than minutes of hands-on time with a turnaround time of to hours. for the most part, the sensitivity and specificity of these multiplex tests are comparable; however, sensitivity and specificity of the individual targets can vary by platform. multiplexed molecular panels that can target up to pathogens have the potential to simplify ordering for the physician, as well as workflow in the laboratory, and require less expertise on both ends as a single automated test. as new faster and simpler technologies are introduced for multiplexed platforms, there has been continued growth in adoption of these tests for clinical diagnosis. however, there are limitations to this shotgun approach that are associated with high financial costs as reimbursements continue to decrease, as well as test interpretation dilemmas, especially in the context of low prevalence rates. a point-counterpoint paper was recently published on large multiplex panels as first-line tests for respiratory and gi pathogens [ ] . a proposed advantage was the potential to provide timely results for targeted therapy. however, detecting more pathogens might not impact treatment at all, as low sensitivity for certain targets can result in missed diagnoses with additional consequences. also, low prevalence rates for many of the targets may lead to false positives followed by unnecessary treatment and potentially delayed diagnosis. diagnostic errors caused by inappropriate ordering can cause delays in care or harm patients [ ] . pre-test probability is important with sensitive molecular assays. a tuberculosis meningitis case that was misdiagnosed as herpes simplex virus (hsv- ) infection presented by gomez et al. [ ] underscored the risk of using syndromic multiplex assays without fully understanding the limitations associated with them. the patient's true diagnosis was delayed because of an initial hsv- -positive filmarray meningitis/encephalitis (me) panel result, which ultimately contributed to severe neurological sequelae. on the other end of the spectrum, another recent article reported that the meningitis panel demonstrated reduced sensitivity for hsv detection from pediatric cerebrospinal fluid specimens [ ] . positive results due to panel detection of colonization in a gastrointestinal panel with c. difficile and long-term shedding of organisms such as norovirus or rotavirus can also lead to inappropriate therapeutic decision making [ , , ] . the selection of the platforms that laboratories implement is usually based on accuracy, cost, hands-on time, level of complexity, staffing, throughput, and convenience. however, we also need to think about how we are going to use the test once we implement it, whether to restrict ordering of these tests to only the sickest patients or to offer them to everyone as a first-line test. for a highvolume laboratory, using a costly multiplex platform as a first-line test is not feasible. patient outcome data based on large multiplex tests has been slow to evolve [ , ] . additional data are needed to determine which patients will benefit from this type of testing. for respiratory infections, testing needs may vary by season and geography. during flu season, it may be more cost effective to perform a targeted influenza/rsv panel on patients presenting with respiratory symptoms before testing for a broad panel of organisms. panels may be better suited to the critically ill or immunocompromised populations. implementation of a testing algorithm for laboratory utilization of molecular multiplex panels with decision support built into ordering may be needed to avoid substituting one set of unintended consequences for another. education and mandated improved test utilization will hopefully improve economic outcomes for the laboratory and decrease the financial burden on the patient. clia-waived status is being obtained for multiplex platforms, with a number of implications. in october , biofire diagnostics received fda clearance and clia waiver for the filmarray respiratory panel ez, which requires only minutes of hands-on time and has a run time of hour. the ez panel is the clia-waived version of the fda-cleared respiratory panel, which tests for viral and bacterial pathogens, adenovirus, coronavirus, human metapneumovirus, human rhinovirus/enterovirus, the influenza viruses, parainfluenza virus, respiratory syncytial virus (rsv), bordetella pertussis, chlamydia pneumoniae, and mycoplasma pneumoniae. there are numerous questions that arise from the availability of these expensive multiplex tests for placement outside the central laboratory without required oversight by technical experts. it will be necessary to determine what algorithms will be used by physicians to decide which patients to test and how results will be interpreted, particularly if multiple targets are positive. until recently, multiplexed molecular panels have been one size fits all. panels with fixed prices based on fixed targets may be excessive and may not necessarily include all the pathogens being considered by the physician. multiple platforms may be required in order to address the needs of the physician in such cases. this scenario becomes a very expensive approach to diagnostic testing. testing needs to fit the medical center and be tailored to the population that the laboratory services. the diagnostic needs of a children's hospital can be very different from those of a medical center that caters to a large elderly population. likewise, a cancer center or a transplant center may have very specific diagnostic needs. nanosphere has fda clearance for its verigene respiratory pathogens flex nucleic acid test (rp flex) on the automated, sample-to-result verigene system, which allows flexibility in testing and is the first multiplex test that is scalable. each rp flex cartridge contains viral and bacterial targets. the physician can order any combination of targets for testing. laboratories pay for only the targets that are ordered. results for other targets not initially ordered on the panel can be reflexed at an additional cost without having to re-run the test. for example, one possible scenario during influenza season is to first order only influenza virus targets or influenza virus plus rsv from the panel. if the result is negative, adenovirus, human metapneumovirus, rhinovirus, and parainfluenza virus can be ordered and the results released. bordetella sp. targets can be ordered separately based on clinical suspicion. medicare recently proposed universal non-coverage for respiratory multiplex panels, which will make it even more challenging for laboratories to utilize the technology. there has been a lot of discussion surrounding multiplex gi panels and whether this is clinically meaningful testing. in may , medicare administrative contractor palmetto gba posted draft local coverage determinations (lcd) for two types of multiplex infectious disease tests [ ] . this decision would provide limited coverage for nucleic acid amplification-based gi pathogen panels and a non-coverage decision for multiplex pcr respiratory viral panels. the lcd proposed coverage for molecular panels to detect gi pathogens would be limited to targets (salmonella, campylobacter, shigella, cryptosporidium, and shiga toxin-producing escherichia coli), which represent the majority of foodborne pathogens. current infectious diseases society of america guidelines for infectious diarrhea suggest a selective approach to workup based on whether the patient has traveler's diarrhea with fever or blood, hospital-acquired diarrhea, or persistent diarrhea [ ] . a flex platform may be more suitable for testing of diarrheal illnesses. regardless of the number of analytes on a gi panel, the cost when reimbursement is limited to a maximum of targets, may be affected only by the actual cost of the panel itself. the different approach for multiplex pcr testing for respiratory viruses, apart from influenza a/b viruses, with or without inclusion of rsv, is being applied. the reasoning for non-coverage included the fact that the pathogen targets in such panels do not represent a common syndrome and that targets can be very rare. the notice said that a "one size fits all testing approach is screening and not a medicare benefit" and went on to say that "one size fits all panels contribute to test over-utilization, and increased cost to health care without specific benefit to a given patient. testing should be limited to organisms with the greatest likelihood of occurrence in a given patient population, and if results are negative, with a reflexive testing to more exotic organisms." examples are c. pneumoniae or b. pertussis in combination with rhinovirus, influenza viruses, and rsv [ ]. telemedicine and remote diagnostics can take on several roles. today with total laboratory automation (tla) and digital microbiology, laboratories have the capability to read and review slides and plates from facilities that are miles or oceans away. a recent clinical microbiology newsletter article highlighted the impact of telemedicine on gram stains in the health care system in arizona [ ] . telemedicine companies like vsee (www.vsee.com) have set up field kits with multiple devices that enable remote diagnosis. through the use of software like ehealth opinion, rural patients and physician experts in the u.s. and china are connected through the virtual doctor project [ ] . such projects are expanding in many parts of the developing world [ ] . telemedicine companies like doctor on demand (www.doctorondemand.com) offer virtual doctor's visits through tablet computers or smartphones. other areas of remote diagnostics being explored are internetbased programs and self-collected specimens for mail-in testing. there are currently fda-approved ct/ng naat assays for self-collected specimens in clinical settings. internet-based mailin programs for sexually transmitted infection (sti) screening has been successfully implemented in a public health system (www. iwantthekit.com), as well as through private companies (mylabbox.com) [ ] . public health england in published a guidance document on commissioning an internet-based chlamydia screening program [ ] . such strategies are aimed at diagnostic testing and improving access over the continuum of care. with this new way of delivering care comes the question of validating at-home self-collected specimens and the stability of a specimen mailed through the post. while sti programs may be a starting point for specimen self-collection, it begins a conversation that would expand the realm of consumerism in health care to a new level. one could argue that no one is better able to properly collect a specimen than the person with the greatest interest in the results, the patient. clinical studies comparing clinician-collected and self-collected specimens in a clinical setting for ct/ng have demonstrated that self-collected vaginal specimens have equivalent performance with acceptable patient satisfaction [ , ] . for a recent review of self-collected specimens for infectious disease testing, see tenover et al. [ ] . internet-based programs have the potential to triage non-critical medical needs while reducing visits to traditional brick-and-mortar clinics. at kaiser permanente, virtual visits have been used for several years through secure e-mails, telephone calls, and some video encounters. in the northern california kaiser permanente region, which has over , physicians and over . million members, virtual visits grew from . million in to . million in , with projections that virtual visits will soon exceed physical visits [ ] . near-patient testing for sti programs, such as the dean street clinic in london, offering walk-in sti testing and treatment with an short message service or sms text on a cell phone to let patients know their results (www.dean.st/testing), are also available. investment in such programs is evolving, yet what is lacking is the return on investment (roi) analysis, which is needed to further policies that could help provide financial support for the evolution of technology in daily practice. ngs has had one of the most significant impacts on microbial sciences since the advent of pcr. through initiatives like the cdc's advanced molecular diagnostics (amd) and response to infectious disease outbreaks, public health microbiology has started to transform into the next generation of thinking for the investigation, prevention, and control of infectious diseases. ngs has provided insight into questions that just was not possible through previous technology. for a review of ngs technologies and amd see maccannell [ ] . ngs platforms like the minion (oxford nanopore) can provide portable real-time ngs analysis. the system is miniature in size, plugs into the usb port of a laptop, and offers minimal sample preparation at a low cost (https://nanoporetech.com/products/ minion). the potential of such technology is just beginning to be realized. applications such as the direct detection of mycobacterium tuberculosis from sputum for identification and antimicrobial susceptibility prediction available the same day have been described [ ] . barriers are bioinformatics, interoperability of results, and building a workforce with a new skill set and infrastructure to support it. given the debate around reimbursement and multiplex panels, it will be interesting to see where the conversation leads with ngs. ngs will provide much more information than a -plex respiratory or stool panel. the technology is already changing practice in the public health laboratory, and the clinical microbiology laboratory is following [ , ] . twenty years ago, the cdc created pulsenet, a molecular-subtyping network of federal, state, and local public health laboratories designed to facilitate the identification of and response to outbreaks caused by bacterial foodborne pathogens. the specific objectives of pulsenet are to detect foodborne disease case clusters through comparison of pulsed field gel electrophoresis (pfge) "fingerprint" patterns, to facilitate early identification of commonsource outbreaks, and to help food regulatory agencies identify areas where implementation of new measures is likely to improve the safety of the food supply. at the time, pfge was considered cutting-edge technology. to celebrate the th anniversary of puslenet, the economic impact of the program was recently published [ ] . pulsenet costs roughly $ . million to operate but saves more than $ million annually in medical and productivity costs avoided [ ] . this roi is impressive, but the fact that it was years before this economic analysis was published is surprising given the program's success. with federal budget cuts to critical programs that support national infrastructure, evaluating and communicating the value of technology to the health economics of the nation should be part of the national strategy. looking ahead, it is clear that it is only a matter of time before pfge will be replaced by ngs for such foodborne outbreak investigations in the pulsenet system. the economic impact of ngs should be analyzed in a timely manner so that the roi of this powerful technology can be communicated to the appropriate funding agencies. the same is true for the clinical microbiology laboratory. while it sounds very appealing to place an mpoc influenza virus platform nearer to the patient in the ed or in urgent care, the initial investment to place and maintain that testing may be a daunting sell to administrators. the question around this roi is where the cost avoidance is over the continuum of care. for patients coming through the ed during influenza season the greatest impact to patient management would be avoiding a hospital admission. the average cost of a hospital admission due to pneumonia is $ , , according to the agency for healthcare research and quality (rockville, md) [ ] . compared to the cost of a tamiflu prescription, which is roughly $ , the avoidance of hospital admission would clearly have the greatest financial impact. when one adds the implementation costs of the mpoc instrument and reagents over the course of a flu season, the roi can become a more comprehensive sell to the c-suite or the corporation's senior executives. tables to demonstrate the estimated cost of implementing an mpoc influenza assay in a hospital system with medical centers, each with an ed. the total cost of implementation for instrument and reagents over months of the respiratory disease season adds up to $ , ( table ). the number of admissions that would need to be avoided to break even on the cost of implementation is , or roughly per ed ( table ). this number is equal to . % of the estimated , tested patients over the course of the respiratory disease season, which would equate to an roi of < months (table ) . another factor to consider when thinking about a rapid mpoc test is that placing testing correctly in the system may actually be cost neutral, because testing is being shifted without the need to bring on any additional testing. outcome studies looking at technology placement are forthcoming [ ] . in , the original patent for pcr was issued, with kary mullis listed as the inventor. in , he was awarded the nobel prize for pcr. these accolades came only after the article reporting the invention was rejected by both nature and science. it was finally published in methods in enzymology [ ] . as one reflects on the impact of technology like pcr, it is easy to lose sight of how far technology has come. the conversation is now focused on where we need to go. in the world of instant gratification that we have become so accustomed to living in, it is important to remember that changes in medicine take time and require data built on evidence. shifting practice also requires buy-in by stakeholders that the laboratory may not be considering. during the lifespan of technology, the stakeholders will range from biotechnology companies to laboratories, physicians, regulators, policymakers, guideline committees (steered by industry thought leaders), payers, and patients. these stakeholders will influence the maturity of technology application over time. thus, the laboratory community must assess and factor in key drivers that address need, satisfy administration, and influence health economics. properly designed pilot studies remain an important step in assessment. publishing these results is key to moving the field forward. sharing information that may be initially considered only for internal quality improvement projects is essential. laboratories could benefit from more coordinated collaboration from stakeholders, who have a vested interest in such data and the impact on patient care and health economics. at the end of the day, we are all consumers of health care. we should all be looking around asking, "what are our expectations?" with the aca, we have more patients to take care of and fewer health care dollars to do it with in an imperfect health care system. we have improved and 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ritchie, hannah title: a cross-country database of covid- testing date: - - journal: sci data doi: . /s - - - sha: doc_id: cord_uid: ihq gdwj our understanding of the evolution of the covid- pandemic is built upon data concerning confirmed cases and deaths. this data, however, can only be meaningfully interpreted alongside an accurate understanding of the extent of virus testing in different countries. this new database brings together official data on the extent of pcr testing over time for countries. we provide a time series for the daily number of tests performed, or people tested, together with metadata describing data quality and comparability issues needed for the interpretation of the time series. the database is updated regularly through a combination of automated scraping and manual collection and verification, and is entirely replicable, with sources provided for each observation. in providing accessible cross-country data on testing output, it aims to facilitate the incorporation of this crucial information into epidemiological studies, as well as track a key component of countries’ responses to covid- . across the world, researchers and policymakers look to confirmed counts of cases and deaths to understand and compare the spread of the covid- pandemic. however, data on cases and deaths can only be meaningfully interpreted alongside an accurate understanding of the extent and allocation of virus testing . two countries reporting similar numbers of confirmed cases may in fact have very different underlying outbreaks: other things being equal, a country that tests less extensively will find fewer cases. many countries now publish official covid- testing statistics, but the insights offered by these numbers remain relatively unexplored both in public discourse and scientific research. this may be because of barriers limiting access to this data: the statistics are scattered across many websites and policy documents, in a range of different formats. no international authority has taken on the responsibility for collecting and reporting testing data. we developed a new global database to address this lack of access to reliable testing data, thereby complementing the available international datasets on death and case counts . the database consists of official data on the number of covid- diagnostic tests performed over time across countries (as of august ). we rely on figures published in official sources, including press releases, government websites, dedicated dashboards, and social media accounts of national authorities. we do not include in our database figures that explicitly relate to only partial geographic coverage of a country (such as a particular region or city). the resulting database is (i) updated regularly through a combination of automated scraping and manual collection and verification, and (ii) entirely replicable, with sources provided for each observation. in addition, the database includes extensive metadata providing detailed descriptions of the data collected for each country. such information is essential due to heterogeneity in reporting practices, most notably regarding the units of measurement (people tested, cases tested, tests performed, samples tested, etc). series also vary in terms of whether tests pending results are included, the time period covered, and the extent to which figures are affected by aggregation across laboratories (private and public) and subnational regions. the comprehensiveness of our database enables comparisons of the extent of testing between countries and over time -in absolute terms, but also relative to countries' population, and to death or confirmed case counts (fig. ) . such variation offers crucial insights into the pandemic. at the most basic level, it is clear that a country that tests very few people -such as the democratic republic of congo, or nigeria (fig. a ) -can only have very few ( ) : | https://doi.org/ . /s - - - www.nature.com/scientificdata www.nature.com/scientificdata/ confirmed cases. the number of performed tests should be seen as an upper limit for the number of confirmed cases. further, high positive test rates ( fig. -see reference lines) may help identify severe underreporting of cases. the relationship between test positivity rate and case underreporting has been explored in the context of other infectious diseases . in terms of covid- , this link is discussed by ashish jha and colleagues at the harvard global health institute, who provide a sketch of the relationship between cases, deaths and the positivity rate in the united states (see https://globalepidemics.org/ / / /why-we-need- -tests-per-d ay-to-open-the-economy-and-stay-open). in a more formal analysis, golding et al. find that their modelling estimates of the case ascertainment rate are weakly correlated (kendall's correlation coefficient of . ) with the number of tests per case -the inverse of the test positivity rate -derived from our database, with a positive relationship evident in the range of - tests per case . the institute for health metrics and evaluation (ihme) www.nature.com/scientificdata www.nature.com/scientificdata/ include testing data sourced from our database in their covid- models (www.healthdata.org/covid/faqs#dif-ferences% in% modeling). in bringing this data together, our hope is that we will facilitate future research in this direction. more generally, our aim is to provide an essential complement to counts of confirmed cases and deaths. these are the figures that guide public policy, both in the initiation of control measures and as they start to be relaxed. but without the context provided by data on testing, reported cases and deaths may offer a very distorted view on the true scale and spread of the covid- pandemic. the database consists of two parts, provided for each included country: ( ) a time series for the cumulative and daily number of tests performed, or people tested, plus derived variables (discussed below); ( ) metadata including a detailed description of the source and any available information on data quality or comparability issues needed for the interpretation of the time series. for most countries, a single time series is provided: either for the number of people tested, or the number of tests performed. for a few countries for which both are made available, both series are provided. in such cases, metadata is provided for each separate series. data collection methods. the time series data is collected by a combination of manual and automated means. the collection process differs by country and can be categorized into three broad categories. firstly, for a number of countries, figures reported in official sources -including press releases, government websites, dedicated dashboards, and social media accounts of national authorities -are recorded manually as they are released. secondly, where such publications are released in a regular, machine-readable format, or where structured data is published at a stable location, we have automated the data collection via r and python scripts that we execute every day. these are regularly audited for technical bugs by checking their output against the original official sources (see 'technical validation' , below). lastly, in some instances where manual collection has proven prohibitively difficult, we source data from non-official groups collecting the official data, most often on github. these are also regularly audited for accuracy against the original official sources (see 'technical validation' , below). any available information on data quality or comparability issues needed for the interpretation of the time series is gathered and summarized manually into detailed metadata for each series, guided by a checklist of data quality questions (see data records, below). general been the basis for covid- case confirmation, in line with who recommendations . since the primary purpose of the database is to provide information on testing volumes specifically to aid the interpretation of data on confirmed cases, it is exclusively this category of testing technologies that the database aims to include. in order to be included, a data point for a given country must report an aggregate figure that includes both negative tests (or negatively tested individuals) plus positive tests (or confirmed cases). the units (whether the number of tests or individuals is being counted) must be consistent across positive and negative outcomes. the aggregate figure must refer to a known time period -for instance, the number of tests performed in the last day or week. however, where a cumulative total is provided, it is not a requirement that the specific start date to which the cumulative count relates must be specified, provided that it is clear that the figure aims to capture the whole of the relevant outbreak period. figures relating to testing 'capacity' or to rough indications of average testing output, or to the number of tests that have been distributed (rather than actually performed) are not included in the database. where figures for pending tests are provided separately by a source these are excluded from our counts. where they cannot be separated, the figures including pending tests are reported. details concerning pending tests for individual countries can be found in the metadata. the database provides a time series for both the cumulative number of tests (or people tested) and for daily new tests. exactly how these series are derived depends on the way the raw data is reported by the source. where a source provides a complete time series for daily tests, we derive an additional cumulative series as the simple running total of the raw daily data. where a source provides cumulative figures, we derive an additional daily series as the day-to-day change observed in consecutive observations. in many cases the source data is not available at a daily frequency (fig. ) . in order to facilitate cross-country comparisons over time, we derive an additional 'smoothed' daily testing series calculated as the seven-day moving average over a complete, linearly interpolated daily series (described in more detail in the data records section below). retrospective revisions in the source data. due to the efforts to produce timely data, official testing figures are subject to frequent retrospective revisions. this can occur for instance where some laboratories have longer reporting delays than others, and previously uncounted tests are then subsequently included. this issue presents no difficulties where sources provide an updated time series within which such revisions are appropriately incorporated; for instance, by backdating the additional tests to the date they were performed. however, a number of the sources we rely on provide only a 'snapshot' of the current cumulative figure, with no time series. we construct our cumulative and daily testing time series from the sequence of these 'snapshots' . for these cases, retrospective revisions do impact our data since revisions to the data are included on the day the revision is made, not when the revised tests occurred. typically, this results in only small deviations in the www.nature.com/scientificdata www.nature.com/scientificdata/ cumulative figure in proportional terms, but the derived daily testing series can be impacted more meaningfully. at the extreme, in a few cases, such revisions result in a fall in the cumulative total from one day to the next, implying a negative number of tests for that day. this issue is mitigated in two ways. firstly, given that much of retrospective revision relates to testing conducted over the last few days, the 'smoothed' daily time series we derive reduces some of the artificial volatility introduced. secondly, we alert the user as to which data is subject to such concerns as part of the information included in the metadata (see below). a copy of the database has been uploaded to figshare . this provides a version of the database as it stood at the time of submission, on august . a live version of the database, which continues to be updated, can be downloaded from a public github repository (https://github.com/owid/covid- -data/tree/master/public/data/testing) in csv, xlsx, and json formats, which may be imported into a variety of software programs. structure. the database consists of two components: a time series file including observations of cumulative and daily testing (covid-testing-all-observations.csv), and metadata (covid-testing-source-details.csv). each row in the metadata table provides source details (discussed below) corresponding to a given country-series (i.e. the combination of country and series fields make up a unique id within covid-testing-source-details.csv). the time series for cumulative and daily testing for each country-series is then provided in the covid-testing-all-observations.csv file. in addition, we provide the raw data (raw-collected-data.csv), as collected from the source, in order to make it plain how our time series data is constructed from the original observations. we also provide the united nations population data for (un- -population.csv) used to derive the per capita measures included in the time series. raw-collected-data.csv. country. each observation relates to testing conducted within the indicated country. we do not include in our database figures that explicitly relate to only partial geographic coverage of a country (such as a particular region or city). the country's -letter iso - code is also provided as a separate field. units. a short description of the unit of observation of the collected testing figures, selected out of three possible categories: "people tested", "tests performed", "samples tested". series for which it was not possible to discern the category are labelled as "units unclear". series. multiple series (e.g. people tested and samples tested) are included for some countries, and are demarcated by this field. common to covid-testing-all-observations.csv and raw-collected-data.csv. date. depending on the source, this may relate to the date on which samples were taken, analyzed, or registered, or simply the date they were included in official figures (see 'retrospective revisions in the source data' , above). in general, sources try to provide testing data relating to a given, stable cut-off time each day. where significant changes in reporting windows have been found, these have been noted in the notes field (see below). www.nature.com/scientificdata www.nature.com/scientificdata/ cumulative total. the reported cumulative amount of testing as of date. the specific date to which the cumulative figures date back to, if known, is provided in the metadata (see below). in many cases this is not explicitly stated by a source, but only figures that appear to intend to capture the entire period of the testing response to covid- outbreak within the country are included in the database. in covid-testing-all-observations.csv, for those sources only providing daily testing figures, this field is derived as the running total of the raw daily data, and is also provided per thousand people of the country's population. daily change in cumulative total. broadly, this field may be interpreted as the number of new tests (or people tested) per day. for sources that report new tests per day directly, this field in covid-testing-all-observations. csv is identical to the raw data presented in raw-collected-data.csv. for sources that report only cumulative testing figures, the field is derived as the day-to-day change observed in consecutive observations of the raw cumulative total data. this may fail to correspond to the true number of new tests for that date where the source has included retrospective revisions in the cumulative totals (see 'retrospective revisions in the source data' , above). in covid-testing-all-observations.csv, this series is also provided per thousand people of the country's population. source url. a url at which the specific observation of the corresponding raw data can be found. source label. the name of the source for the observation. notes. contains any notes to aid the interpretation of this specific observation (above and beyond details that apply to the whole series, which are provided in covid-testing-source-details.csv). specific to covid-testing-all-observations.csv. -day smoothed daily change. as an outbreak progresses, flows of new tests per day, rather than cumulative figures, become more relevant for understanding trends. daily testing figures however suffer from volatility created by reporting cycles. moreover, since many sources do not provide data at daily intervals, figures for new tests per day are available with more limited coverage. to aid the cross-country analysis of testing volumes over time, we provide this short-term measure of testing output that aims to mitigate these two problems. it is calculated as the right-aligned rolling seven-day average of a complete series of daily changes. for countries for which no complete series of daily changes is available because of the reporting frequency of our source, we derive it by linearly interpolating the daily cumulative totals not available in the raw data, up to a maximum interval of days. the exact code used to derive the -day smoothed daily change is available online (see 'code availability' , below). specific to covid-testing-source-details.csv. number of observations. the number of days for which raw observations are available. detailed description. a written summary of available information concerning the nature and quality of the source data needed for proper interpretation and cross-country comparison. the collation of this information is guided by a 'checklist' of data quality questions regarding: the unit of observation; which testing technologies figures relate to; whether tests pending results are included; the time period covered; and the extent to which figures are affected by aggregation across laboratories (private and public) and subnational regions. in practice the documentation we are able to provide is limited by that made available by the official source. we aim to include any information provided by the original source needed for the interpretation and comparison with other countries. coverage. the database includes observation for countries, covering % of the world's population. because of differences in the frequency at which countries publish testing data, coverage is somewhat lower for more recent periods: % of the world's population is covered with figures relating to - august ; % is covered with figures relating to - august (fig. ). the database represents a collation of publicly available data published by official sources. as such, the key quality concern for the database itself is whether it represents an accurate record of the official data. we employ four main strategies for ensuring this. firstly, all automated collection of data, whether obtained from official channels or from third-party repositories of official data, is subject to initial manual verification when it is added to our database for the first time. secondly, we employ a range of data validation processes, both for our manual and automated time series. we continually check for invalid figures such as negative daily test figures, out-of-sequence dates, or test positivity rates above % (by comparing testing data to confirmed case data), and we monitor each country for abrupt changes in daily testing rates. abrupt positive or negative daily changes are sometimes the result of data corrections in the official data, in which case our database includes them without alteration. these changes can be due, for example, to the deduplication of double-counted tests, or the addition of testing data that was previously not captured by the national system (see table ). in order to mitigate against large impacts due to reporting lags, we automatically exclude the most recent observation for a country if its daily number of new tests is less than half that of the previous observation. this is only applied to the most recent day in each time series: as soon as data for subsequent days becomes available, the data point is reinstated if the sharp fall is still present. www.nature.com/scientificdata www.nature.com/scientificdata/ thirdly, to monitor the ongoing reliability of third-party repositories of official data, we apply a continuous audit process, which will remain active as long as this dataset is updated. each day, three observations are randomly drawn out of all observations in the database that have been obtained via third-party sources. for each selected observation, the recorded figure is manually checked against the direct official channel from which the repository purports to obtain the data. the sampling rate means that each third-party source we make use of is checked around once a week. given that any discrepancies with official channels are likely to be clustered within particular sources, this provides a high degree of quality control on these sources on a timely basis. where any discrepancies are noticed, we switch sources (for the entire time series) to either a different repository or to manual data collection directly from the official channel. finally, the testing data included in the database is viewed by tens of thousands of people every day, including many health researchers, policymakers and journalists, from which we receive a large amount of feedback concerning the data. this serves as a final, 'crowd-sourced' method of verification that has proven very effective, enabling any discrepancies between our data and that published in official channels to be flagged and resolved quickly. code used for the creation of this database is not included in the files uploaded to figshare. our scripts for data collection, processing, and transformation, are available for inspection in the public github repository that hosts our data (https://github.com/owid/covid- -data/tree/master/scripts/scripts/testing). changes observed in the source data as of august case-fatality rate and characteristics of patients dying in relation to covid- in italy an interactive web-based dashboard to track covid- in real time malaria burden through routine reporting: relationship between incidence and test positivity rates reconstructing the global dynamics of under-ascertained covid- cases and infections advice on the use of point-of-care immunodiagnostic tests for covid- : scientific brief this project was funded from multiple sources, including general grants and donations to our world in data. the following is a list of funding sources and affiliations. grants: our world in data has received grants from the bill and melinda gates foundation, the department of health and social care in the united kingdom, and the german philanthropist susanne klatten. sponsors: in addition to grants, our world in data has also received donations from several individuals and organizations: center for effective altruism -effective altruism meta fund, templeton world charity foundation, effective giving, the camp foundation, the rodel foundation, the pritzker innovation fund diana beltekian -data recording, verification and analysis. charlie giattino -data recording, verification and analysis. bobbie macdonald -data recording, verification and analysis. esteban ortiz-ospina -data recording, verification and analysis the authors declare no competing interests. correspondence and requests for materials should be addressed to j.h.reprints and permissions information is available at www.nature.com/reprints.publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons license, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons license, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this license, visit http://creativecommons.org/licenses/by/ . /.the creative commons public domain dedication waiver http://creativecommons.org/publicdomain/zero/ . / applies to the metadata files associated with this article. key: cord- - qlk y authors: rahmandad, h.; lim, t. y.; sterman, j. title: estimating the global spread of covid- date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: qlk y limited and inconsistent testing and differences in age distribution, health care resources, social distancing, and policies have caused large variations in the extent and dynamics of the covid- pandemic across nations, complicating the estimation of prevalence, the infection fatality rate (ifr), and other factors important to care providers and policymakers. using data for all countries with reliable testing data (spanning . billion people) we develop a dynamic epidemiological model integrating data on cases, deaths, excess mortality and other factors to estimate how asymptomatic transmission, disease acuity, hospitalization, and behavioral and policy responses to risk condition prevalence and ifr across nations and over time. for these nations we estimate ifr averages . % ( . %- . %). cases and deaths through june , are estimated to be . and . times official reports, respectively, at . ( - . ) million and ( - ) thousand. prevalence and ifr vary substantially, e.g., ecuador ( %; . %), chile ( . %; . %), mexico ( . %; . %), iran ( . %; . %), usa ( . %; . %), uk ( . %; . %), iceland ( . %, . %), new zealand ( . %, . %), but all nations remain well below the level needed for herd immunity. by alerting the public earlier and reducing contacts, extensive testing when the pandemic was declared could have averted . ( . - . ) million cases and ( - ) thousand deaths. however, future outcomes are less dependent on testing and more contingent on the willingness of communities and governments to reduce transmission. absent breakthroughs in treatment or vaccination and with mildly improved responses we project ( - ) million cases and . ( . - . ) million deaths in the countries by spring . explanatory mechanisms: a) differences in population density, lifestyle, and interaction patterns create variations in reproduction number. b) risk perception, behavioral change and policy responses alter transmission rates endogenously. c) testing is prioritized based on symptoms and risk factors, so detection rates depend on both testing rates and current prevalence. d) limited hospital capacity is allocated based on symptoms, influencing fatality rates. e) weather may have a role in transmission ( ) while age, socio-economic status, and pre-existing conditions impact severity ( , ) , with the poor and minorities suffering disproportionately ( ) . prior research has addressed different parts of this puzzle, including estimating the infection fatality rate (ifr) in well-controlled settings ( ) or using statistical extrapolation ( ) , assessing the asymptomatic fraction in smaller populations or through random testing ( , ) , and estimating prevalence using random antibody testing in highly affected cities and regions ( ) . yet we lack a global view of the pandemic that is both consistent with these more focused findings and simultaneously explains the large variance in official cases and fatality across different countries. in this paper we build and estimate a multi-country model of the covid- pandemic at global scale. our model captures transmission dynamics for the disease, as well as how, at the country level, transmission rates vary in response to risk perception and weather, testing rates condition infection and death data, and fatality rates depend on demographics and hospitalization. estimating this model using data from every country with more than cases for which testing data is available, we infer some of the key characteristics of covid- pandemic globally and inform how alternative control policies may have played out across the globe. we use a multi-country modified seir model to simultaneously estimate the transmission of covid- in countries. the model tracks community transmission, excluding the global travel network and instead separately estimating the date of introduction of patient zero for each country. within each country, the core of the model tracks the population through susceptible, pre-symptomatic, infected pre-testing, infected post-testing, and recovered states. basic transmission dynamics reflect a classical seir process, with a baseline transmission rate, incubation period, and duration of infection. building on this basic structure the model explicitly represents the dynamics of covid testing, including demand for tests, sensitivity of pcr based testing, and allocation of test capacity between positive and negative cases, as well as the dynamics of hospital system capacity, both with concomitant effects on transmission and mortality. it also endogenously generates population-level behavioral and policy responses due to the perceived risks and government intervention. infected people and those with other risk factors (e.g. hospital workers) or similar symptoms due to other illnesses. we assume, based on prior research ( ) , that infected individuals are potentially tested on average days after the onset of symptoms. on any given day, individuals with more severe symptoms get priority for testing. following ( ) , this prioritization exerts a selection effect that results in different average severity of covid in the tested vs. untested infected populations. we also assume a % false negative rate for pcr-based covid tests ( , ) . a positive test results in reduced contact rates for tested individuals, changing the transmission rates endogenously. thus the model tracks various mechanisms generating the observable measures: a daily reported infection rate that combines the total positive results from each day's tests with daily post-mortem infection confirmations, and a daily reported death rate of confirmed cases. unobserved parameters, such as ifr and asymptomatic fraction, can then be estimated by fitting the model against data for observables. we estimate the effective hospital capacity for each country as a function of total hospital beds available, modified for population density. this modification approximates the effect of geographic heterogeneity in demand for hospital capacity -in larger and less densely populated countries, geographic heterogeneity in the progression of the epidemic means that some areas (e.g. new york city) may be overwhelmed with demand even when other parts of the country have unused hospital capacity. as with testing, hospital capacity is allocated between more severe covid cases (both those tested and those not tested) and demand from non-covid patients. hospitalization can reduce the mortality rate for covid patients, while other determinants of fatality rates are the severity of symptoms and the age distribution of the population ( , ) . each country also exhibits a response to the perceived risk of covid. the response is endogenously driven by a weighted combination of reported and actual hazard of infection. perceived risk drives reduction in contact rate and hence transmission rates through non-pharmaceutical interventions such as social distancing measures. specific government policies are not explicitly represented, but treated as part of this endogenous risk response. different countries could vary in their risk perception, response time, as well as the magnitude of their response based on the perceived risk. overall each country is represented by a system of ordinary differential equations tracking seven population stocks (susceptible, pre-symptomatic infected, infected pre-testing, and four groups of infected post-testing -positively tested or not × hospitalized or not) and a state variable for perceived risk. the model also includes multiple additional state variables for measurement and accounting of e.g. deaths and recoveries. model parameters are specified based on prior literature and formal estimation. main parameters adopted from the literature include incubation period ( days ( , ) ), onset-to-detection delay ( days ( ) ), sensitivity of pcr-based testing ( % ( , ) ), and post-detection illness duration ( days ( ) ). we estimate the remaining parameters using a maximum likelihood approach. using testing rate time series and various country-level data points (e.g. population, hospital capacity, comorbidities, age distribution), the model endogenously simulates confirmed new daily cases and deaths over time and matches them against observed data by maximizing the likelihood of observing those data given the model parameters. we use a negative binomial likelihood function to accommodate excess dispersion in infection and death flows compared to more common gaussian specifications. where data on mean) are . % ( . % for median across countries, med) and . % (med: . %) for cumulative infections and deaths, respectively. r-square values exceed . for % of country-specific cumulative and incidence time series. our projections are also consistent with excess mortality data, where available (see appendix s ). main findings include estimated parameters of covid- epidemics across countries, as well as trajectories of key measures. for estimated parameters we report a) the mean of most likely values across countries (mean); b) the standard deviation of those values (std), which quantifies variability of the underlying concept across countries; and c) the mean of country-level interquartile ranges (miqr), which captures the inherent uncertainty in parameter estimates for each country. the model brings together infection, testing, risk perception, behavioral and policy responses, hospitalization, and fatality using data from across the globe. here we focus on three main results. first, the magnitude of epidemic is widely under-reported with much variation globally. we estimate the asymptomatic fraction to be % (mean; std: . %; miqr: . %). combined with a sensitivity of % ( , ) for pcr tests, the fraction of infections that could potentially be identified without mass testing is limited to %. most countries do not reach this upper bound, however, and testing is the binding constraint. figure -a reports the ratio of estimated to reported infections and deaths, ranging between . and for infections and . to for deaths. in our sample of countries (total population of . billion), we estimate total infections at . ( - . , % credible interval (ci)) million and (ci: - ) thousands by june , . and . times larger than reported numbers respectively. under-counting has been larger earlier in the epidemic. for example, usa faced peak infection rate (of thousands per day) when detection rate was less than % of daily new cases. the most affected countries (based on percent infected) to date include ecuador ( %), peru ( . %), chile ( . %), mexico ( . %), iran ( . %), qatar ( . %), spain ( . %), usa ( . %), uk ( . %), and netherlands ( . %) (see figure -b) . despite the order-of-magnitude under-reporting of cases, however, herd immunity due to infection remains far from reach (figure -b) . the closest a a b . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint country has come to herd immunity is chile, which at its peak infection rate was (ci: days away from infection of % of its total population. second, we quantify both significant heterogeneity, and notable consistency, across countries in terms of basic parameters of the epidemic. the estimated initial reproduction number re ranges between . (indonesia) and . (iran), with the median of . (iceland) (re estimates include significant uncertainty; see figure s for details). even absent endogenous reductions in contact due to realized risk, these initial rates may be higher than longer-term levels for most countries because of early exposures happening in denser social networks. cross-country variations also reflect differences in population density, cultural practices, hygiene, as well as the timing of infection and thus early preparedness. we find support for the impact of weather on reproduction number, with the multiplier (rw) developed by xu and colleagues ( ) explaining transmission rates closely (rw . ). we estimate the global infection fatality rate (ifr) to have been . % (ci: . %- . %), with a wide range (figure -c) between . % (ci: . - . ; qatar) and . % (ci: . - . ; italy). the variations in ifr are primarily due to demographics with elderly having much higher risks ( ) . hospital availability and treatment effectiveness provide a second mechanism affecting fatality rates. we find that hospitalization can bring down risk of death to . % (std: . %; miqr: . %) of baseline. the model explains much variability in ifr with minimum country-level variability in basic fatality parameters. nevertheless, the quality of fit deteriorates in a handful of countries. for example, a ratio of simulated to reported deaths below one in a handful of countries signals that the model expected fewer deaths than observed. notably, we find it hard to reconcile, using only the model's mechanisms, the low fatality rates in qatar, singapore, and thailand relative to infection statistics, and high fatality rates in belgium and france. third, testing regulates transmission dynamics though a few mechanisms. by providing early warning, testing sets in motion the behavioral and policy responses essential to reducing transmission rate and controlling the epidemic. the exponential nature of contagion amplifies small early differences, such that a few days' difference in response time can lead to large differences in peak infection and final epidemic size. behavioral and policy responses to changes in infection risk are adopted rapidly, on average reducing effective contact (and thus transmission) rates in . (std: . ; miqr: . ) days. those responses are relaxed when risks attenuate, though down-regulating risk perception is slower (mean: . ; std: . ; miqr: . days). given limited data on rebounds in infections to date, how quickly perceived risk is downgraded is a major source of uncertainty in projecting the future of the pandemic. we also find that those with a positive test reduce their infectious contacts to a fraction of the original level (mean: . % of original contact rate; std: . %; miqr: . %). these reductions are especially important because asymptomatic individuals are estimated to be less infectious than symptomatic ones (mean: %; std: . %; miqr: . %). finally, by regulating infection rates through the previous two channels, testing also 'flattens the curve', allowing a larger fraction of those in need of medical care to be hospitalized. together, these mechanisms create an early race between testing and the spread of infection ( figure ). when infection is ahead, detection is compromised (moving up into the darker shades in figure) , responses lag further, and exponential infection growth can overwhelm hospital capacity. high early test capacity and its rapid expansion (moving to the right in the figure), brings the epidemic to light, activates policy responses, and allow for control. (panels a and b) shows one alternative testing scenario and counter-factual trajectories of pandemic to date. in this scenario, all countries shift their testing rates from baseline to . % of population per day (a rate currently achieved by multiple countries, e.g. usa, australia, in figure ). the shift happens on march , (the date covid- was officially designated as a pandemic). such enhanced testing would have reduced total cases from . millions to . (ci: . - . ) millions. corresponding reduction in deaths would have been from k to k(ci: k- k). by making additional assumptions on future testing and responses, the model can inform future trajectories. we explore a few projections out to spring that exclude vaccine and treatment availability. figure (panels c and d) shows projections under three scenarios: i) using the current country-specific testing rates and response functions moving forward; ii) if enhanced testing (of . % per day) is adopted on july st p; and iii) if sensitivity of contact rate to perceived risk is set to (approx. th percentile of estimated value across countries), leaving testing at current levels. contrary to the impacts of early differences in testing ( figure -a) , the reductions in future cases from additional testing (ii) are rather modest (from . in i to . billions in ii), because recognition of epidemic is no longer the bottleneck to response. both these scenarios project a very large burden of new cases in the fall , with hundreds of millions of cases concentrated in a few countries estimated a b c d . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint to have insufficient responses given perceived risks (primarily india, but also bangladesh, pakistan, and usa). in contrast, changes in response policies would make a major difference. scenario iii brings down future cases sharply, to as low as (ci: - ) millions (cumulatively) by the end of winter. across scenarios, we find that the infection rate in each country usually peaks and then stabilizes at a lower and slowly declining linear rate, in some cases after damped oscillations (i.e. second waves). these (approximately) steady-state infection rates are at levels that motivate just enough policy and behavioral response to bring effective reproduction number re to . faster rates lead to exponential growth, raise alarms and bring down contacts; slower ones lead to relaxation of policies bringing the reproduction number back up to . those post-peak infection rates vary widely across countries and depend on risk perception parameters, time constants, and contact sensitivity to risk, as well as weather and susceptible population size. in this scenario we shift both testing and contact sensitivity to perceived risks to arguably more realistic values between current ones and those in scenarios ii and iii in figure -c. specifically, on july st we shift test rates to a value % between the current rates and . % per day (which increases testing in most countries and reduces it in a few). similarly, sensitivity of contacts to perceived risk is shifted to % of the way between estimated country-level values and a high value of . resulting infection and death rates at the end of this period reflect the post-peak burden of the disease discussed above and are estimated at . % (ci: . - . ) and . e- % (ci: . e . appendix s provides projections for all countries. note that projections are highly sensitive to assumed testing, behavioral, and policy responses in the scenario. as such they should be interpreted as indicators of potential risk and not precise predictions of future cases; more rigorous testing and reductions in contacts in response to risk perception will significantly reduce future cases while laxer response and normalization of risks can lead to overwhelming breakouts. to enable empirical estimation and considering limits to data availability at a global scale, the model includes important simplifications and uncertainties that should temper the interpretation of the results. first, by analyzing an aggregate, country-level model, we abstract away much heterogeneity, from social networks to super-spreaders and local events. moreover, we offer no explanation for the underlying heterogeneity in reproduction numbers across countries. second, lacking hospitalization data across the world, the model's hospital sector includes additional uncertainty. similarly, our estimated behavioral and policy response functions do not tease apart the impact of various determinants such as national and local policies, business and event closures, use of personal protective equipment, reductions in physical interactions, and a host of other contributors. thus, results are not informative about the effectiveness of specific policies, and extrapolation of response function in future scenarios includes unknown uncertainties. for example, if normalization of risk reduced response magnitude in the second wave, our projections would miss that and prove optimistic. finally, absent explicit travel network our results would under-estimate the risk of the reintroduction of the disease in locations that have contained the epidemic. this paper provides a systemic view of the covid- pandemic globally. by incorporating testing capacity and prioritization, hospitalization, and risk perception and responses into an epidemiological model, we are able to closely match widely varying country-specific trajectories of the epidemic. our model explains the observed heterogeneities primarily through three pathways. first, estimates point to much variance in initial reproduction numbers across countries. this heterogeneity is not surprising given that reproduction number is very much a function of human behaviors and interaction is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . environments. nevertheless, our study was not designed to tease out the sources of that heterogeneity, an important task that requires other types of data and analysis. second, the course of the epidemic is also significantly impacted by risk perception and behavioral and policy responses that vary notably across different countries. finally, we show that differences in testing rates play an important role in shaping those trajectories. despite those variations, we also find much that is consistent across the globe: a) we estimate that just over half of the infections are asymptomatic, consistent with detailed estimates from smaller samples ( , , ) . b) we estimate that asymptomatic individuals are about a third as infective as symptomatic patients. c) in our model, hospitalization brings down fatality substantially, highlighting the crucial importance of keeping cases below hospital capacity. d) we find an average global infection fatality rate close to . %. this is consistent with growing evidence on ifr ( , ) . our estimates for ifr change predictably with age, and require few other predictors and no country-specific factors to stay consistent with the data. e) an order of magnitude under-reporting of cases is the norm across most countries, with a few percent of population already infected across many nations; nevertheless, herd immunity remains distant. f) finally, absent notable improvements in country level responses or breakthroughs in vaccination or treatment, the outlook for the epidemic remains grim, with most nations settling into a steady state of cases and deaths that, while below their peaks, are troublingly large. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . the model simulates the evolution of covid- epidemic, risk perception and response, testing, hospitalization, and fatality at the level of a country. here we explain key equations and structures in each sector, followed by complete listing of model equations and parameters in s . the model is a derivative of the well-known seir (susceptible, exposed, infectious, recovered) framework for simulating infection dynamics. figure s provides an overview of key population groups and the population movements among them . . we assume demand for testing and hospitalization are driven by symptoms, so all asymptomatic patients will be in the latter category. in the equations below we use short-hands to simplify mathematical notations. the full model documentation uses full variable names. table s provides the mapping between the short-hands and the full names, as well as the sources and equations for those variables and parameters discussed below. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint from these infectious categories, resolution flows (r…) take individuals to either recovered (r…) or dead (d…) states, with corresponding subscripts u, c, ch, and uh for stocks and uu, uhch etc. for flows. given the differences in severity and potential survival extension due to hospitalization, we distinguish between resolution delay for those in hospital (hospitalized resolution time; τh) and those not hospitalized (post-detection phase resolution time; τr). we use first order exponential delays for all lags, though sensitivity analyses showed very little impact of using higher order delays. the infection rate (rsp) controls the flow from s to p and depends on infectious contacts (ci), fraction of total population (n) that is susceptible, and weather effect on transmission (w). the latter is a function of rw, the country-level projections for impact of weather on covid- transmission risk year-round developed by xu and colleagues ( ) and a parameter, sensitivity to weather (sw), to be estimated: infectious contacts depend on the reference force of infection (β), various infectious sub-populations (and their relative transmission rates; ma for asymptomatic and mt for confirmed), and contacts relative to normal (fc), which captures behavioral and policy responses as a fractional multiplier to baseline infectious contacts: in this equation we separate various stocks (of i and p) into asymptomatic (a superscript) and symptomatic (s superscript). that distinction is treated analytically using a zero-inflated poisson distribution that is discussed in the next section. in light of evidence on the short serial interval for covid- , likely below the incubation period ( , ), we do not distinguish the infectivity of pre-symptomatic individuals from those post onset. contagion dynamics start from patient zero arrival time, t , another estimated parameter. the key mechanisms regulating the population flows among these stocks are discussed below, and a schematic of important relationships is provided in figure s . five parameters are estimated in the equations discussed above. one of them (sw) is global (i.e. assumed identical across countries; see the estimation section below for details on the distinction between global and country-specific parameters) and the remaining four are country-specific: β, mt, ma, and t . . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . covid- infection varies in acuity, from asymptomatic to life-threatening. acuity of disease affects notonly baseline fatality risk, but also testing and hospitalization decisions which impact official records of infection and fatality rates. since movement between population groups via testing or hospitalization is itself a function of acuity, to allow for consistent inference of mean acuity across different population groups, we use an analytical framework to track acuity levels. this framework, which we adapted from prior research ( ) , obviates the need to disaggregate the population by different acuity levels (which would prohibitively raise the computational costs for estimation). specifically, we represent acuity using a zero-inflated poisson distribution. this distribution combines two subpopulations -one with poisson-distributed acuity levels with mean covid acuity (αc), and another additional asymptomatic fraction with zero acuity, which is the zero-inflated component. the sum of those with zero acuity from the poisson part of the population and the second group is the total asymptomatic fraction (a). we assume this asymptomatic group is not given priority in testing or hospitalization, and is not at risk of death. thus they will always follow the → → → → pathway. the pathways for the remaining population depend on acuity and its impacts on testing, hospitalization, and death. note that the concept of acuity defined here only needs to have a monotonic relationship with tangible symptoms and risk factors and it does not have a one-to-one relationship with any real world measure of acuity, and as such is better seen as a mathematical construct that informs modeling rather than a real-world variable with clinical definition. from this framework two parameters, a and αc, are estimated as country specific parameters with limited variability across countries. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint the testing sector reads the active test rate (tt) for each country as exogenous input data (see appendix s for pre-processing details for this data). a fraction of this total test rate, typically small, is allocated to postmortem testing of covid- victims who have not been previously confirmed (post mortem tests total, tpm). specifically, of the deaths of unconfirmed infectious individuals (whether hospitalized or not), a certain fraction of fatalities screened post mortem (npm) will be identified true post-mortem tests. we anchor the npm to fraction covid death in hospitals previously tested (ndch). the rationale for this anchoring is that on the margin if there are many unidentified covid patients in hospitals, the chances are that the system lacks enough testing capacity and thus post-mortem testing should also be less thorough: we experimented other functional forms with a free parameter connecting the two constructs, but following our conservative estimation principle decided against including that free parameter in the final model. we feared that absent clear observables to identify this additional parameter (e.g. on country-specific policies regulating post-mortem testing) the degree of freedom would improve the fit but potentially for the wrong reason. the where the multiplier recent infections to test (mit), captures the sensitivity of negative test demand to recent infection reports. to allocate the available tests (tnet) between these two sources of demand, we use an analytical logic that allocates testing based on acuity of symptoms. the basic idea is that through self selection and screening by testing centers, people who have more symptoms or other signals that correlate with covid infection (e.g. high exposure risk) are more likely to be tested. we assume each unit of acuity increases the likelihood that an individual gets tested, based on a variable prob missing symptom, pms. this variable represents the probability that each acuity unit fails to convince the testing decision process to test a given individual, i.e. how selectively and sparingly tests are conducted. specifically, in this model an individual with k acuity units is tested with probability: we assume the negative test demand is coming from a population with a poisson-distributed, unit average acuity level (αn= ) for symptoms of non-covid influenza-like illnesses. the test demand from covid . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint patients also comes from a poisson distribution of acuity, but with mean αc. with the poisson distribution and given a level of α and pms, one can calculate the fraction of each demand source that would be tested: we therefore need to find the pms that allows test supply to match demand that is satisfied, specifically, by solving the following equation for pms*: having solved for p*ms (numerically), we analytically calculate the average acuity level for those positively tested (αcp: average acuity of positively tested ) and those either not tested or having received a false negative result (αcn). specifically, if test sensitivity was %, the average acuity for those not tested would be: the acuity level for those tested could then be found based on the conservation of total acuity across those positively tested and those not. starting with this basic specification we further account for the sensitivity of covid test (st) to calculate the values of αcp and αcn. we parametrize sensitivity at %, which is the estimated sensitivity for the pcr-based tests used as the primary diagnosis method of current infections of covid- ( , ) . overall, the testing rates that are determined by solving for * , combined with sensitivity of tests, inform the fraction of covid positive individuals transitioning from pre-detection (ip) to confirmed vs. unconfirmed states (ic or ich vs. iu or iuh), while the calculated α values inform the likelihood of hospitalization and fatality rates, as discussed next. the testing sector includes the following two country level parameters that are estimated: nst, mit. the hospitalization sector of the model starts with each country's nominal hospital capacity (hn) in total hospital beds. in practice, geographic variation in hospital density and demand creates imperfect matching of available beds with cases of covid- at any point in time, e.g. because some potential capacity is physically distant from current covid hotspots. this imperfect matching means some of the nominal hospital capacity is effectively unavailable at any time, especially in larger, less densely populated countries. we therefore calculate effective hospital capacity (he) by considering geographic density of hospital beds (bed per square kilometer; dh): where the * represents a large reference hospital density of . beds per km (which is the value of for south korea). the parameter sdh (impact of population density on hospital availability) is estimated. effective capacity is allocated between potential hospital demand (hcd) from covid- cases and the regular demand for hospital beds from all other conditions (which we assume equals pre-pandemic effective hospital capacity). we assume that covid- patients will have higher priority for hospitalization compared to regular demand. specifically, we assume that fraction of regular demand allocated (mhr) would be the . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint square of that for covid demand (mhc), = , and solve the resulting hospital capacity allocation problem analytically: we determine the covid demand for hospitalization based on a screening process similar to that for testing. two types of covid patients may seek hospitalization: those with confirmed test results and those without. the former are more likely to seek hospital treatment. we first calculate a parameter analogous to pms in the testing sector that informs the demand from confirmed covid patients for hospitalization. this parameter, the pmas confirmed for hospital demand (pmhc) is determined based on acuity level of confirmed (αct) and reference covid hospitalization fraction confirmed (rh), an estimated parameter capturing the overall need for hospitalization among covid patients: for unconfirmed covid patients we scale the analogue of this parameter (pmhu) based on how much priority non-covid patients generally receive: this formulation ensures that: ) confirmed covid patients are more likely to be hospitalized, but also that ) if there is ample hospital capacity (mhr~ ), then confirmed and unconfirmed covid patients will receive similar priority for the same level of acuity. in short, the pm. values determine hospital demand by confirmed and unconfirmed covid patients, which add up to hcd. the latter determines the fraction of hospital demand that is met. analogous to the testing sector, this fraction along with demand determines the flow of individuals from the pre-detection (ip) state to hospitalized vs. non-hospitalized states (ich or iuh vs. ic or iu). matching demand to allocated capacity also allows us to calculate the realized probability of missing acuity signal at hospitals (p*m) for confirmed and unconfirmed patients. as in the testing sector, those probabilities let us approximate for the expected acuity levels for covid patients in and out of hospital, as well as tested vs. not-tested, i.e. αct, αch, αu, and αuh. these average acuity levels in turn inform fatality rates for each group. the hospital sector includes two country level estimated parameter with limited variation across countries: sdh and rh. for patients in each of the u, c, ch, and uh groups we specify the infection fatality rate (f), as: the parameter base fatality rate for unit acuity (fb) sets the baseline for fatality rate. sensitivity of fatality rate to acuity (sf) determines how fatality changes with estimated acuity levels; more severe cases are expected to have higher fatality rates. hospitalization reduces fatality rates, expressed as the relative impact of treatment on fatality rate (shf). the function incorporates the impact of age distribution on fatality rates. for age effect, we calculate a risk factor for each country based on its age distribution and the relative fatality risks for covid patients in different ages documented in prior work ( ) . we normalize this factor . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint against its value for china where the original study was conducted. given the well-established impact of age on fatality, this factor is directly multiplied into the infection fatality equations. overall, the fatality sector includes three parameters that are estimated at the country level, with limited variance across countries, those are: , , and . note on comorbidities and fatality: we also explored including three comorbidities but found the estimates unreliable and therefore they are not included in the main specification of the model. those comorbidities include obesity, chronic disease, and liver disease. the effects we explored for each were: (.) = (.) (.) , where we used the following country-level indicators from the world health organization ( ), normalized by the average across all countries (d(.)): for obesity: prevalence of obesity among adults, bmi ≥ (age-standardized estimate) (%) for chronic health issues: probability (%) of dying between age and exact age from any of cardiovascular disease, cancer, diabetes, or chronic respiratory disease for liver disease: liver cirrhosis, age-standardized death rates ( +), per , population in equation we noted that contacts relative to normal (fc) regulates infection rates. this factor ranges between a minimum (min contact fraction; cmin) and as a function of the relative utility from normal activities (un) compared to utility from limited activities (ul) in light of additional risks associated with normal activity patterns: the utilities from normal and limited activities are specified as . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint overall, the risk perception and response sector includes the following five country-specific parameters that are estimated: cmin, τru, τrd, λ, and wr. table s summarizes the main equations discussed in appendix s , providing the mapping between full variable names and the short forms. it also includes all estimated model parameters, as well as those specified based on prior research. table s -mapping between full variable names and their short form for the subset of variables and parameters discussed in s . also included are equations explained above and sources for other variables. is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint the model we estimate is nonlinear and complex, and any estimation framework is unlikely to have clean analytical solutions or provable bounds on errors and biases. therefore, in designing our estimation procedure, we set out to be conservative. specifically: we use a likelihood function that accommodates overdispersion and autocorrelation (negative binomial); we utilize a hierarchical bayesian framework to couple parameter estimates across different countries which reduces the risk of over-fitting the data; and we use the conceptual definitions of parameters and their expected similarity across countries to inform the magnitude of that coupling across countries. compared to more common choices in similar estimation settings, these choices tend to widen the credible regions for our estimates and reduce the quality of the fit between model and data. in return, we think the results may be more reliable for projection, more informative about the underlying processes, and better reflective of uncertainties in such complex estimation settings. the model is a deterministic system of ordinary differential equations with a set of known and unknown parameters. the known parameters are those specified based on the existing literature and do not play an active role in estimation. the unknown parameters can be categorized into those that vary across different countries and those that are the same across all countries (i.e. general parameters). the estimation method is designed to identify both the most likely value and the credible regions for the unknown parameters, given the data on reported cases and deaths (and for a subset of countries, the excess deaths). this is done through a combination of estimating the most likely parameter values in a likelihood based framework, and using markov chain monte carlo simulations to quantify the uncertainties in parameters and projections. we first introduce the different components of the likelihood function we use: the fit to time series data, the random effects component coupling country-level parameters, and the penalty for excess mortality. then we explain the implementation details. define model calculations for expected reported cases and deaths for country i as μij(t) (with index j specifying cases and deaths) and the observed data for those variables as yij(t); the country-level vector of unknown parameters as and the general unknown parameters as ϕ. note that vector includes several parameters, each specifying an unknown model parameter, such as impact of treatment on fatality, or total asymptomatic fraction, for country i. the model can be summarized as a function f that produces predictions for expected cases and deaths for each country given the general and country-specific parameters: we use a negative binomial distribution to specify the likelihood of observing the y values given θ and ϕ. specifically, the logarithm of likelihood for observing the data series y given model predictions μ(θ ,ϕ) is: where (dropping time index for clarity): . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . summing the lt function over time provides the full (log) likelihood for the observed data given a parameterization of the model. the negative binomial likelihood function includes two parameters, μ and ε which determine the mean and the scaling/shape of the observed outcomes. the second parameter, ε, provides the flexibility needed fit outcomes with fat tails and auto-correlation. this parameter could itself be subject to search in the optimization process. specifically, we assume that: thus we create a (set of) country specific parameter(s) ( ) and two general parameters ( ) which should be estimated along with the conceptual model parameters. the country level scale ( ) implicitly assesses the reliability and inherent variability in country level reports, and the general ones inform the variability in case data vs. deaths. we augment the vectors ϕ and θ to include these scaling parameters as well. up to this point we have not included any relationship among country specific parameters, . this independence assumption would allow parameters representing the same underlying concept to vary widely across different countries. such treatment, by providing more flexibility, enhances the model's fit to historical data. however, it ignores the conceptual link that exists for a given parameter across countries, potentially allowing the model to fit the data for the wrong reasons (i.e. using parameter values that do not correspond to meaningful real world concepts). the result would likely be less reliable and also not robust for future projections. we therefore define a hierarchical bayesian framework to account for the potential dependencies among model parameters. specifically, we assume the same conceptual parameters (e.g. impact of treatment on fatality), across different countries, are coming from an underlying normal distribution with an unknown mean (to be estimated) and a pre-specified standard deviation. this assumption is similar to the use of "random effect" models common in regression frameworks, though we deviate from canonical random effect models by pre-specifying the standard deviation. in fact it is possible to estimate the standard deviation across countries as well (and to obtain better fits to data), but adding those degrees of freedom ignores qualitatively relevant insights about the level of coupling across different countries for each parameter, and thus results may fit the data better but for the wrong reasons. for example, some parameters, such as patient zero arrival time, could be very different across countries, whereas parameters reflecting innate properties of the sars-cov- virus itself (e.g. total asymptomatic fraction (a)) or those determining fatality (e.g. base fatality rate for unit acuity (fb)) should be very similar across different countries. allowing the model to determine the variance for the latter will lead to better fits: the model can find baseline fatality rates that easily match fatality variations across countries, and would expand the corresponding variance parameter accordingly. however, as a result the estimation algorithm will have too easy a job: it will not require a precise balancing between hospitalization, impact of acuity on fatality, and post-mortem testing decisions to fit fatality data. thus, the estimates may well be less informative, or further from true underlying processes and the general characteristics of the disease which we care about. the implementation of this random effect introduces another element to the overall likelihood function: here θik represents the k th parameter for country i, and ̅ is the (estimated) average across countries for the k th parameter. σk is the pre-specified allowable variability for the k th parameter across different countries. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint specifying these standard deviations adds a subjective element to the estimation process. however, we note that subjective elements are ultimately indispensable in any modeling activity: from specifying the model boundary to the level of aggregation, use of various functional forms, and choice of likelihood functions, these choices are built on subjective assessments that experts bring to a modeling project. absent our conceptually informed variability factors, we would need to make the assumption that country-level parameters are independent, or that our complex estimation process would correctly identify the true dependencies among those parameters. we think both those alternatives are inferior in the chosen method. so here we focus on transparently documenting and explaining those assumptions. table s summarizes the estimated model parameters, their estimated values (mean across countries and mean of inter-quartile range) and the assumed variability factor (σk) for each. sw sensitivity to weather . (global parameter so the other metrics do not apply) *given the wide range and potential long tail for these parameters the log transformation is used in specifying the dispersion penalty (equation ) and variability factors are reported as σ , where σ is used in equation . ** these parameters are expected to be less variable across countries and thus are assigned small variability allowances compared to their mean. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint finally, we include a likelihood-based penalty term to allow model predictions be informed by excess mortality data collected by various news agencies and researchers for a subset of countries in our sample. these data provide snapshots of excess mortality (compared to a historical baseline) for a window of time in each country. subtracting from total excess mortality the covid- deaths officially recorded in that window offers a data point for excess mortality not accounted for in official data (ei). we can calculate in the model the counter-part for this construct: the simulated mortality that is not included in the simulated reported covid- deaths ( ̅ ). there is uncertainty in these excess mortality data: the historical baselines used by various sources do not adjust for demographic change, excess mortality may be due to factors other than covid- , and some of it may be due to changes in healthcare availability and utilization motivated by covid- but not directly attributable to the disease (for example when surgeries are delayed, hospitalization is avoided, or heart conditions are ignored). excess mortality may also be reduced due to reduced traffic accidents (in light of physical distancing policies) and pollution related deaths. given these uncertainties, we use the following penalty function to keep the simulated unaccounted excess mortality close to data: this penalty could be seen as a likelihood coming from the probability distribution ( ) = should be attributed to covid- deaths, but that there is significant uncertainty around this, so some % variation across this figure is quite plausible ( %- % of data). however, numbers outside of this range start to impose increasingly large penalties, so that very large deviation becomes unlikely. combining these three components, we obtain the full likelihood function used in the analysis: for each country we include the lt component from the first day they have reached . % of their cumulative cases to-date, or a minimum of cumulative cases. this excludes very early rates that are both unreliable and which, given very small estimated model predictions for infection, could lead to unreasonably large likelihood contributions. the model includes a large number of parameters to be estimated: a general parameter for the impact of weather, general parameters for , and parameters for each country that are coupled together based on the random effects framework described above. out of those parameter is for and the rest are informing various features of disease transmission, testing, hospitalization, and risk perception and response. with a sample of countries, this would lead to about parameters to be estimated. a direct optimization approach to this problem suffers from potential risk of getting stuck in local optima, and direct use of mcmc methods to find the promising region of parameter space suffers from the curse of dimensionality. we therefore designed the following -step procedure to find more reliable solutions to both problems. ) we estimate the model with the full parameter vector for a smaller number of countries with larger outbreaks ( - countries). we use the powell direction search method implemented in vensim™ simulation software for this step. the method is a local search approach though it has features that allows it to escape local optima in some cases. we restart the optimization from various random points in the feasible parameter space and track the convergence of those restarts to unique local peaks. we stop this process when we are repeatedly landing on the same local peaks in the parameter . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint space. this procedure showed that local peaks do exist, but they are not many; for example within restarts we may find - distinct peaks. this provides a coherent set of starting points for ϕ and ̅ for next steps. ) we go through iterations of the following two steps: a) conduct country-specific optimizations with restarts to find the vector of θi given the ϕ and ̅ from first optimization or from the step b. b) conduct a global optimization, including all countries but fixing θi and optimizing on ϕ (and ̅ ; though that is simply the mean across country level parameters from previous round). we stop when iterations offer little improvement from one round to the next (less than . % improvement in loglikelihood). ) we conduct a full optimization allowing all parameters (θi, ϕ and ̅ ) to change, starting from the point found in the last iteration of step . this step finds the exact peak on the likelihood landscape which is the best-fitting parameter set for the model. ) for the mcmc, theoretically one should conduct the sampling from all model parameters in the full model. however, our experiments showed that the large dimensionality of the parameter space requires an infeasible number of samples to achieve adequate mixing and ensure reliable credible regions for parameters and projections. to overcome this challenge we note that the parameters of different countries are connected to each other only through ϕ and ̅ , and these general parameters are rather insensitive to dynamics in each country. the insensitivity is due to the fact that a single country only contributes about % to the general parameters' values, and within a typical mcmc the country-level parameters often can't change more than % before the resulting samples become highly unlikely. therefore, one can conduct an approximate country-level mcmc by fixing the general parameters at those from step , and only sampling from the θi for each country. the mcmc algorithm used is one designed for exploring high dimensional parameter spaces using differential evolution and self-adaptive randomized subspace sampling ( ) . using this method we obtain good mixing and stable outcomes (robin-brooks-gelman psfr convergence statistic remaining under . ) after about , samples (the burn-in period). we continue the mcmc for each country for million samples and then randomly take a subsample of those points after the burn-in period for the next step. ) the resulting subsamples for different countries from step are assembled together to create a final sample of parameters for the full model to conduct projections and sensitivity analysis at the global scale. uncertainties in the handful of global parameters is not identified in this procedure, but can be quantified by assessing the sensitivity of the global likelihood surface to changes in those parameters. the process above is automated using a python script that controls the simulation software (vensim). we conduct the analysis using a parallel computing feature of vensim on a windows server with cores. after compiling the simulation model into c++ code (which speeds up calculations significantly), and using a simulation time step of . days, it takes about hours to complete the estimation for countries. full analysis code is available online at https://github.com/tseyanglim/covidglobal. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint s -data pre-processing getting contemporaneous, comprehensive, national-level data on covid- is a challenge. the most widely-cited data aggregators, such as the johns hopkins center for systems science and engineering's covid- database ( ) , ourworldindata portal ( ), and the us-focused covid tracking project ( ), get their data from the same few official sources, such as the us centers for disease control and prevention (cdc), the european cdc (ecdc), and the world health organization (who). these official agencies in turn get their data from national and subnational public health authorities, which ultimately rely on reports from hospitals, clinics, and private and public health labs. as a result, idiosyncrasies in the ground-level data collection processes permeate virtually all sources of aggregate data. most notably, data collection involves time lags, which can differ from source to source. daily death counts could reflect the date of actual death or the date a death is registered or reported; different uk government sources, for instance, use each of these metrics. daily infection or case counts could include the total new cases reported on a given date, or the total cases confirmed from that date; the latter would result in some 'backfill' whereby case counts for previous days can continue to increase for some time as delayed confirmations come in. daily counts of tests conducted could report samples collected, samples processed, results reported, or a mix of these; the us cdc, for instance, reports a mix of testing by date of sample collection and date of sample delivery to the cdc. aside from differences in unit of measure (people vs. tests vs. samples), there may be different time lags involved as well. in addition to these idiosyncrasies, testing data in particular is also patchy for many countries, even as testing has become more widespread. the who does not report country-by-country testing, nor does the jhu covid map outside the us. furthermore, there are sometimes irregular delays in the reporting of test results, which can create occasional unexpected spikes in reported numbers of tests, infections, or both. depending on the specifics of how daily infection and test counts are reported, there can in some cases be a disjunction between the two. because confirmed case counts largely depend on positive test results, test and infection counts should be correlated -ceteris paribus, a day with a lot of samples collected for testing should see more confirmed cases attributed to it, while a day with no sample collection should see no cases. but since cases may not be reported by the date of the test, and tests may not be reported by the date of sample collection, officially reported numbers can get out of sync in either direction. this problem is most salient when there are clear weekly cycles in daily rates. in most of the world, particularly western countries, daily test rates are far lower on weekends than during the week. as a result, infection numbers show a clear weekly cyclical component as well. but the weekly cycles in testing and infection numbers for a given country do not always line up. our model explicitly accounts for the effect of testing on reported infections, but we do not explicitly model the country-level idiosyncrasies of reporting and how they vary between test data and infections. instead we account for any such lags in pre-processing of the data to align testing and case data. the weekly cycle occurs in many countries' death rate data as well, where it presents a different problem. a weekly cycle in testing is a behaviourally realistic part of the data-generation process, as many labs, clinics, or other testing sites for instance may be closed on weekends. as testing provides the window on the state of confirmed infections, a comparable cycle in confirmed cases is to be expected as well. by linking case confirmations to testing, our model explicitly accounts for this limited visibility on the true state of the epidemic. however, a weekly cycle in death rates almost certainly reflects different limitations of the data- https://blog.ons.gov.uk/ / / /counting-deaths-involving-the-coronavirus-covid- / https://www.cdc.gov/coronavirus/ -ncov/cases-updates/previous-testing-in-us.html see e.g. https://www.wcvb.com/article/massachusetts-coronavirus-reporting-delay-due-to-quest-lab-itglitch/ # . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint generation process, typically to do with hospital staffing, which we do not explicitly model. as such we need to address any weekly cycle in death rates through data pre-processing as well. to deal with these challenges, we developed a multi-step algorithm to pre-process our data before feeding it into the model for calibration. the algorithm is described below. it was implemented in python, largely using the pandas and numpy packages, and the code is available in full at: https://github.com/tseyanglim/covidglobal. the algorithm proceeds country-by-country, following these steps on each country. ) examine daily cumulative test data; if data are insufficient ( or fewer data points), drop country from the dataset. ) interpolate any missing daily cumulative test data points using a piecewise cubic hermite interpolating polynomial (pchip) spline. if the first reported infection is before the first reported cumulative test, also extrapolate cumulative tests back to the date of first reported infection. a. extrapolation to the date of first reported infection is necessary since both in the model and, to a large extent, in reality, reported infections require testing for confirmation. b. pchip spline interpolation yields a continuous monotonic function with a continuous first derivative, thus avoiding generating any anomalous rapid change in daily test rate. c. we used the implementation of pchip interpolation from the widely used scipy package for python. ) calculate daily test rate as daily cumulative tests less the preceding day's cumulative test total: ) examine the original daily cumulative test data to estimate how much of the calculated daily test rate is based on interpolated vs. original data. a. daily test rates calculated based on mostly original data should be expected to include any weekly cycles or occasional irregularities that would also be reflected in daily infection counts. conversely, daily test rates calculated from cumulative test counts that are largely interpolated would not be expected to fully reproduce any such cycles or irregularities, since the interpolation produces a relatively smooth function. b. as a rule of thumb, we examine the cumulative test data for the second half of the time from the first test to the latest test. if fewer than half the days in that window have original cumulative test data, we consider the test data to be 'sparse', requiring further processing. it may be argued that there are weekly cycles in large-scale human behaviour that may drive some true weekly cyclicality in the true rates of infection and death, and as such it may be wrong to consider such cycles to be artefacts of the datageneration process. however, we find this unlikely for a few reasons. first, weekly cycles in human interactions, largely driven by the work and school week and weekend, will have been significantly attenuated by widespread adoption of social distancing measures around the world. second and more importantly, variation in incubation period and time before development of symptoms means that any true cyclicality in the timing of initial infection will be further attenuated in the timing of symptom development. by the same logic, wide variability in the delay from symptom development to death means there should be minimal cyclicality, if any, in the timing of deaths, meaning any such cycles visible in the data are due to measurement and reporting lags. https://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.pchipinterpolator.html . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint ) if the test data are not sparse, account for any potential lag or other reporting delay differences between daily test rate and daily infection rate using a time-shift algorithm to estimate any such lags or delays from the data and shift the test rate time series accordingly. the time-shift algorithm ensures that any weekly cycles present in the daily infection rate data are reflected in the daily test rate data and aligned as best as possible on date, thereby accounting for the fact that model-generated reported infections depends on testing but with no time lag between test and result. a. first, identify the weekly component of the time series of daily infection rate and daily test rate using a seasonal-trend decomposition based on loess (stl) procedure. i. stl deconstructs time series data into several components, including a trend and a seasonal component over a specified period (weekly, in this case) as well as a residual. stl is an additive decomposition, and has the advantage of allowing the seasonal component to change over time (rather than being a fixed pattern repeated exactly across the whole time series). ii. we used the stl implementation from the statsmodels package for python. b. shift the time series over a one-week range (from - to + days of lag between test and infection reporting), calculating the cross-correlation between the weekly seasonal component of the daily infection rate data and the daily test rate data for each time shift. c. identify the time shift within this range that maximizes the cross-correlation between the infection rate and test rate data, and shift the test rate data accordingly. ) if the test data are sparse, the spline interpolation will generally cut out some of any weekly cyclicality that may be present. visual inspection of daily test rates for countries with sparse test data also shows large, irregular spikes in reported tests are not uncommon, without necessarily having concomitant irregular spikes in reported daily infection rates. as such, rather than attempting to eliminate differences in reporting lags through the time-shift algorithm described above, we instead apply a data-smoothing algorithm to both daily test rate and daily infection rate, in order to reduce any cyclicality and irregular spikes. this smoothing allows the calibration of the main model to focus on matching the underlying trends in the data. in all cases, whether daily cumulative test data are sparse or not and whether infection and test rate data are smoothed or not, since weekly cycles in death data are reflective of reporting lags not captured in the model, daily death rate data is smoothed using the same algorithm. ) the smoothing algorithm used is designed first to conserve the total number of reported cases (tests, infections, or deaths), and second to preserve some degree of variation in the time series, as some noise may be informative and retaining some is important to the calibration of the model. a. starting from when the time series of daily rate (test or infection) exceeds a specified minimum value ( /day), calculate the rolling mean of the daily rate, using a centred moving window of days. b. calculate the residual between each day's data point and the rolling mean for that day, and divide by the square root of the rolling mean, to get an adjusted deviation value: i. dividing by the square root of the rolling mean reflects a heuristic assumption that each daily rate (of infections, deaths, or tests) behaves as a poisson process (stdev of pois() =  . ). is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint ii. the functional result of this adjustment is that both absolute and relative magnitudes of deviations from the rolling mean are given some weight -large relative deviations when absolute values are small (and data are noisier) are not ignored, but neither do they outweigh larger absolute (but smaller relative) deviations that occur when the mean is large, which is important since most of the time series data are growing significantly over the time horizon of the model. c. calculate thresholds for identifying dips and peaks in the data based on the median of the adjusted deviations, ± one median absolute deviation (mad) of the adjusted deviations: i. using the median absolute deviation to determine thresholds for peaks and dips is robust to outliers in the deviations, which do arise occasionally in the data. ii. a threshold width of one mad is relatively narrow for outlier detection, but by inspection of the data, is about right for identifying most of the peaks and dips caused by weekly cycles in test, infection, and death rates, as well as larger outliers. d. once thresholds are calculated, iterate through the data points in the time series first forward in time from oldest to newest, filling in any 'dips' (data points with adjusted deviations below the lower threshold), then backward in time from newest to oldest, smoothing out any 'peaks' (data points with adjusted deviations above the upper threshold) that remain. repeat the process until all data points' adjusted deviations are within the originally calculated thresholds for the time series. i. we infer that the underlying processes generating dips and peaks are somewhat different. dips are generally the result of weekly cycles in the data, e.g. lower rates of testing or longer lags in death reporting that occur on weekends. peaks arise to some extent due to the same weekly processes, e.g. some deaths that occur on weekends only being recorded at the start of the next week. however, some peaks, especially larger ones, may result from irregular random delays in reporting, such as large batches of tests being held up due to logistical issues and then getting processed all at once. as such the smoothing procedure for dips vs. peaks is slightly different. e. the dip-filling step fills a fraction of each dip (specified as a smoothing factor) by redistributing data counts based on a multinomial draw from the subsequent few days following each dip. i. first, calculate the amount to fill based on the deviation and the smoothing factor specified, in this case . : ii. calculate the amount redistributed from each of the following few ( ) days + , + , … + , = , based on a multinomial distribution as follows: where + , + , … + are calculated as: iii. this formulation allows some redistribution from any of the subsequent few days whose adjusted deviations exceed the focal day's adjusted deviation, but with more redistribution from days with higher adjusted deviations. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint f. the peak-smoothing step similarly redistributes a fraction of each peak, specified by the smoothing factor, to the preceding several days based on another multinomial draw. i. first, calculate the amount to redistribute similarly to the dip-filling step: ii. calculate the amount redistributed to each of the preceding several ( ) iii. this formulation redistributes peaks to preceding days based on the calculated rolling mean counts of those days, on the assumption that the irregular delays that generate random spikes in counts are essentially random and equally likely to affect any given unit of data over a several-day span. as such, the probability that a unit showing up in a spike due to such delays comes from a given preceding day is simply proportional to the expected count for that day, as approximated by the rolling mean. g. by filling dips first before smoothing peaks, the combined algorithm largely addresses any peaks that are due primarily to weekly cycles during the dip-filling stage, such that remaining peaks that get smoothed tend to be the larger, irregular ones. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint table s reports two quality of fit metrics for different countries and different time series. the first four columns report mean absolute error normalized by mean (maen) and the last four report the r-squared measures. errors for cumulative infection and deaths are followed by those for the new cases and deaths (flow variables). . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint figure s shows the visualization of fit between data and simulations for all the countries in our sample. these graphs include data and model outputs for reported new cases (blue; left axis in thousands per day) and deaths (red; right axis in thousands per day) starting from the beginning of the epidemic in each country until june . figure s -comparison of data and simulation. new cases in blue (left axis, in thousands per day) and new deaths (red, right axis). . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint estimates for true cumulative cases (blue; left axis in millions) and deaths (red; right axis in thousands) across different countries up to june are reported in figure s . figure s shows the ratio of estimated excess deaths, i.e. covid- fatalities not reported as such, to reported excess deaths, i.e. deaths over historical baseline not accounted for by reported covid- deaths, for the countries for which such data are available. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint figure s -ratio of estimated excess deaths to reported excess deaths. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint figure s shows the initial reproduction number (re) occurring in each country. reproduction numbers are changing dynamically and transient dynamics may lead to larger than equilibrium numbers if maximum re values were used. we therefore use the th percentile of simulated reproduction number in this graph. also note the large credible intervals for these estimates, partly coming from changes in what is included in the th percentile (sometimes it includes the highest values and sometimes it does not), as well as the inherent uncertainty when both reproduction number and behavioral and policy responses are estimated: one can have smaller initial re and smaller response functions, or larger values for both, and stay consistent with the data. figure s -maximum reproduction number re for each country's outbreak . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint parameter estimates figure s reports most likely estimates for the vector of country-specific parameters (θi). the figure also includes % credible intervals for these parameter estimates. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint figure s -parameter estimates and % credible regions for country-specific parameters. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint figure s reports country-level projections for new cases and deaths based on the following assumptions (consistent with those reported in figure -d in the main paper). we shift both testing and contact sensitivity to perceived risks to arguably more realistic values between current ones that capture some improvements but not a completely different behavior. specifically, on july st we shift test rate to a value % between the current rates and . % per day (which increases testing in most countries and reduces it in a few). similarly, sensitivity of contacts to perceived risk is shifted to % of the way between estimated country-level values and a high value of that is. figure s -country level projections until spring . daily cases (in thousands, blue, left axis) and daily deaths (red, right axis) are graphed. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted june , . . https://doi.org/ . / . . . doi: medrxiv preprint spread of sars-cov- in the icelandic population clinical characteristics and imaging manifestations of the novel coronavirus disease (covid- ): a multi-center study in wenzhou city detection of sars-cov- in different types of clinical specimens sensitivity of chest ct for covid- : comparison to rt-pcr stability issues of rt-pcr testing of sars-cov- for hospitalized patients clinically diagnosed with covid- weather conditions and covid- transmission: estimates and projections. medrxiv clinical characteristics of coronavirus disease in china characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention covid- exacerbating inequalities in the us suppression of covid- outbreak in the municipality of vo estimating the asymptomatic proportion of coronavirus disease (covid- ) cases on board the diamond princess cruise ship universal screening for sars-cov- in women admitted for delivery incubation period and other epidemiological characteristics of novel coronavirus infections with right truncation: a statistical analysis of publicly available case data modeling the rework cycle: capturing multiple defects per task data analysis using regression and multilevel/hierarchical models accelerating markov chain monte carlo simulation by differential evolution with self-adaptive randomized subspace sampling most equations are self-explanatory. the "[…]" notation is used to subscript variables over a set of members. for example, the subscript "rgn" is used to identify different countries. therefore [rgn] indicates that a variable is defined separately for each member of the set "rgn". other subscript ranges used in the equations are: expnt: used for numerically solving the probability of missing symptoms equation. pdim: used for setting policy levels for a few variables. priors: used for implementing the random effects estimation components. each estimated parameter is mapped into an element of this subscript to simplify vector-based calculations tststs: the test status including those confirmed ('tested') and those unconfirmed complete equations and units potential test demand from susceptible population[rgn] , positive candidates interested in testing poisson subset adj active test rate[rgn] = if then else ( time < new testing time , datatestrate[rgn] , external test rate initial( inputave[priorendoave] * ( -sw endoave ) + sw endoave * calcave activities allowed by government additional asymptomatic post detection[rgn] = weighted infected post detection gate[rgn] * additional asymptomatic relative to symptomatic[rgn] / ( + additional asymptomatic relative to symptomatic additional asymptomatic relative to symptomatic[rgn] = zidz ( total asymptomatic fraction net[rgn] -exp ( -covid acuity[rgn] ) , -total asymptomatic fraction net all recovery[rgn] = recovery of confirmed[rgn] + recovery of untested[rgn] + sum ( hospital discharges expected positive poisson covid patients[rgn] + sqrt ( expected positive poisson covid patients[rgn] ^ + * effective hospital capacity[rgn] * effective hospital capacity[rgn] ) ) / ( * effective hospital capacity allocated fration noncovid hospitalized[rgn] = smoothi ( allocated fraction covid hospitalized = min ( maxalp , ialp * alpr = min ( , talp * alpr[rgn] ) units: dmnl ) alpr area of region[rgn] = get vdf constants(constant data file average acuity of positively tested[rgn] * xidz ( ( -probability of missing acuity signal at hospitals[rgn,tested] * fraction poisson not hospitalized[rgn,tested] ^ ) , -fraction poisson not hospitalized average acuity of untested poisson subset[rgn] * ( -probability of missing acuity signal at hospitals[rgn,notest] * fraction poisson not hospitalized[rgn,notest] ^ ) , -fraction poisson not hospitalized average acuity not hospitalized[rgn,notest] = zidz ( average acuity not hospitalized poisson[rgn,notest] * infectious not tested or in hospitals poisson average acuity not hospitalized[rgn,tested] = average acuity not hospitalized poisson average acuity not hospitalized poisson[rgn,tested] = max ( , probability of missing acuity signal at hospitals[rgn,tested] * average acuity of positively tested[rgn] * fraction poisson not hospitalized probability of missing acuity signal at hospitals[rgn,notest] * average acuity of untested poisson subset[rgn] * fraction poisson not hospitalized -prob missing symptom[rgn] * fraction interested not tested[rgn] ^ ) , -fraction interested not tested[rgn] , * prob missing symptom average acuity of untested poisson subset[rgn] = zidz ( poisson subset reaching test gate[rgn] * covid acuity[rgn] -positive tests of infected[rgn] * average acuity of positively tested[rgn] , poisson subset not tested passing gate positive candidates interested in testing poisson subset adj[rgn] -potential test demand from susceptible population[rgn] , positive candidates interested in testing poisson subset adj base fatality rate for unit acuity base fatality rate for unit acuity net[rgn] = initial( base fatality rate for unit acuity baseerror = units: person baseline daily fraction susceptible seeking tests demographic impact on fatality relative to china[rgn] * base fatality rate for unit acuity net baseline risk of transmission by asymptomatic[rgn] = initial( baseline transmission multiplier for untested symptomatic * multiplier transmission risk for asymptomatic net baseline transmission multiplier for untested symptomatic = units: dmnl bed per square kilometer[rgn] = initial( nominal hospital capacity[rgn] / area of region beds per thousand population[rgn] = get vdf constants(constant data file zidz ( lnymix deaths of symptomatic untested[rgn] -post mortem test rate[rgn] * frac post mortem from untreated chronic death rate[rgn] = get vdf constants(constant data file chronic impact on fatality[rgn] = initial cml death frac in hosp[rgn] = xidz ( cumulative deaths at hospital cml death fraction in hospitals large enough = sum ( if then else ( cml death frac in hosp cml known death frac hosp[rgn] = xidz ( cumulative deaths at hospital cmlterrpw = units: dmnl cmltpenaltyscl = units: dmnl constant data file :is: 'covidmodelinputs -constantdata contacts relative to normal[rgn] = min ( voluntary reduction in contacts[rgn] , activities allowed by government reaching testing gate[rgn] -symptomatic infected to testing[rgn] -untested symptomatic infected to hospital excess death start count[rgn] = :na:, , if then else ( time >= excess death start count flu acuity * covid acuity relative to flu net covid acuity relative to flu net[rgn] = initial( covid acuity relative to flu total covid hospitalized[rgn] , infectious not tested or in hospitals poisson[rgn] + infectious confirmed not hospitalized[rgn] + total covid hospitalized cumulative cases[rgn] = integ( new cases[rgn] , ) units: person cumulative confirmed cases[rgn] = infectious confirmed not hospitalized[rgn] + hospitalized infectious[rgn,tested] + cumulative deaths of confirmed confirmed recovered[rgn] + cumulative recovered at hospitals cumulative death fraction cumulative deaths at hospital[rgn,tststs cumulative deaths of confirmed[rgn] = cumulative deaths at hospital[rgn,tested] + cumulative deaths of confirmed untreated cumulative deaths of confirmed untreated[rgn] = integ( deaths of confirmed cumulative deaths untested untreated cumulative fraction total cases hospitalized[rgn] = zidz ( sum ( cumulative deaths at hospital[rgn,tststs!] + cumulative recovered at hospitals[rgn,tststs!] + hospitalized infectious[rgn,tststs!] ) , cumulative cases cumulative missed death[rgn] = integ( count missed death[rgn] , ) units: person cumulative negative tests cumulative recovered at hospitals[rgn,tststs] = integ( hospital discharges cumulative recoveries[rgn] = integ( all recovery cumulative tests conducted cumulative tests data current test rate per capita dalp = . units: dmnl data excess deaths[rgn] = get vdf constants(constant data file , 'dataconstants[rgn]', ) units: person data pseudo case fatality raw: := datacmltinfection raw: := datacmltdeath raw: units: person/day raw: := dataflowinfection raw: := dataflowdeath raw: := datatestrate raw: units: person/day cumulative confirmed cases new testing time ) ) ) units: person/day datalimitfromtime = if then else ( time > max time data used , , ) units: dmnl = units: day/year death rate[rgn] = deaths of confirmed[rgn] + deaths of symptomatic untested[rgn] + sum ( hospitalized infectious deaths tested untreated resolution[rgn] * fatality rate untreated post-detection phase resolution time" * fatality rate untreated delay order = units: dmnl demographic impact on fatality relative to china[rgn] = get vdf constants(constant data file discount rate annual = . units: /year discount rate per day = initial( discount rate annual / days per year ) units: /day dread factor in risk perception dread factor in risk perception net[rgn] = if then else ( response policy time on < time , dread factor policy * response policy weight[dfcp] + ( -response policy weight[dfcp] ) * dread factor in risk perception[rgn] , dread factor in risk perception dread factor policy = units: dmnl effective hospital capacity[rgn] = nominal hospital capacity[rgn] * normalized hospital density[rgn] ^ impact of population density on hospital availability excess death end count[rgn] = get vdf constants(constant data file excess death mean frac = . units: dmnl excess death range frac = . units: dmnl zidz ( cumulative missed death[rgn] -excess death mean frac * data excess deaths[rgn] , excess death range frac * data excess deaths excess death start count[rgn] = get vdf constants(constant data file expected positive poisson covid patients[rgn] = sum ( potential hospital demand[rgn,tststs!] ) * "post-detection phase resolution time" units: person ) expnt external test rate[rgn] = population[rgn] * policy test rate utility from normal activities[rgn] / ( utility from limited activities[rgn] + utility from normal activities units: dmnl baseline fatality multiplier[rgn] * impact of treatment on fatality rate[rgn] * average acuity hospitalized baseline fatality multiplier[rgn] * average acuity not hospitalized poisson[rgn,tststs] ^ sensitivity of fatality rate to acuity net final test rate per capita[rgn] = initial( current test rate per capita[rgn] + weight max in test goal * ( max test rate per capita -current test rate per capita final time = units: day flu acuity relative to covid deaths of symptomatic untested fraction covid death in hospitals previously tested[rgn] = zidz ( hospitalized infectious deaths fraction covid hospitalized positively tested[rgn] = zidz ( hospitalized infectious fraction interested not tested[rgn] = -zidz ( total test on covid patients[rgn] , positive candidates interested in testing poisson subset fraction interseted not correctly tested[rgn] = -( -fraction interested not additional asymptomatic relative to symptomatic[rgn] / ( + additional asymptomatic relative to symptomatic fraction of fatalities screened post mortem[rgn] = indicated fraction post mortem testing[rgn] * switch for government response fraction of population hospitalized for covid[rgn] = total covid hospitalized fraction poisson not hospitalized[rgn,tested] = exp ( -average acuity of positively tested[rgn] * ( -probability of missing acuity signal at hospitals fraction poisson not hospitalized[rgn,notest] = exp ( -average acuity of untested poisson subset[rgn] * ( -probability of missing acuity signal at hospitals fraction seeking test fraction tests positive[rgn] = zidz ( positive tests of fraction tests positive data[rgn] = min ( , zidz ( dataflowinfection[rgn] , active test rate[rgn] ) ) units: dmnl ) fractional value of limited activities = . units: dmnl global cases = sum ( cumulative cases[rgn!] ) units: person global deaths = sum ( cumulative deaths[rgn!] ) units: person global deaths , global cases ) units: dmnl government response start time hazard of symptomatic infection[rgn] = infection rate[rgn] / susceptible[rgn] * ( -total asymptomatic fraction net herd immunity fraction = . units: dmnl hospital admission infectious[rgn,tststs] = hospital admits all hospital admit ratio[rgn,tststs] = xidz ( hospital admits all hospital admits all[rgn,tested] = hospital demand from tested[rgn] * allocated fraction covid hospitalized hospital admits all[rgn,notest] = hospital demand from not tested[rgn] * allocated fraction covid hospitalized poisson subset not tested passing gate[rgn] * ( -exp ( -average acuity of untested poisson subset[rgn] * ( -pmas unconfirmed for hospital demand positive tests of infected[rgn] * ( -exp ( -average acuity of positively tested[rgn] * ( -pmas confirmed for hospital demand = ( -fatality rate treated[rgn,tststs] ) * hospital outflow covid positive hospital outflow covid positive[rgn,tststs] = hospitalized infectious[rgn,tststs] / hospitalized resolution time units cumulative deaths at hospital hospitalized infectious deaths hospitalized infectious deaths[rgn,tststs] = fatality rate treated[rgn,tststs] * hospital outflow covid positive hospitalized resolution time = units: day zidz ( sum ( hospitalized infectious deaths[rgn,tststs!] ) , sum ( hospital outflow covid positive zidz ( sum ( cumulative deaths at hospital[rgn,tststs!] ) , sum ( cumulative deaths at hospital[rgn,tststs!] + cumulative recovered at hospitals units: day flu acuity * ( prob missing symptom indicated fraction post mortem testing[rgn] = fraction covid death in hospitals previously tested[rgn] ^ sensitivity post mortem testing to capacity indicated risk of life loss[rgn] = min ( , switch for government response[rgn] * perceived hazard of infection[rgn] * dread factor in risk perception net[rgn] * pseudocfr / discount rate per day ) units: dmnl symptomatic infected to testing[rgn] -untested symptomatic infected to hospital[rgn] , ) units: person ) transmission multiplier presymptomatic[rgn] + infected pre detection[rgn] * transmission multiplier pre detection[rgn] + ( additional asymptomatic post detection[rgn] + "poisson not-tested asymptomatic transmission multiplier for confirmed[rgn] + sum ( hospitalized infectious[rgn,tststs!] * transmission multiplier for hospitalized[rgn,tststs!] ) ) * reference force of infection infectious not tested or in hospitals poisson constant data file , 'dataconstants[rgn]', ) units: person ) initial time = units known death fraction in hospitals large enough = sum ( if then else ( cml known death frac hosp[rgn!] < minhspdtreshadv , , ) * advcntrs liver disease impact on fatality[rgn] = initial( ( liver disease rate liver disease rate[rgn] = get vdf constants(constant data file , 'dataconstants[rgn]', ) units: dmnl max test rate per capita = . units: /day max time data used = units: day ) maxalp = units: dmnl units: person maxrtresh = units: dmnl constant data file , 'meanchronic', ) units: dmnl constant data file , 'meanliver', ) units: dmnl constant data file , 'meanobesity', ) units: dmnl min contact fraction minadjt = units: day multiplier recent infections to test multiplier transmission risk for asymptomatic multiplier transmission risk for asymptomatic net[rgn] = initial( multiplier transmission risk for asymptomatic + alp negative test results new cases[rgn] = infection rate new testing time = units: day nominal hospital capacity[rgn] = initial( initial population[rgn] * beds per thousand population[rgn] / ) units: person normalized hospital density[rgn] = initial( bed per square kilometer[rgn] / reference hospital density ) units: dmnl not too few susceptibles = sum ( if then else ( suscfrac[rgn!] < minsusctresh , , ) ) units: dmnl sens obesity impact net infection rate[rgn] , incubation period , , delay order ) units: person/day ) onset to detection delay = units overall death fraction[rgn] = zidz ( death rate[rgn] , all recovery[rgn] ) units: dmnl patient zero arrival[rgn] = if then else ( time < patient zero arrival time patient zero arrival time units: person ) payoff = units: dmnl ) pdim : tstp,dfcp,dgtp,scup perceived hazard of infection[rgn] = ( weight on reported probability of infection[rgn] * reported hazard of infection[rgn] + ( -weight on reported probability of infection[rgn] ) * hazard of symptomatic infection indicated risk of life loss[rgn] -perceived risk of life loss[rgn] ) / if then else ( indicated risk of life loss[rgn] > perceived risk of life loss pmas confirmed for hospital demand[rgn] = ( -reference covid hospitalization fraction confirmed[rgn] ) ^ ( / average acuity of positively tested pmas confirmed for hospital demand[rgn] + ( -pmas confirmed for hospital demand[rgn] ) * untested pmas gap with tested infectious not tested or in hospitals poisson[rgn] * exp ( -average acuity not hospitalized poisson poisson subset not tested passing gate[rgn] = poisson subset reaching test gate[rgn] -positive tests of infected poisson subset reaching test gate[rgn] = reaching testing gate[rgn] / ( + additional asymptomatic relative to symptomatic policy test rate[rgn] = if then else ( time < new testing time , current test rate per capita[rgn] , final test rate per capita infected unconfirmed post-detection"[rgn] + susceptible[rgn] + recovered unconfirmed[rgn] + confirmed recovered[rgn] + infectious confirmed not hospitalized[rgn] + "pre-symptomatic infected positive candidates interested in testing poisson subset[rgn] = poisson subset reaching test gate[rgn] * fraction seeking test positive candidates interested in testing poisson subset adj[rgn] = max ( . * potential test demand from susceptible population[rgn] , positive candidates interested in testing poisson subset positive testing of infected untreated[rgn] = positive tests of infected[rgn] * fraction poisson not hospitalized positive tests of infected[rgn] = positive candidates interested in testing poisson subset[rgn] * ( -fraction interseted not correctly tested post mortem test rate[rgn] = post mortem tests total[rgn] * sensitivity of covid test units post mortem test untreated[rgn] = post mortem test rate[rgn] * frac post mortem from untreated deaths of symptomatic untested[rgn] + hospitalized infectious deaths[rgn,notest] ) * fraction of fatalities screened post mortem post mortem tests total[rgn] = min ( post mortem testing need[rgn] , active test rate[rgn] ) units: person/day hospitalized infectious[rgn,notest] / minadjt , post mortem test rate[rgn] * ( -frac post mortem from potential hospital demand[rgn,notest] = hospital demand from not tested potential hospital demand[rgn,tested] = hospital demand from recovered unconfirmed[rgn] + cumulative recovered at hospitals[rgn,notest] ) * ( baseline daily fraction susceptible seeking tests[rgn] * fraction seeking test[rgn] + multiplier recent infections to test infection rate[rgn] + patient zero arrival[rgn] -onset of symptoms[rgn] , ) units: person ) priorendoave : upadj mtrasym ) priors : upadj prob missing symptom probability of missing acuity signal at hospitals[rgn,tested] = zidz ( ln average acuity of untested poisson subset[rgn] ) + units: dmnl ) pseudocfr units: dmnl effective reproduction rate[rgn] = zidz ( infection rate[rgn] , total weighted infected population reaching testing gate realistic r = sum ( if then else ( r effective reproduction rate recovery of untested[rgn] , ) units: person ) recovery of confirmed[rgn] = tested untreated resolution[rgn] * ( -fatality rate untreated post-detection phase resolution time" ) -deaths of symptomatic untested reference covid hospitalization fraction confirmed units: person/(km*km) regionalinputs[rfi,rgn] = reference force of infection sensitivity post mortem testing to capacity baseline daily fraction susceptible seeking tests weight on reported probability of infection multiplier recent infections to test min contact fraction confirmation impact on contact impact of population density on hospital availability impact of treatment on fatality rate log ( dread factor in risk perception reference covid hospitalization fraction confirmed base fatality rate for unit acuity net covid acuity relative to flu net sensitivity of fatality rate to acuity net total asymptomatic fraction net sens obesity impact net sens chronic impact net sens liver impact net multiplier transmission risk for asymptomatic net relative risk of transmission by hospitalized = units: dmnl relative risk of transmission by presymptomatic = units: dmnl reported hazard of infection[rgn] = positive tests of infected response policy time on = units: day response policy weight[pdim] = units: dmnl ) rgn : albania saveper = units: day sens chronic impact = e- units: dmnl sens chronic impact net[rgn] = initial( sens chronic impact * ( -sw gen sens liver impact = e- units: dmnl sens liver impact net[rgn] = initial( sens liver impact * ( -sw gen sens obesity impact = e- units: dmnl sens obesity impact net[rgn] = initial( sens obesity impact * ( -sw gen senscoviduntestedadmission = units: dmnl sensitivity of contact reduction to utility sensitivity of contact reduction to utility policy * response policy weight[scup] + ( -response policy weight[scup] ) * sensitivity of contact reduction to utility sensitivity of contact reduction to utility policy = units: dmnl sensitivity of covid test = . units: dmnl sensitivity of fatality rate to acuity sensitivity of fatality rate to acuity net[rgn] = initial( sensitivity of fatality rate to acuity sensitivity post mortem testing to capacity ^ cmlterrpw ) / ( baseerror + datacmltovertime sim pseudo case fatality[rgn] = zidz ( cumulative deaths of confirmed[rgn] , cumulative confirmed cases simcmltovertime[rgn,infection] = cumulative confirmed cases post mortem test rate[rgn] + positive tests of infected post mortem test rate total simulated tests = if then else ( flowresiduals[rgn,series] = :na:, :na:, flowresiduals units: dmnl units: dmnl ) switch for government response[rgn] = if then else ( time > government response start time symptomatic fraction in poisson[rgn] = initial( -exp ( -covid acuity[rgn] ) ) units: dmnl symptomatic fraction negative symptomatic infected to testing[rgn] = positive testing of infected untreated[rgn] + hospital admission infectious testing capacity net of post mortem tests[rgn] = active test rate positive candidates interested in testing poisson subset[rgn] * symptomatic fraction in poisson[rgn] + potential test demand from susceptible population[rgn] * symptomatic fraction negative testing on living[rgn] = min ( testing capacity net of post mortem tests indicated fraction negative demand tested[rgn] * potential test demand from susceptible population[rgn] , indicated fraction negative demand tested[rgn] * potential test demand from susceptible population[rgn] + indicated fraction positive demand tested[rgn] * positive candidates interested in testing poisson subset tests per million[rgn] = cumulative tests data[rgn] / initial population time step = . units: day time to adjust testing = units: day time to downgrade risk time to downgrade risk policy * response policy weight[dgtp] + ( -response policy weight[dgtp] ) * time to downgrade risk time to downgrade risk policy = units: day time to herd immunity[rgn] = xidz ( herd immunity fraction * susceptible time to upgrade risk total asymptomatic fraction total asymptomatic fraction net[rgn] = initial( total asymptomatic fraction total covid hospitalized[rgn] = sum ( hospitalized infectious total disease duration = onset to detection delay + "post-detection phase resolution time" + incubation period units: day total simulated tests[rgn] = post mortem tests total[rgn] + testing on living total test on covid patients[rgn] = max ( , min ( positive candidates interested in testing poisson subset total to official cases simulated[rgn] = zidz ( cumulative cases[rgn] , simcmltovertime[rgn,infection] ) units: dmnl pre-symptomatic infected transmission multiplier for confirmed[rgn] = initial( baseline transmission multiplier for untested symptomatic * confirmation impact on contact transmission multiplier for hospitalized[rgn,tststs] = initial( baseline transmission multiplier for untested symptomatic * relative risk of transmission by hospitalized * if then else ( tststs = , confirmation impact on contact transmission multiplier pre detection[rgn] = initial( baseline transmission multiplier for untested symptomatic * ( -total asymptomatic fraction net[rgn] ) + total asymptomatic fraction net[rgn] * baseline risk of transmission by asymptomatic baseline transmission multiplier for untested symptomatic * relative risk of transmission by presymptomatic ) * ( -total asymptomatic fraction net[rgn] ) + total asymptomatic fraction net[rgn] * baseline risk of transmission by asymptomatic[rgn] * relative risk of transmission by presymptomatic ) units: dmnl active test rate[rgn] units: person/day ) tststs : tested untested pmas gap with tested[rgn] = ( -allocated fration noncovid hospitalized[rgn] ) ^ senscoviduntestedadmission units: dmnl untested symptomatic infected to hospital[rgn] = hospital admission infectious utility from limited activities[rgn] = exp ( sensitivity of contact reduction to utility net[rgn] * fractional value of limited activities ) units: dmnl utility from normal activities[rgn] = exp ( sensitivity of contact reduction to utility net[rgn] * ( -perceived risk of life loss voluntary reduction in contacts[rgn] = f[rgn] / f [rgn] * ( -min contact fraction[rgn] ) + min contact fraction zidz ( sum ( average acuity hospitalized[rgn,tststs!] * hospitalized infectious[rgn,tststs!] ) , sum ( hospitalized infectious weather effect on transmission weight max in test goal = units: dmnl infected unconfirmed post-detection"[rgn] + infectious confirmed not hospitalized[rgn] + sum ( hospitalized infectious[rgn,tststs!] ) * "post-detection phase resolution time" / hospitalized resolution time units spread of sars-cov- in the icelandic population clinical characteristics and imaging manifestations of the novel coronavirus disease (covid- ): a multi-center study in wenzhou city detection of sars-cov- in different types of clinical specimens sensitivity of chest ct for covid- : comparison to rt-pcr stability issues of rt-pcr testing of sars-cov- for hospitalized patients clinically diagnosed with covid- weather conditions and covid- transmission: estimates and projections. medrxiv clinical characteristics of coronavirus disease in china characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention covid- exacerbating inequalities in the us estimating the infection and case fatality ratio for coronavirus disease (covid- ) using age-adjusted data from the outbreak on the diamond princess cruise ship estimating the infection fatality rate among symptomatic covid- cases in the united states. health aff (millwood) suppression of covid- outbreak in the municipality of vo estimating the asymptomatic proportion of coronavirus disease (covid- ) cases on board the diamond princess cruise ship universal screening for sars-cov- in women admitted for delivery incubation period and other epidemiological characteristics of novel coronavirus infections with right truncation: a statistical analysis of publicly available case data modeling the rework cycle: capturing multiple defects per task data analysis using regression and multilevel/hierarchical models accelerating markov chain monte carlo simulation by differential evolution with self-adaptive randomized subspace sampling an interactive web-based dashboard to track covid- in real time simulation-based estimation of the early spread of covid- in iran: actual versus confirmed cases estimates of the severity of coronavirus disease : a model-based analysis. the lancet infectious diseases serial interval of covid- among publicly reported confirmed cases serial interval of novel coronavirus (covid- ) infections an interactive web-based dashboard to track covid- in real time key: cord- -h uwj authors: kiechle, frederick l.; arcenas, rodney c.; rogers, linda c. title: establishing benchmarks and metrics for disruptive technologies, inappropriate and obsolete tests in the clinical laboratory date: - - journal: clin chim acta doi: . /j.cca. . . sha: doc_id: cord_uid: h uwj benchmarks and metrics related to laboratory test utilization are based on evidence-based medical literature that may suffer from a positive publication bias. guidelines are only as good as the data reviewed to create them. disruptive technologies require time for appropriate use to be established before utilization review will be meaningful. metrics include monitoring the use of obsolete tests and the inappropriate use of lab tests. test utilization by clients in a hospital outreach program can be used to monitor the impact of new clients on lab workload. a multi-disciplinary laboratory utilization committee is the most effective tool for modifying bad habits, and reviewing and approving new tests for the lab formulary or by sending them out to a reference lab. laboratory test overutilization is estimated to represent . % to % of all laboratory tests internationally. efforts have been made to reduce the demand for or utilization of these over utilized tests [ ] [ ] [ ] [ ] [ ] [ ] . the most efficient outcomes have involved the formation of a laboratory utilization committee [ , ] or a laboratory formulary committee [ ] based on the hospital pharmacy and therapeutics committee's organizational structure. this committee evaluates the clinical value of laboratory tests using an evidence-based review of the appropriate medical literature. this same literature is reviewed by numerous professional specialty medical organizations as well as healthcare insurance carriers to determine what tests or procedures should be performed and reimbursed. the conclusions based on these reviews need to be updated on a regular basis. "the quality of guidelines is only as good as the published studies on which they are based" [ ] . often relevant studies evaluating laboratory tests demonstrate negative findings and are not published [ , ] . this phenomenon is referred to as positive publication bias or publication bias. tzoulaki et al. [ ] demonstrated publication bias during a review of reports evaluating emerging cardiovascular biomarkers. therefore, misinterpretation is a potential impact of failing to publish studies with negative results during a review of evidence-based literature. readers beware. tests may be obsolete and should be retired from clinical use, while others may be inappropriately used for specific disease categories. the playing field is not level. there are at least six newer game-changing disruptive technologies being evaluated [ ] [ ] [ ] which will result in modifications of clinical practice and laboratory testing modalities. these newer disruptive technologies may replace obsolete or inappropriate tests. lab utilization benchmarks and metrics are under continuous flux as a consequence. in the case of evolving newer technology, it is imperative to explore their impact early in their development to anticipate and monitor their impact on laboratory testing. the three authors have reviewed the current literature related to laboratory test utilization with an emphasis on where do the definitions of obsolete or inappropriate test utilization originate. we evaluated whole genome sequencing, next generation sequencing and proteomics as examples of high impact disruptive technologies that generate large quantities of data that need software to reduce to clinically useful results. practical examples of obsolete and inappropriate tests are reviewed as potential metrics to monitor improvement in test utilization. another useful metric is test utilization by clients in a hospital outreach program which can be used to monitor the impact of new clients on laboratory workload. finally, the result of published data from the work of laboratory utilization committees is summarized. benchmarks and metrics for laboratory utilization will be reviewed for three disruptive technologies as well as obsolete and inappropriately used tests. medical practice as well as pathology is in the midst of the rapid development of at least six major game-changing disruptive technologies. they include genetics, proteomics, digital pathology, informatics, therapeutic pathology and in vivo diagnostics [ ] [ ] [ ] . all six of these disruptive technologies share similar issues like resolution of best applications for routine clinical use, paucity of evidence-based outcome literature for review, education of practitioners and physician users of the clinical information generated and software to convert big databases the method generates into clinical useful information [ ] [ ] [ ] . the utilization of these techniques will increase as these barriers or obstacles to clinical use are overcome. an example of a disruptive technology is next generation sequencing or massively parallel sequencing [ ] [ ] [ ] . this technique is currently not cleared by the u.s. food and drug administration [ ] . it has been used to generate genome wide sequences and one of the authors (flk) has had his genome sequenced at the clia approved laboratory at illumina (san diego, ca). the results revealed . million variants compared with the reference method and , of these variants were in the exome or in the coding elements. the study interrogated genes causally associated with conditions as recommended by the american college of medical genetics. in that limited number of genes, , variants were detected and classified as clinically significant ( ), carrier status ( ), variants of unknown significance ( ), likely benign variants ( ) and benign variants ( ). the definition of these variants calls and the failure of this technique to detect deletions, insertions, interspersed repeats and tandem repeats (repeats adjacent to each other like triplet repeats [ ] ) may lead to inappropriate interpretation of the results and expensive follow up clinical and laboratory evaluation. for example, a clinically significant pathogenic variant reported in at least unrelated cases with control data may be found in additional genome studies in other populations [ ] to be a benign variant that is also found with a new variant which contains the mutation that leads to the most significant deleterious effect on gene function. the software application for variant significance assignment, like datagenno [ ] , will need to be up-to-date with the latest genotype/phenotype associations to prevent false positive findings and inappropriate follow-up testing. in the highest rate of reported cancers was prostate, lung and bronchus and colon and rectum for men with female breast replacing prostate for women in the u.s. [ ] . the annual incidence rate was cases per , individuals. comprehensive sequencing of numerous human cancers have revealed driver genes, to such genes per tumor, which alter intracellular signal transduction pathways related to the cells future death or survival and/or genome maintenance [ , ] . there are at least fda approved cancer therapies based on the inhibition of these tumor-activated intracellular pathways [ ] . for example, the braf kinase inhibitor, vemurafenib, has shown a response rate in % of patients with metastatic melanoma that have the braf valine to glutamic acid mutation at codon (v e) [ ] . this v e mutation is associated with aggressive clinical course in patients with thyroid papillary microcarcinoma [ ] . in one study of a hybrid score composed of one molecular diagnostic (v e) and histopathologic parameters were used to predict this tumor's clinical course with a sensitivity of % and specificity of % [ ] . the selection of the correct molecular diagnostic tests for specific tumors is aided by published guidelines. immunohistochemistry detection of estrogen and progesterone receptors in breast cancer from american society of clinical oncology and college of american pathologists [ ] and selection of lung cancer patients for egfr and alk tyrosine kinase inhibitors from the international association for study of lung cancer, association for molecular pathology and college of american pathologists [ ] . whole genome sequencing of a tumor will provide access to all known and unknown variants related to the tumor's survival skills [ ] . the development of software [ ] which will convert the patient's raw genome sequence into a medically relevant assessment of therapeutic targets and drug metabolism based on the tumor's body site will be very useful. from this genome analysis, the clinician wants to know what anticancer drug or drugs will this patient respond to as well as the dose. maldi-tof (matrix assisted laser desorption ionization-time of flight) spectroscopy is a relatively new technology to the clinical microbiology laboratory. pathogen identification has always relied on visual and biochemical interrogation where the summary of results may point to a specific identification (genus and species) or sometimes to at least the genus level. visual and biochemical results can sometimes yield variable results meaning in some cases the id may change depending on the result. the use of maldi-tof allows the clinical microbiology laboratory to identify bacteria once an isolate has been cultured potentially without performing any biochemical testing [ , , ] . the implications are quicker pathogen identifications to clinicians and the potential to affect antibiotic treatment before susceptibility results are available. the ability to obtain a quicker answer will disrupt the testing workflow and require a re-evaluation of that workflow to optimize the use of maldi-tof and antibiotic susceptibility testing [ , , ] . benchmarks and subsequent metrics for monitoring laboratory test utilization have been developed by professional subspecialty medical organizations in the format of recommendations and guidelines [ ] . examples include guidelines for hypothyroidism in adults from the american association of clinical endocrinologists and the american thyroid association [ ] , definition of myocardial infarction from the american college of cardiology foundation and american heart association [ ] , definition of diabetes mellitus from the american diabetes association [ ] , pharmacogenetics as well as follow-up testing for metabolic diseases identified by expanded newborn screening using tandem mass spectrometry from the national academy of clinical biochemistry [ , ] , and use of bone metabolic markers from the japan osteoporosis society [ ] . thirty-five of these specialty societies have joined the choosing wisely project organized by the american board of internal medicine. societies are asked to provide five specific, evidence-based recommendations on when tests and procedures may be appropriate or inappropriate for patient care (www.choosingwisely.org). a review of the lists from specialty societies revealed recommendations. laboratory tests were referenced in items or . % of the total. only one organization, american society of clinical pathology, had a list of laboratory test-related recommendations [ ] . kale et al. [ ] reviewed the national annual savings if outpatient visits to the primary care physicians did not include unnecessary or inappropriate laboratory tests including cbc ($ . million), urinalysis ($ . million) and basic metabolic panel ($ . million). those three procedures yield an annual cost savings of $ . million compared to the elimination of inappropriate pap tests at an annual savings of $ . million. these figures illustrate the magnitude of healthcare savings by implementing simple laboratory test ordering practices which reduce duplication and/or inappropriate testing. collaboration by subspecialty medical societies in disruptive technology development and improvements in routine clinical laboratory test utilization will be a fertile area for the development of benchmarks and metrics for future laboratory test utilization. the appropriateness of laboratory tests and the appropriate utilization of laboratory tests are always important for patient care, but require increased scrutiny in the era of containment of healthcare costs. objective criteria for the judging of appropriateness of tests and their utilization have not been universally developed or applied, so it is not always easy to define these terms [ ] . insurance companies are recognizing the medical and the financial burden of unnecessary testing and are taking action. many companies have posted information on their websites defining obsolete and unreliable lab tests which are readily accessible on the internet, including aetna [ ] , united healthcare [ ] and amerihealth [ ] . one criterion for judging the appropriateness of a test is to determine if it is obsolete. the definition of "obsolete" as noted in the merriam-webster on-line dictionary at http://www.merriam-webster. com/dictionary/ is "no longer in use or no longer useful". synonyms include: antiquated, archaic, dated, démodé, demoded, fossilized, and kaput. over time, with advances in medical technology, laboratory tests become outdated. although it is difficult to remove a test from a laboratory's formulary, there are good reasons to do so. reasons include the availability of a more sensitive, specific, or accurate test or new guidelines recommend the elimination of a test with the replacement of another. there are tests in clinical pathology that must be considered for obsolescence. these include t uptake and lactic acid dehydrogenase (ldh) isoenzymes in the clinical chemistry lab and bleeding time in hematology. obsolete tests in the microbiology laboratory include bacterial antigen detection tests, group b streptococcus antigen (gbs) testing and hiv- western blot. t uptake and free thyroxine index (fti) are still ordered by physicians, despite the fact that alternative tests have been available for many years. t uptake is an old test designed with a purpose of indirectly measuring free thyroxine (t ). it was developed before the availability of direct assays able to accurately measure free t levels [ ] . standardization of free t assays has been reported using the time-consuming equilibrium dialysis in combination with isotope dilution-liquid chromatography/tandem mass spectrometry [ ] . t uptake is an assessment of unsaturated (unbound to thyroxine) thyroid binding proteins in serum and is used with total t to calculate fti. the fti is obtained by multiplying the (total t ) times (t update). there is no longer a need to estimate free t when there are assays for the direct measurement of free t in every laboratory. supporting evidence for the obsolescence of t update and fti has been available for decades [ ] . current guidelines for the diagnosis and management of hypothyroidism [ ] , hyperthyroidism [ ] , and thyroid disease in pregnancy [ ] , no longer include the assessment of t update or fti. the analysis of lactic acid dehydrogenase (ldh) isoenzymes by electrophoresis has been utilized as an aid in the diagnosis of myocardial infarction. with the development of a more specific test for myocardial damage, troponin, there is little use for this insensitive and time-consuming electrophoretic assay. current guidelines clearly establish that the preferred marker for cardiac injury is troponin [ ] . bleeding time is a crude test of hemostasis (the arrest or stoppage of bleeding). it is an indication of how well platelets interact with blood vessel walls to form blood clots. indirectly assesses platelet function. it is performed by making a small incision on the skin and measuring, in seconds, the time taken for bleeding to stop. the test was designed to assess platelet function or exclude von willebrand disease. this test is labor intensive, invasive, poorly reproducible, and insensitive [ ] . historically it was performed because screening tests with a higher sensitivity for platelet dysfunction and von willebrand disease (vwd) were unavailable. bleeding time has been replaced by instrumentation that can assess platelet function in whole blood by aggregation studies [ , ] . available instrumentation includes the pfa- (platelet function analyzer, siemens usa), the verifynow (accumetrics), the plateletworks (helena), the impact (diamed) and the thromboelastograph (teg) (haemonetics). initial tests for a bleeding disorder rule out more common causes of bleeding. these tests include complete blood and platelet counts, ptt, pt, and possibly fibrinogen level or thrombin time. additional tests for von willebrand disease (vwf: antigen, ristocetin cofactor activity. factor viii clotting activity) can confirm the disease [ ] . bacterial antigen detection tests should be considered obsolete. they have historically been used as an adjunct to other laboratory tests for the diagnosis of bacterial meningitis. the test's purported advantages were the rapid detection of h. influenza, n. meningitides, s. pneumoniae, and s. agalactiae. overall, the sensitivity is essentially the same as that of a gram-stained smear of a cyto-centrifuged csf specimen [ , ] . with the advent of vaccines to h. influenza type b and n. meningitides (a, c, y, and w- ) the antigen testing is even less useful. the literature confirms that the use of direct antigen testing from the csf is neither sensitive nor specific [ , ] . more importantly, the gram stain and cultures still need to be performed regardless of the initial antigen test result. based on the data reviewed, our laboratory has discontinued this testing in-house. this is an example of testing that was removed from the market based on recommendations from the centers for disease control (cdc) stating that the rapid antigen detection tests for gbs are not sensitive enough to replace the culture based prenatal screening or to use in place of the risk-based approach when culture results are unknown at the time of labor [ ] . because of the poor performance of the rapid antigen testing, cdc has recommended intrapartum chemoprophylaxis antibiotics be administered to women who have certain risk factors [ ] . our laboratory looked at internal data for our patient population and found the sensitivity of the rapid antigen test that was being used was %. forty-one patients were missed on the rapid antigen test were detected only by culture. data from the literature show an average sensitivity of . % among various labs surveyed [ ] . this is an example where cdc recommendations and assessment of testing performance within your laboratory supports moving a test into obsolescence. the hiv- western blot (wb) has been a constant as one of the confirmatory tests for hiv antibody testing. however, the wb is moving its way into obsolescence as newer generation antigen/antibody and molecular assays become part of the new hiv testing algorithms. hiv- wbs have always had issues with indeterminate results due to a myriad of factors (false positives and/or lack of specificity, kit design, etc.), which required either re-testing at a later time and/or molecular testing for hiv- nucleic acid [ ] . the cdc/aphl, who, and france each have different interpretation criteria for defining a positive confirmatory result which indicates a lack of standardization for defining a patient as positive for hiv- [ ] . the immune response to hiv- is well known to produce antibodies that cross react on the hiv- wb which could lead to a false positive hiv- result [ ] . the lack of improvements or advancements of the wb compared to other antibody based assays has been nicely shown by masciotra et al. [ ] . they demonstrate that the rapid hiv tests actually detect hiv- antibodies several days earlier before the wb becomes positive [ ] . the introduction of th generation antigen/antibody testing has allowed clinicians to detect reactive patients earlier in their disease course compared to rd generation testing effectively narrowing the window of serological detection by approximately - days [ ] . because of these new developments, clsi and aphl have recommended new algorithms that incorporate antigen/antibody combination tests, rapid tests, and molecular testing [ , ] . the wb should be a test that will be obsolete as laboratories adopt the newer algorithms for hiv testing. in addition to obsolete tests, tests may be inappropriately used. inappropriate utilization includes the failure to follow current practice guidelines for the diagnosis and management of disease, thus ordering the incorrect test, panel of tests, or algorithm of tests; ordering tests too frequently or lack of medical rationale for the test. the problem and the resolution need to be reshaped as a way to "improve patient outcomes and lower costs" [ ] . the acknowledgement of the laboratory test utilization problem has been known and published for more than decades [ - , ] studies have been done to estimate and document the percentage of unnecessary tests [ , ] . a typical scenario for inappropriate test ordering occurs with thyroid function testing in the diagnosis and management of hypothyroidism. the guidelines are clear on the appropriate tests [ ] . thyroid stimulating hormone (tsh) is regarded as the best screening test, followed by free thyroxine (free t ) if the tsh is abnormal. additional tests are often ordered including total t . there is no need for a total t measurement if a free t is provided. furthermore, adding a total t level may confuse the diagnosis if changes in binding proteins via disease or drug therapy result in a total t that is inconsistent with other test results. tests may be ordered inappropriately or at other times, the wrong test is ordered. vitamin d testing is known to result in both inappropriate and erroneous ordering [ ] . the correct test for the routine assessment of vitamin d status or deficiency is -hydroxy vitamin d. the test , -dihydroxy vitamin d is often mistakenly ordered. the dihydroxy form of vitamin d is occasionally ordered in patients with kidney disease (decreased levels are one of the earliest changes to occur in persons with early kidney failure). however, most of the orders for , -dihydroxy vitamin d are simply erroneous. tests for both vitamin d and d are unnecessary for the assessment of vitamin d status. there is no need to differentiate between the d and d forms other than in the research setting. viral cultures have traditionally been the gold standard for virological detection in the clinical microbiology laboratory. direct viral detection direct from patient samples have also been utilized with monoclonal antibodies to detect viral antigen(s) with the intent of obtaining a result in a timelier manner than viral cultures. molecular technologies have now become established in the clinical microbiology laboratory. with the increased sensitivity and specificity [ ] and almost always a shorter turn-around-time, it is reasonable to ask "why do viral cultures?" [ , ] . one example of molecular testing that helps to answer this question are panels developed for respiratory viruses. there are several commercial companies that offer their version of an rvp (respiratory virus panel). our laboratory offers a rvp assay that detects viral targets. not only are results obtained sooner than traditional virology testing, but our molecular rvp offers greater sensitivity and specificity than our prior direct fluorescence assay (dfa) that was sent out to a reference laboratory. because of the increased sensitivity, the rvps have allowed us to document co-viral infections, which have not been fully appreciated before with dfa or culture based testing [ ] . there have been reports of increased severity of disease, as well as reports of decreased severity of disease in the setting of co-viral infections [ ] . much more research must be done to understand the potential interactions of different respiratory viruses in the setting of a respiratory infection. our laboratory publishes a "virogram" during the respiratory virus season and related viral coinfections (figs. and and table ). the "virogram" charts the respiratory virus prevalence among the patient populations tested to give an idea what is circulating in the community. another example of molecular testing replacing viral cultures is the detection of enterovirus (ev) from csf. ev pcr has been shown to have greater sensitivity over culture [ ] . a study (unpublished) performed within our institution looked at the utility of an in-house ev pcr and its affect on length of stay (los) and cost on ev pcr negative and ev pcr positive patients. those with an ev pcr negative result had an average los of . days greater than those that were ev pcr positive and had an estimated $ , of additional cost related to in-patient care. viral cultures still have importance in growing the virus for the purposes of subtyping, identifying new strains, or antiviral testing. however, these should remain in specialty or research labs and not be routine for clinical diagnostic testing. pcr testing for the causative agent of lyme disease may initially make sense, but the life cycle of b. burgdorferi is such that pcr detects borrelia dna in the blood in less than half of patients that are in the early acute stage of disease when the characteristic erythema migrans is present [ ] . therefore, pcr is not recommended as a first line test for making the initial diagnosis of lyme disease. a review article showed that the median percent sensitivities of pcr testing from blood, skin biopsy, csf, and synovial fluid are - %, - %, - %, and - %, respectively [ ] . the current recommendation for diagnostic testing involves a two-tiered algorithmic approach involving antibody testing [ ] . there may be clinical utility for pcr, but only if the serology testing is negative or inconclusive and clinical history and symptoms strongly suggest lyme disease. hospitals have introduced outreach programs that market laboratory services to physician offices, nursing homes, and other hospitals [ , ] to increase test volumes and reduce unit costs per test. this effort generates increased laboratory test utilization which should be monitored by average number of specific tests ordered per subspeciality physician per month ( [ ] , table . ). the data is collected from patient requisitions that are processed each day in the accessioning area of the outreach specimen receiving area. the sales force will introduce outreach administration to the projected number of new client accounts to be opened each month. the impact of the laboratory can be estimated by multiplying the volume of a specific test per physician for an office practice of multiple physicians. these volumes will estimate the utilization of tests per laboratory section and predict the future need for additional analyzers and/or personnel to perform the laboratory test procedures as the outreach client number increase. utilization data varies by medical subspeciality. for example, urology had requisitions/physician, . procedures/requisition and procedures/physician with the psa being the highest test volume. compare that to the nursing homes with requisitions/physician, . procedures/requisition and procedures/physician with electrolytes being the highest test volume [ ] . this data is used primarily for planning the best strategies to absorb the increased workload new clients will bring to the outreach business. it can also be used to monitor the use of obsolete and inappropriate lab tests to develop educational efforts to improve test utilization practices by subspeciality among outreach clients. an excellent review of laboratory test utilization, understanding the many factors involved, and steps to implement changes are provided in a recent publication [ ] . the author provides insight and guidelines to assist the laboratory in initiating improvements in laboratory utilization. ultimate goals include: developing and adopt more-effective testing algorithms, reducing testing costs, use new technologies cost-effectively, and shorten the time to diagnosis. interventions for hospitals and laboratories focus on changing physicians' test ordering behavior and include: . eliminating obsolete tests and modifying requisition forms. the laboratory can alter test-requisition forms to steer clinicians in the right direction. one such option is an "out of sight, out of mind" approach in which certain tests simply don't appear on the menu. . assisting in the education to promote appropriate lab testing can be part of a hospitals continuing medical education (cme) program for clinicians through grand rounds, newsletters, and cme lectures. . reinforcing positive changes by auditing clinicians' use of new protocols and offering feedback. . a two tier review process for molecular send out tests is a useful tool for pathologists to learn and advice on the wisdom of molecular assays [ ] . finally, all hospitals should implement a laboratory utilization or formulary committee to help in overseeing testing and promoting good testing practices, similar to pharmacy and therapeutics committees. this approach has been met with great success [ , , ] . the use of molecular methods for respiratory virus testing has allowed us to detect patients with more than virus present. the presence of multiple viruses within a patient sample is currently underappreciated and the effect on the overall disease presentation is currently unknown. managing utilization of new diagnostic tests clinical laboratory tests not performed in a central hospital laboratory managing the demand for laboratory testing: options and opportunities demand management and test request rationalization laboratory test utilization program. structure and impact in a large academic medical center changing physician behavior in ordering diagnostic tests biomarkers in cardiovascular medicine. the shame of publication bias bias in association 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clinical practice guidelines for hypothyroidism in adults accf expert consensus document on practical considerations in the interpretation of troponin elevations. a report of the american college of cardiology foundation task force on clinical expert consensus documents diagnosis and classification of diabetes mellitus laboratory analysis and application of pharmacogenetics to clinical practice follow up testing for metabolic diseases identified by expanded newborn screening using tandem mass spectrometry guidelines for the use of bone metabolic markers in the diagnosis and treatment of osteoporosis when less is more for patients in laboratory testing top " lists top $ billion do we know what inappropriate laboratory utilization is? a systematic review of laboratory clinical audit aetna clinical policy bulletin: obsolete and unreliable tests and procedures united healthcare's policy number . . obsolete or unreliable tests amerihealth's medical policy bulletin # . . d. obsolete or unreliable diagnostic tests and medical services comparison of three free t (ft$) and free t (ft#) immunoassays in healthy subjects and patients with thyroid diseases and severe non-thryoid illnesses use of frozen sera for ft standardization: investigation by equilibrium dialysis combined with isotope dilution-mass spectrometry and immunoassay a reappraisal of the free thyroxine index hyperthyroidism and other causes of thyrotoxicosis: management guidelines of the american thyroid association and guidelines of the american thyroid association for the diagnosis and management of thyroid disease during pregnancy and postpartum standardization of platelet function testing by aggregometry through new clsi guideline diagnosis and management of von willebrand disease: guidelines for primary care comparison of bacterial antigen test and gram stain for detecting classic meningitis bacteria in cerebrospinal fluid rapid bacterial antigen detection is not clinically useful prevention of perinatal group b streptococcal disease infections in international pregnancy study: performance of the optical immunoassay test for detection of group b streptococcus frequency, causes, and new challenges of indeterminate results in western blot confirmatory testing for antibodies to human immunodeficiency virus comparison of alternative interpretive criteria for the hiv- and hiv- infections evaluation of an alternative hiv diagnostic algorithm using specimens from seroconversion panels and persons with established hiv infections evaluation of the performance of the abbott architect hiv ag/ab combo assay criteria for laboratory testing and diagnosis of human immunodeficiency virus infection; approved guideline, clsi document m -a silver spring, maryland: the association of public health laboratories order patrol -how to rein in test requests professional review of laboratory utilization ready, fire! aim! an enquiry into laboratory test ordering vitamin d testing-what's the right answer? role of cell culture for virus detection in the age of technology detection of respiratory viruses by molecular methods an analytical comparison of four commercial respiratory virus panels. clinical virology symposium poster diagnosis of enteroviral meningitis by use of polymerase chain reaction of cerebrospinal fluid, stool and serum specimens diagnosis of lyme borreliosis notice to readers: recommendations for test performance and interpretation from the second national conference on serological diagnosis of lyme disease outreach implementation requirements: a case study hospital laboratory outreach: benefits and planning clinical requests for molecular tests. the -step evidence check clinical labs of hillview hillview avenue phd university of alberta hospital . walter mackenzie centre th street edmonton ab t g b canada key: cord- -d cpe yl authors: gonzalez, t.; de la rubia, m. a.; hincz, k. p.; comas-lopez, m.; subirats, laia; fort, santi; sacha, g. m. title: influence of covid- confinement on students’ performance in higher education date: - - journal: plos one doi: . /journal.pone. sha: doc_id: cord_uid: d cpe yl this study analyzes the effects of covid- confinement on the autonomous learning performance of students in higher education. using a field experiment with students from three different subjects at universidad autónoma de madrid (spain), we study the differences in assessments by dividing students into two groups. the first group (control) corresponds to academic years / and / . the second group (experimental) corresponds to students from / , which is the group of students that had their face-to-face activities interrupted because of the confinement. the results show that there is a significant positive effect of the covid- confinement on students’ performance. this effect is also significant in activities that did not change their format when performed after the confinement. we find that this effect is significant both in subjects that increased the number of assessment activities and subjects that did not change the student workload. additionally, an analysis of students’ learning strategies before confinement shows that students did not study on a continuous basis. based on these results, we conclude that covid- confinement changed students’ learning strategies to a more continuous habit, improving their efficiency. for these reasons, better scores in students’ assessment are expected due to covid- confinement that can be explained by an improvement in their learning performance. the coronavirus covid- outbreak disrupted life around the globe in . as in any other sector, the covid- pandemic affected education in many ways. government actions have followed a common goal of reducing the spread of coronavirus by introducing measures limiting social contact. many countries suspended face-to-face teaching and exams as well as placing restrictions on immigration affecting erasmus students [ ] . where possible, traditional classes are being replaced with books and materials taken from school. various e-learning platforms enable interaction between teachers and students, and, in some cases, national television shows or social media platforms are being used for education. some education systems announced exceptional holidays to better prepare for this distance-learning scenario. a a a a a in terms of the impact of the covid- pandemic on different countries' education systems many differences exist. this lack of homogeneity is caused by such factors as the start and end dates of academic years and the timing of school holidays. while some countries suspended in-person classes from march/april until further notice, others were less restrictive, and universities were only advised to reduce face-to-face teaching and replace it with online solutions wherever practicable. in other cases, depending on the academic calendar, it was possible to postpone the start of the summer semester [ ] . fortunately, there is a range of modern tools available to face the challenge of distance learning imposed by the covid- pandemic [ ] . using these tools, the modification of contents that were previously taught face-to-face is easily conceivable. there are however other important tasks in the learning process, such as assessment or autonomous learning, that can still be challenging without the direct supervision of teachers. all these arguments end in a common topic: how to ensure the assessment's adequacy to correctly measure students' progress. thus, how can teachers compare students' results if they differ from previous years? on one hand, if students achieve higher scores than in previous years, this could be linked with cheating in online exams or with changes in the format of the evaluation tools. on the other hand, lower grades could also be caused by the evaluation format change or be attributable to autonomous learning as a less effective teaching method. the objective of this article is to reduce the uncertainty in the assessment process in higher education during the covid- pandemic. to achieve this goal, we analyze students' learning strategies before and after confinement. altogether, our data indicates that autonomous learning in this scenario has increased students' performance and higher scores should be expected. we also discuss the reasons underneath this effect. we present a study that involves more than students enrolled in subjects from different degrees from the universidad autónoma de madrid (spain) during three academic years, including data obtained in the / academic year, when the restrictions due to the covid- pandemic have been in force. e-learning has experienced significant change due to the exponential growth of the internet and information technology [ ] . new e-learning platforms are being developed for tutors to facilitate assessments and for learners to participate in lectures [ , ] . both assessment processes and self-evaluation have been proven to benefit from technological advancement. even courses that solely offer online contents such as massive open online courses (moocs) [ , ] have also become popular. the inclusion of e-learning tools in higher education implies that a greater amount of information can be analyzed, improving teaching quality [ ] [ ] [ ] . in recent years, many studies have been performed analyzing the advantages and challenges of massive data analysis in higher education [ ] . for example, a study of gasevic et al. [ ] indicates that time management tactics had significant correlations with academic performance. jovanovic et al also demonstrated that assisting students in their management of learning resources is critical for a correct management of their learning strategies in terms of regularity [ ] . within few days, the covid- pandemic enhanced the role of remote working, e-learning, video streaming, etc. on a broad scale [ ] . in [ ] , we can see that the most popular remote collaboration tools are private chat messages, followed by two-participant-calls, multiperson-meetings, and team chat messages. in addition, several recommendations to help teachers in the process of online instruction have appeared [ ] . furthermore, mobile learning has become an alternative suitable for some students with fewer technological resources. regarding the feedback of e-classes given by students, some studies [ ] point out that students were satisfied with the teacher's way of delivering the lecture and that the main problem was poor internet connection. related to autonomous learning, many studies have been performed regarding the concept of self-regulated learning (srl), in which students are active and responsible for their own learning process [ , ] as well as being knowledgeable, self-aware and able to select their own approach to learning [ , ] . some studies indicated that srl significantly affected students' academic achievement and learning performance [ ] [ ] [ ] . researchers indicated that students with strongly developed srl skills were more likely to be successful both in classrooms [ ] and online learning [ ] . these studies and the development of adequate tools for evaluation and self-evaluation of learners have become especially necessary in the covid- pandemic in order to guarantee good performance in e-learning environments [ ] . linear tests, which require all students to take the same assessment in terms of the number and order of items during a test session, are among the most common tools used in computerbased testing. computer adaptive test (cat), based on item response theory, was formally proposed by lord in [ ] [ ] [ ] , as is the case with linear testing. some platforms couple the advantages of cat-specific feedback with multistage adaptive testing [ ] . the use of cat is also increasingly being promoted in clinical practice to improve patient quality of life. over the decades, different systems and approaches based on cat have been used in the educational space to enhance the learning process [ , ] . considering the usage of cat as a learning tool, establishing the knowledge of the learner is crucial for personalizing subsequent question difficulty. cat does have some negative aspects such as continued test item exposure, which allows learners to memorize the test answers and share them with their peers [ , ]. as a solution to limit test item exposure, a large question bank has been suggested. this solution is unfeasible in most cases, since most of the cat models already require more items than comparable linear testing [ ]. the aim of this study is to identify the effect of covid- confinement on students' performance. this main objective leads to the first hypothesis of this study which can be formulated as h : covid- confinement has a significant effect on students' performance. the confirmation of this hypothesis should be done discarding any potential side effects such as students cheating in their assessment process related to remote learning. moreover, a further analysis should be done to investigate which factors of covid- confinement are responsible for the change. a second hypothesis is h : covid- confinement has a significant effect on the assessment process. the aim of the project was therefore to investigate the following questions: . is there any effect (positive or negative) of the covid- confinement on students' performance? . is it possible to be sure that the covid- confinement is the origin of the different performance (if any)? . what are the reasons for the differences (if any) in students' performance? . what are the expected effects of the differences in students' performance (if any) in the assessment process? we have used two online platforms. the first one is e-valuam [ ] , an online platform that aims to increase the quality of tests by improving the objectivity, robustness, security and relevance of assessment content. e-valuam implements all the cat tests described in the following sections. the second online platform used in this study is the moodle platform provided by the biochemistry department from universidad autónoma de madrid, where all the tests that do not use adaptive questions are implemented. adaptive tests have been used in the subjects "applied computing" and "design of water treatment facilities". traditional tests have been used in the subject "metabolism". . . cat theoretical model. let us consider a test composed by n q items. in the most general form, the normalized grade s j obtained by a student in the j-attempt will be a function of the weights of all the questions α and the normalized scores ψ (s j = s j (α, φ)), and can be defined as: where the φ i is defined as where δ is the kronecker delta, a i the correct answer and r i the student's answer to the i-question. by using this definition, we limit φ i to only two possible values: and ; φ i = when the student's answer is correct and φ i = when the student gives a wrong value. this definition is valid for both open answer and multiple-choice tests. in the case of multiple-choice test with n r possible answers, φ i can be reduced to consider the random effect. in this case: independently of using eqs or , to be sure that s j (α, φ) is normalized (i.e. < = s j (α, φ)< = ), we must impose the following additional condition on α: in the context of needing a final grade (fg) between and a certain value m, which typically takes values such as or , we just need to rescale the s j (α, φ) value obtained in our model by a factor k, i.e. fg j = k s j (α, φ). we will now include the option of having questions with an additional parameter l, which will be related to the level of relevance of the question. l is a number that we will assign to all the questions included in the repository of the test (i.e. the pool of questions from where the questions of a j-test will be selected). the concept of relevance can take different significances depending on the context and the opinion of the teachers. in our model, the questions with lower l values will be shown initially to the students, when the students answer correctly a certain number of questions with the lower l value, the system starts proposing questions from the next l value. by defining n l as the number of possible l values, the l value that must be obtained in the k-question of the j-test can be defined as: where trunc means the truncation of the value between brackets. it is worth noting that l k is proportional to the sum of the student's answers to all the previous questions in the test. this fact means that, in our model, the l k depends on the full history of answers given by the student. l k is inversely proportional to n q , which means that it takes a higher number of correct answers to increase l k . once l k is defined, a randomly selected question is shown to the student. another important fact that implies the use of eq in the adaptive test is that we will never have l k