key: cord- -oj e wo authors: kaeuffer, charlotte; ruch, yvon; fabacher, thibaut; hinschberger, olivier; mootien, joy; eyriey, magali; greigert, valentin; meyer, icolas; fafi-kremer, samira; lefebvre, nicolas; hansmann, yves; martinot, martin; danion, françois title: the bas²ic score: a useful tool to identify patients at high risk of early progression to severe covid- date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: oj e wo we developed a score, based on easily accessible data (age, sex, bmi, dyspnea and inflammatory parameters), to predict the risk of rapid progression to severe disease in hospitalized patients with covid- . using a cut-off of > points, the negative and positive predictive values were % and %, respectively. the coronavirus disease (covid- ) was declared a pandemic by the world health organization (who) on march [ ] . on an average, less than % of infected individuals are hospitalized, among which % require intensive care. overall, . % of patients with covid- died [ ] . rapid identification of patients at a high risk of developing severe covid- appeared to be crucial to help clinicians closely monitor such patients and for triage. in a previous multicenter study involving , hospitalized patients with confirmed covid- , we identified several independent risk factors, such as advanced age, obesity and inflammation, associated with the early development of severe disease [ ] . in the present study, we aimed to develop a practical score for estimating the risk of rapid progression to severe disease in a cohort of patients hospitalized for covid- . we used data collected from a prospective non-interventional cohort study, which included adult patients with confirmed covid- hospitalized in march in strasbourg university and mulhouse hospitals (france) [ ] . severe disease was defined as admission to the intensive care unit (icu) or death within days after admission. overweight and obesity were defined according to the who as a body mass index (bmi) of ≥ kg/m² and ≥ kg/m², respectively. dyspnea was defined as a score > according to the modified medical research council breathlessness scale. we chose an early time-point at day as majority of icu transfers or deaths occurred within the first week of hospitalization. in the derivation cohort, we have performed a bayesian logistic regression to identify risk factors for severe covid- . all demographic, clinical and biological variables with a pr(diff> ) < . or a pr(diff> ) > . in the univariate analysis, or of clinical relevance, were included in the multivariate model. variables collected were: age, sex, bmi, comorbidities (hypertension, diabetes, chronic lung disease, immunosuppression, chronic kidney disease, chronic heart failure, chronic hepatic failure, cancer, hematological malignancy, active smoking), pregnancy, symptoms at admission (fever, dyspnea, headache, chills, cough, fatigue, myalgia, chest pain, diarrhea, abdominal pain, confusion, anosmia or ageusia, oxygen level at admission), biological markers (c-reactive protein, neutrophil count, lymphocyte count, aspartate aminotransferase, alanine aminotransferase, hemoglobin level, platelet count, serum creatinine, serum sodium, lactate), radiological findings (chest computed tomography (ct) described as typical, bilateral involvement, ground-glass opacities, micronodules), treatments in the previous month (non-steroidal anti-inflammatory drugs, angiotensin-converting enzyme inhibitors, angiotensin- receptor antagonists, insulin, corticosteroids, hydroxychloroquine), antibiotic in the seven days prior to admission (betalactam, macrolide). [ ] . to build the score, these coefficients have been multiplied by and rounded to the nearest half-integer. the score was evaluated (positive predictive value [ppv], negative predictive value [npv] , sensitivity, specificity) on the derivation cohort and clinically relevant cut offs (npv > % and ppv > %) were determined. missing data were imputed using prior distributions derived from the observed data. the performance of this score was validated using an external cohort of patients hospitalized for covid- during the same period in colmar hospital, france. the study was approved by the ethics committee of the university hospital of strasbourg (n°ce- - ). written consent was waived in the context of an emerging infection. the patients who refused to participate in this study were not included. in the derivation cohort of , patients, the mean age was years (standard deviation [sd], ), and patients ( . %) were men (supplementary table based on previously identified prognostic factors [ ] , we then defined a prognostic bas²ic score including bmi, age, sex, shortness of breath and inflammatory parameters to screen patients at a risk of developing early severe disease (table ). in the receiver-operating characteristics analysis, the area under the curve was . ( . - . ) (figure ). using a cut-off > points, the npv and ppv were % and %, respectively, with a sensitivity of % and a specificity of %. using a cut-off > points, the npv was %, the ppv was %, sensitivity was % and specificity of %. in the validation cohort, including adult patients, the mean age was years (sd, ). among them, ( . %) were men and ( . %) were overweight. in this cohort, ( %) patients have developed severe disease. using a cut-off > points, the npv, ppv, sensitivity and specificity were %, %, % and %, respectively (figure ). using a cut-off > points, the npv, ppv, sensitivity and specificity were %, %, % and %, respectively. a suggestion on management was proposed depending of these cut offs (table b ). in this study, we established a new practical score, the bas²ic score, to easily evaluate the risk of developing early severe covid- among patients hospitalized due to severe covid- . the score was validated on an external cohort, providing a similar performance. patients with a score ≤ points could be considered at a low risk of developing severe disease, with a npv of %; hence, this score may help to decide which patients can be discharged. on the contrary, those with score > were considered to have a high risk, requiring rapid implementation of appropriate measures, such as hospitalization and consideration of specific therapeutics (e.g. dexamethasone, remdesivir) [ , ] . the bas²ic score has several advantages over previously published scores [ ] [ ] [ ] . this score was based on a large multicenter prospective cohort. it can predict the development of early complications, and it relies on clinical and laboratory parameters, all of which are simple, inexpensive and easily accessible. this score could be easily implemented in routine clinical practice to help clinicians classify patients at low risk and those at high risk, who should be closely monitored and thus, might benefit quickly from the relevant therapy. this is particularly important in the context of a rapid increase in the number of cases saturating health care facilities and in cases where identifying patients at high risk of developing a severe disease might help optimize medical resources. moreover, this score includes overweight parameter and certain inflammatory parameters, two important risk factors that have not been taken into account in previously published scores [ , ] . the use of inflammatory parameters is of particular relevance in terms of the results of dexamethasone administration for covid- treatment [ ] . however, the bas²ic score has some limits. first, the performance level of this score is not very high. some risk factors, such as high levels of d-dimer and interleukine- , which are associated with a poor outcome, were not taken into account when elaborating our score [ , ] . the efficacy of the score would probably have been even better if these parameters had been included. however, we believe that since these parameters are not tested for in routine clinical practice, adding them to the bas²ic score would have rendered the score difficult to use for clinicians. the etiology of death or admission to the icu among the elderly is multifactorial and often linked to the decompensation of underlying diseases. comorbidities, such as diabetes, immunosuppression and chronic kidney disease, were not associated with severe disease in our previous analysis but were associated with death alone [ ] . as this study was conducted in march , the beginning of the outbreak in france, very few patients benefited from specific therapy, such as corticosteroids or immunomodulatory treatments. this could have had an impact on the number of patients with severe disease. finally, this score is a helpful tool for clinicians, but it should not replace common clinical sense for deciding whether the patients require hospitalization or specific therapy. other parameters, such as the duration of symptoms, decompensation of comorbidities, need for oxygen, extension of lesions on computed tomography, and others, may be taken into account. further studies are needed to confirm the performance of the bas²ic score and validate our proposal for covid- management depending on the score. we developed the predictive bas²ic score, which is easy to implement and use in routine clinical practice, to help clinicians identify patients at high risk of developing early severe covid- . this simple score may be useful for triage of patients with covid- and to identify those who should be closely monitored. who director-general's opening remarks at the media briefing on covid- - estimating the burden of sars-cov- in france risk factors associated with severe covid- in eastern france: analysis of cases remdesivir for the treatment of covid- -preliminary report dexamethasone in hospitalized patients with covid- -preliminary report development and validation of a clinical risk score to predict the occurrence of critical illness in hospitalized patients with covid- prediction for progression risk in patients with covid- pneumonia: the call score host susceptibility to severe covid- and establishment of a host risk score: findings of cases outside wuhan clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study prognostic value of interleukin- , c-reactive protein, and procalcitonin in patients with covid- the authors would like to thank enago (www.enago.com) for the english language review. the authors declare no conflict of interest. key: cord- - g n j authors: frey, sharon e; shakib, sepehr; chanthavanich, pornthep; richmond, peter; smith, timothy; tantawichien, terapong; kittel, claudia; jaehnig, peter; mojares, zenaida; verma, bikash; kanesa-thasan, niranjan; hohenboken, matthew title: safety and immunogenicity of mf -adjuvanted cell culture–derived a/h n subunit influenza virus vaccine: dose-finding clinical trials in adults and the elderly date: - - journal: open forum infect dis doi: . /ofid/ofz sha: doc_id: cord_uid: g n j background: a/h n influenza viruses have high pandemic potential; consequently, vaccines need to be produced rapidly. mf ® adjuvant reduces the antigen required per dose, allowing for dose sparing and more rapid vaccine availability. methods: two multicenter, phase ii trials were conducted to evaluate the safety and immunogenicity of an mf -adjuvanted, cell culture–derived, a/h n vaccine (ah n c) among adult ( – years old) and elderly (≥ years old) subjects. participants were equally randomized to receive full-dose ( . μg of hemagglutinin antigen per dose) or half-dose ah n c vaccinations weeks apart. outcomes were based on center for biologics evaluation research and review (cber) and committee for medicinal products for human use (chmp) licensure criteria (titers ≥ : and seroconversions on day ). solicited reactions and adverse events were assessed (www.clinicaltrials.gov: nct and nct ). results: cber and chmp criteria were met by both age groups. cber criteria for hemagglutination titers were met for the full-dose formulation. solicited reaction frequencies tended to be higher in the full-dose group and were of mild to moderate intensity. no vaccine-related serious adverse events occurred. conclusions: in adult and elderly participants, the full-dose ah n c vaccine formulation was well tolerated and met us and european licensure criteria for pandemic vaccines. periodic influenza pandemics pose serious threats to global health and economies [ ] . the highly pathogenic avian influenza virus h n causes severe human disease and death [ ] and has a higher case fatality rate than seasonal influenza infections [ , ] . of the h n cases reported to the world health organization between and , (~ %) were fatal [ ] . sporadic cases of human h n virus infection have been associated with close contact with infected poultry. moreover, circulation of h n virus in bird flocks allows for potential mutations that can facilitate bird-to-human and human-to-human viral transmission [ ] . overall, the h n virus retains pandemic potential because it has spread to most continents, and most humans are unlikely to be immune to the virus [ ] . rapid and efficient production of pandemic influenza vaccines is essential to meet the anticipated global demand [ , ] . new cell culture-based production methods can eliminate dependency on egg supply and poultry flocks, which are also vulnerable to h n infection. cell culture-based vaccine manufacturing techniques shorten production times and increase production capacity [ , ] . manufacturing capacity may also benefit from the use of a vaccine adjuvant to enhance immunogenicity. mf ® (novartis international ag, basel, switzerland) is a proprietary oil-in-water emulsion adjuvant that has been used in several registered pandemic and seasonal influenza vaccines since . it has a well-established safety profile [ ] , allows for reduced antigen content per dose ( . μg of hemagglutinin [ha] in pandemic formulations vs μg of ha per strain in seasonal formulations [ , [ ] [ ] [ ] ), promotes the production of cross-reactive antibodies that may provide heterologous immunity against antigenically divergent strains [ , , ] , and improves vaccine efficacy in elderly adults and children, who are particularly vulnerable to influenza infection [ ] . based on a previous phase i dose-ranging study of an adjuvanted, cell culture-derived, h n subunit influenza virus vaccine, antigen-sparing formulations were evaluated in phase ii studies [ ] . we present safety, tolerability, and immunogenicity data from healthy adult and elderly subjects to establish the optimal vaccine formulation for these age groups. here we present primary and secondary outcome data from these -month studies, up to study day . the adult (nct ) and elderly (nct ) trials were phase ii, randomized, observer-blind, multicenter studies, conducted in australia, new zealand, the united states, and thailand. the design, objectives, and endpoints were identical for both studies. the study protocols were approved by the ethics review committees of the participating centers, and the studies were conducted in compliance with good clinical practices guidelines and the declaration of helsinki. written informed consent was obtained from subjects before enrollment. subjects were randomized at a : ratio to receive vaccinations with either full-dose or half-dose mf -adjuvant, cell culture-derived, h n vaccine (ah n c) given weeks apart ( figure ). the primary immunogenicity outcomes evaluated hemagglutination inhibition (hi) assay antibody responses in terms of the percentages of subjects achieving seroconversion and hi titers ≥ : on day . each subject was followed for months (day ) after the second vaccine dose to assess safety and immunogenicity. in the respective studies, adult (aged - years) and elderly subjects (aged ≥ years) were enrolled. the main exclusion criteria were presence of serious chronic or progressive disease, pregnancy or breastfeeding, prior receipt of any h n vaccine, receipt of any other influenza vaccines within days before enrollment, body temperature ≥ . °c and/or any acute illness within days of receiving study vaccines, and a body mass index ≥ kg/m (see clinicaltrials.gov for all exclusion criteria). both the adult and elderly studies used mf -adjuvanted, cell culture-derived, monovalent, inactivated, subunit, h n vaccines containing a/turkey/turkey/ / (h n )-like strain (nibrg- ) antigen (seqirus inc., holly springs, nc; f/k/a novartis influenza vaccines gmbh, marburg, germany). one . ml dose (full-dose formulation) contained . μg of ha antigen with . ml of mf . one . ml dose (half-dose formulation) contained . μg of ha with . ml of mf . vaccines were administered on day and day as single intramuscular injections in the nondominant arm. sera samples were obtained for immunogenicity analyses before each vaccination (day and day ) and on day and day (stored at - °c). immunogenicity was assessed by hi assay against the h n vaccine strain according to standard methods [ ] and expressed as the percentage of subjects achieving seroconversion, the percentage of subjects with an hi titer ≥ : , geometric mean hi titers (gmts), and the geometric mean ratios (gmrs) of hi titers. seroconversion was defined as hi titers ≥ : for subjects who were seronegative at baseline (hi titer < : on day ) or a minimum -fold increase in hi titer for subjects who had detectable baseline hi titers (≥ : ). for both studies, the primary immunogenicity outcomes were assessed on day and were based on the licensure criteria for pandemic influenza vaccines established by the center for biologics evaluation research and review (cber) [ ] . for the adult population, the following cber criteria were applied: ( ) the lower limit (ll) of the -sided . % confidence interval (ci) for the percentage of subjects achieving seroconversion for hi antibody responses should be ≥ %; ( ) the ll of the -sided . % ci for the percentage of subjects achieving an hi antibody titer of ≥ : should be ≥ %. for the elderly population, the values for the criteria described above were ( ) ≥ % and ( ) ≥ %, respectively. the secondary immunogenicity outcomes were also assessed on day and were based on the licensure criteria for pandemic influenza vaccines established by the committee for medicinal products for human use (chmp) [ ] . for the adult population, the following chmp criteria applied: ) the ll of the -sided . % ci for the percentage of subjects achieving seroconversion for hi antibody responses should be ≥ %; ) the ll of the -sided . % ci for the percentage of subjects achieving an hi antibody titer of ≥ : should be ≥ %; ) gmr should be > . . for the elderly population, the values for the criteria described above were ( ) ≥ %, ( ) ≥ %, and ( ) > . , respectively. after each vaccination, subjects were observed for minutes to monitor for immediate reactions. solicited local and systemic reactions were recorded by the subjects on diary cards for days after each vaccination. solicited local reactions included injection site induration, erythema, ecchymosis, and pain. solicited systemic reactions included nausea, generalized myalgia, generalized arthralgia, headache, fatigue, loss of appetite, malaise, and fever (body temperature ≥ °c). the severity of solicited reactions was categorized as mild (transient with no limitation in normal daily activity), moderate (some limitation in normal daily activity), or severe (unable to perform normal daily activity). all unsolicited adverse events (aes) were collected for days after each vaccination. serious adverse events (saes), the new onset of chronic diseases, medically attended aes, aes of special interest, aes leading to study withdrawal, and the administration of concomitant medications associated with these events were recorded throughout the study. the causal relationships of aes to the study vaccines were assessed by the investigators as being either nonrelated, possibly related, or probably related. sample sizes for the adult and elderly studies were planned as and evaluable subjects per group (assuming a study dropout rate of %), respectively. the percentages of subjects achieving seroconversion and the percentages of subjects with hi titers ≥ : , along with the associated . % clopper-pearson cis, were calculated as log -transformed values using analysis of covariance (ancova) with factors for dose, group, baseline titer, and study center. gmts, gmrs, and the associated -sided adjusted % cis were calculated using ancova with factors for race, gender, and study center. although the cber criteria involve the lower limits of % cis, a . % ci was calculated because there were vaccine formulations tested in the study, and the . alpha was distributed across tests. the immunogenicity analyses were performed on full analysis set (fas) data, which included all subjects who received at least dose of study vaccine and provided at least serum sample at both prevaccination and postvaccination time points. analyses of vaccine reactogenicity and safety were performed on data from subjects who had received at least study vaccination and provided either postvaccination ae or reactogenicity data (safety data set). all safety analyses were descriptive. of the enrolled adult and elderly subjects, (> %) and (> %) received at least dose of study vaccine, respectively ( figure ). overall, % of adult subjects ( of in the full-dose group and of in the half-dose group) and % of elderly subjects ( of in the full-dose group and of in the half-dose group) remained in the study and provided sera for immunogenicity analyses on day (fas data) (figure ). approximately % of adult subjects and % of elderly subjects were excluded from the immunogenicity fas data due to the absence of sera data. subject demographics and baseline characteristics were well balanced between groups within the respective study populations (table ). in both studies, more females were enrolled than males ( % vs % in the adult study and % vs % in the elderly study, respectively). at day , % ( . % ci, %- %) and % ( . % ci, %- %) of adult subjects in the full-dose and half-dose groups, respectively, achieved seroconversion; the cber and chmp criteria for seroconversion were met for both treatment groups (table ) [ , ] . in the elderly population, % ( . % ci, %- %) and % ( . % ci, %- %) of subjects in the full-dose and half-dose groups achieved seroconversion at day , respectively; the cber and chmp criteria for seroconversion were met for both treatment groups. at day , % ( . % ci, %- %) and % ( . % ci, %- %) of adult subjects in the full-dose and half-dose groups achieved hi titers ≥ : , respectively ( table ). the ll of the -sided . % ci for the percentage of subjects achieving an hi antibody titer ≥ : exceeded the cber and chmp requirements of % in the full-dose group, but not in the half-dose group. in the elderly population, % ( . % ci, %- %) of subjects in full-dose group and % ( . % ci, %- %) of subjects in the half-dose group achieved hi antibody titers ≥ : at day . the ll of the -sided . % ci exceeded the cber and chmp criterion of % in the fulldose group, but not in the half-dose group. at baseline, gmts within each study population were comparably low between the respective vaccine groups. among adult subjects, weeks after doses of ah n c (day ), gmts rose to ( % ci, %- %) and ( % ci, %- %) in the full-dose and half-dose groups, respectively (figure a) . the day to day gmrs for the full-dose and half-dose groups were ( % ci, %- %) and ( % ci, %- %), respectively, and exceeded the chmp gmr criterion of . . among elderly subjects, gmts rose to ( % ci, %- %) and ( % ci, %- %) by day in the full-dose and half-dose groups, respectively ( figure b ). the day to day gmrs for the elderly full-dose and half-dose groups were ( % ci, %- %) and . ( % ci, %- %), respectively, exceeding the chmp criterion of . ( table ). the rates of any solicited reactions within minutes of administration of the first vaccine dose were low and comparable between the vaccine groups in each age population, with no increase in reactogenicity after administration of the second dose (adults % vs % following first and second doses; elderly % vs % following first and second doses, respectively). in both age populations, the frequencies of solicited local reactions reported within days of each vaccination were higher for the abbreviations: ci, confidence interval; gmr, geometric mean ratio; hi, hemagglutination inhibition; seroconversion, defined as positivity or significant increase. a outcome met cber criterion [ ] for age group. b outcome met chmp criterion [ ] for age group. c gmr was a secondary end point in the adult study and was not adjusted for multiplicity; therefore, gmr ( . % ci) data are not available. positivity conversion was defined as postvaccination hi titer ≥ : for subjects negative (titer < : ) at baseline or a minimum -fold increase in hi titer for subjects seropositive (titer ≥ : ) at baseline; significant increase in antibody titer was defined as a minimum -fold increase in hi titer for subjects seropositive (titer ≥ : ) at baseline. full-dose groups compared with the respective half-dose groups, with no increase in reactogenicity after administration of the second doses (table ) . for both age populations, injection site pain was the most frequently reported solicited local reaction. within each age population, frequencies of individual solicited systemic reactions reported within days of each vaccination were comparable between the respective full-dose and halfdose groups (table ) . among adults, after each vaccination, the most commonly reported systemic reactions were headache and fatigue, followed by malaise, with no difference between the full-dose and half-dose groups. among elderly subjects, the most commonly reported systemic reactions after each vaccination were fatigue and malaise, with no difference between the full-dose and half-dose groups. after the second vaccination, frequencies of solicited systemic reactions were lower. between day and day , unsolicited aes were reported by up to % of subjects in the adult population and up to % of subjects in the elderly population, with comparable frequencies between the vaccine groups in each study. following first or second vaccinations, % and % of subjects in the adult and elderly populations reported an unsolicited ae that was judged to be possibly or probably related to the study vaccine, respectively. injection site bruising was the most commonly reported unsolicited ae in both age groups. at least sae was reported by (< %) subjects (appendicitis, pyelonephritis, and nerve compression) in the adult population, and by ( %) subjects (atrial fibrillation, adenocarcinoma of left lung, transient ischemic attack, cholecystitis, benign positional vertigo, right inguinal hernia, acute kidney injury, infected wound of left leg, fractured ribs, and syncope) in the elderly population; none of the reported saes were considered to be possibly or probably vaccine-related. one elderly subject (< %) withdrew prematurely from the study due to an unsolicited ae. three (< %) subjects in the adult population and ( %) subjects in the elderly population were diagnosed with the new onset of chronic diseases up to day . only sae had a fatal outcome (non-vaccine-related, elderly half-dose group; lung adenocarcinoma; occurred on day ). we evaluated the immunogenicity and safety of an mf adjuvanted, cell culture-derived, h n subunit influenza virus vaccine in phase ii studies; vaccine was administered as either a full-or half-dose formulation to healthy adult or elderly subjects. for both age populations, all cber criteria (seroconversion and hi titer ≥ : ) were met for the fulldose group, whereas the half-dose group only met the criteria for seroconversion. similarly, for both age groups, all chmp criteria (seroconversion, hi titer ≥ : , and gmr) were met for the full-dose group, whereas the half-dose group met of the criteria (seroconversion and gmr). although both vaccine formulations were immunogenic and well tolerated in each age population, the full-dose ( . μg of h n ha antigen with . ml of mf ) ah n c vaccine appears preferable-in terms of higher immunogenicity-for future clinical development. overall, postvaccination immunogenicity outcomes (seroconversion, percentages of subjects with hi titers ≥ : , and gmts) were higher among adults compared with elderly subjects, regardless of vaccine formulation. the generally lower postvaccination antibody responses observed in the elderly population may partly be attributed to immunosenescence. in both studies, the proportions of subjects who reported solicited reactions trended higher for the full-dose group compared with the half-dose group (mainly due to incidence of pain at the site of injection). subjects ≥ years of age appeared to report fewer solicited local and systemic reactions in each vaccine group compared with adult subjects. irrespective of vaccine formulation, and for each age group, the majority of reported reactions were mild to moderate in severity, with no evidence of increased frequency of reactions following a second dose. in both age groups, there were no appreciable differences in unsolicited aes between the full-dose and half-dose groups, in terms of both frequencies and specific conditions. the immunogenicity data for the full-dose formulation are consistent with those of previous studies conducted in healthy adult and elderly individuals, in which subjects received doses of mf -adjuvanted h n vaccine ( . μg of h n ha per dose) [ , , , , ] . whereas in the present study the half-dose formulation (containing . μg of h n antigen and a lower-than-standard quantity of mf per dose) did not meet all the licensure criteria evaluated, many studies conducted to assess the immunogenicity of half-doses ( . μg of antigen with a reduced quantity of mf ) administered weeks apart have consistently demonstrated that either or half-doses were sufficiently immunogenic to meet the cber and/or chmp licensure criteria; these studies included subjects of all ages and ethnicities, cell-and egg-derived vaccines, and a/h n [ ] , a/h n [ ] , and a/h n [ , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] strains. overall, the reactogenicity and safety data presented here are similar to and are in agreement with the results of previous studies of mf adjuvanted h n vaccine when administered to healthy adult and elderly subjects [ , ] . there were some limitations to the study. first, because a non-h n control group was not included, interpretation of the safety data is somewhat limited. however, the safety profile of the full-dose formulation observed in this study is consistent with that reported from a recent placebo-controlled trial of an egg-based, mf -adjuvanted, h n vaccine (aflunov, seqirus vaccines ltd., liverpool, uk [f/k/a novartis influenza vaccines ltd., liverpool, uk]; . μg of h n ha per dose) conducted in adult and elderly subjects [ ] . second, the study assessed only short-term antibody responses; analyses of mid-term ( -month) responses and long-term antibody persistence are either ongoing or planned. third, the relatively short follow-up period does not allow for the possible detection of rare, delayed aes. nonetheless, in a separate study of a cell culture-derived, mf -adjuvanted h n vaccine in adults, no vaccine-related aes were reported throughout the study period [ ] . in conclusion, two . -μg doses of a cell culture-derived, mf -adjuvanted h n vaccine administered weeks apart were well tolerated and highly immunogenic, raised no safety concerns, and induced robust antibody responses in adult and elderly subjects that met all the immunogenicity criteria required for pandemic vaccine licensure by both the us and european regulatory authorities. these results support the further development of the full-dose ( . μg), mf -adjuvant, cell culture-derived h n vaccine formulation for adult (age ≥ years) pandemic preparedness programs. avian influenza fact sheet recognizing true h n infections in humans during confirmed outbreaks world health organization. cumulative number of confirmed human cases for avian influenza a(h n ) reported to who cumulativenumberh n cases.pdf?ua= . accessed world health organization. pandemic influenza risk management who interim guidance influenza: options to improve pandemic preparation a randomised, single-blind, dose-range study to assess the immunogenicity and safety of a cell-culture-derived a/h n influenza vaccine in adult and elderly populations mf -adjuvanted versus non-adjuvanted influenza vaccines: integrated analysis from a large safety database mf -adjuvanted h n vaccine induces immunologic memory and heterotypic antibody responses in non-elderly and elderly adults effects of adjuvants on the safety and immunogenicity of an avian influenza h n vaccine in adults antigen sparing and cross-reactive immunity with an adjuvanted rh n prototype pandemic influenza vaccine: a randomised controlled trial fast rise of broadly cross-reactive antibodies after boosting long-lived human memory b cells primed by an mf adjuvanted prepandemic vaccine antigenically distinct mf -adjuvanted vaccine to boost immunity to h n the comparative effectiveness of adjuvanted and unadjuvanted trivalent inactivated influenza vaccine (tiv) in the elderly dose ranging of adjuvant and antigen in a cell culture h n influenza vaccine: safety and immunogenicity of a phase ½ clinical trial immunogenicity of avian influenza a/ anhui/ / (h n ) vaccine with mf adjuvant: a randomized clinical trial guidance for industry: clinical data needed to support the licensure of pandemic influenza vaccines note for guidance on harmonisation of requirements for influenza vaccines (cpmp/bwp/ / ) a phase ii, randomised clinical trial to demonstrate the non-inferiority of low-dose mf -adjuvanted pre-pandemic a/h n influenza vaccine in adult and elderly subjects safety and immunogenicity of an mf (®)-adjuvanted a/h n pre-pandemic influenza vaccine in adults and the elderly safety and immunogenicity of cell culture-derived a/h n variant influenza vaccines: a phase i randomized, observer-blind, dose-ranging study assessment of the immunogenicity and safety of varying doses of an mf ®-adjuvanted cell culture-derived a/h n pandemic influenza vaccine in japanese paediatric, adult and elderly subjects a randomized clinical trial to identify the optimal antigen and mf (®) adjuvant dose of a monovalent a/h n pandemic influenza vaccine in healthy adult and elderly subjects immunogenicity and safety of cell-derived mf ®-adjuvanted a/h n influenza vaccine for children immunogenicity and tolerability of an mf -adjuvanted, egg-derived, a/h n pandemic influenza vaccine in children - months of age safety and immunogenicity of an mf -adjuvanted a/h n pandemic influenza vaccine in children from three to seventeen years of age identification of antigen and adjuvant doses resulting in optimal immunogenicity and antibody persistence up to year after immunization with a pandemic a/h n influenza vaccine in children to < years of age a dose-ranging study of mf (®)-adjuvanted and non-adjuvanted a/h n pandemic influenza vaccine in young to middle-aged and older adult populations to assess safety, immunogenicity, and antibody persistence one year after vaccination comparison of half and full doses of an mf -adjuvanted cell culture-derived a/h n v vaccine in japanese children potential conflicts of interest. authors c.k., p.j., z.m., b.v., and n.k-t. were permanent employees of novartis group companies at the time the study was conducted (novartis' influenza vaccine business was acquired by the csl group on july , , and is currently operating as seqirus inc.). m.h. is a permanent employee of seqirus inc. (f/k/a novartis' influenza vaccine business), cambridge, ma. pr has served on advisory boards for glaxosmithkline, sanofi, and janssen and has received institutional funding to undertake multicenter vaccine trials from novartis, glaxosmithkline, csl, and janssen. s.f., s.s., e.s., t.s., p.c., and t.t. do not have any conflicts of interest to declare. mf is a registered trademark of novartis international ag, basel, switzerland. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -o zfilcl authors: laidler, matthew r.; thomas, ann; baumbach, joan; kirley, pam daily; meek, james; aragon, deborah; morin, craig; ryan, patricia a.; schaffner, william; zansky, shelley m.; chaves, sandra s. title: statin treatment and mortality: propensity score-matched analyses of – and – laboratory-confirmed influenza hospitalizations date: - - journal: open forum infect dis doi: . /ofid/ofv sha: doc_id: cord_uid: o zfilcl background. annual influenza epidemics are responsible for substantial morbidity and mortality. the use of immunomodulatory agents such as statins to target host inflammatory responses in influenza virus infection has been suggested as an adjunct treatment, especially during pandemics, when antiviral quantities are limited or vaccine production can be delayed. methods. we used population-based, influenza hospitalization surveillance data, propensity score-matched analysis, and cox regression to determine whether there was an association between mortality (within days of a positive influenza test) and statin treatment among hospitalized cohorts from influenza seasons (october , to april , and september , to april , ). results. hazard ratios for death within the -day follow-up period were . ( % confidence interval [ci], . –. ) for a matched sample from the – season and . ( % ci, . – . ) for a matched sample from the pandemic. conclusions. the analysis suggests a protective effect against death from influenza among patients hospitalized in – but not during the pandemic. sensitivity analysis indicates the findings for – may be influenced by unmeasured confounders. this analysis does not support using statins as an adjunct treatment for preventing death among persons hospitalized for influenza. . deaths have been estimated to range between ( ) ( ) and ( ) ( ) annually [ ] . influenza-associated mortality in pandemic years can be higher still and typically shifts toward younger age groups [ ] . this result was especially evident during the pandemic because cross-protective immunity to the pandemic strain was present among older adults [ ] . during the recent influenza pandemic, % of the deaths occurred in persons < years of age, with children and young adults and middle-aged adults having rates of hospitalization and death to times and to times greater, respectively, than estimates from the years - [ ] . the best available strategy to prevent and control influenza is through influenza vaccination. in the united states, all persons ≥ months of age are recommended to receive influenza vaccine annually. however, influenza vaccine effectiveness can vary from season to season, depending on the match between the vaccine influenza strains and the circulating strains and host factors. in addition, during influenza pandemics, the development and deployment of an influenza vaccine may be delayed. influenza antiviral therapy for persons with severe influenza illness or who are at risk for complications is an important adjunct intervention to the influenza vaccination program, reducing morbidity and mortality during seasonal or pandemic influenza [ ] [ ] [ ] [ ] [ ] [ ] . nonetheless, there is always the possibility of widespread circulation of an influenza virus strain resistant to available antiviral agents, and, in a pandemic situation, the risk of antiviral shortages is ever present. the use of immune-modulating drugs, particularly statins, has been postulated as an additional tool for the treatment and prophylaxis of influenza, especially in countries where influenza vaccine and antiviral agents are not readily available [ , ] . statins have wide-ranging down-regulatory effects on inflammatory and immune mechanisms [ ] [ ] [ ] , and there is some evidence that statin treatment may beneficially alter the clinical course of some infectious diseases [ ] [ ] [ ] [ ] . to date, no randomized clinical trials have been conducted to address whether statins could reduce complications of influenza, although some observational studies have suggested protective effects [ ] [ ] [ ] [ ] . a study by vandermeer et al [ ] , using data from a populationbased influenza surveillance system, found a protective effect of statin use on mortality among patients hospitalized with laboratory-confirmed influenza during the - influenza season. nonetheless, due to the observational nature of the study, biases could potentially explain this association, even after controlling for confounders. we sought to repeat the - influenza season analysis of vandermeer et al [ ] and to analyze the influenza a (h n ) pandemic data from the same surveillance platform to study the possible association between influenza-associated mortality and statin treatment. in this analysis, we take into account potential treatment indication biases through the use of propensity score-matched analysis. this study was conducted with data from the centers for disease control and prevention's (cdc) emerging infections program (eip) influenza hospitalization surveillance. the eip influenza hospitalization surveillance system collects data on persons hospitalized with laboratory-confirmed influenza from october through april of the following year, because influenza typically circulates in the fall to spring months in the northern hemisphere. the exception to this was the influenza pandemic, in which hospitalization data were collected from september , through april , . the eip network comprises selected counties in us states (california, colorado, connecticut, georgia, maryland, minnesota, new mexico, new york, oregon, and tennessee) and includes a catchment area of approximately million people. cases were identified through active surveillance from reports from hospitals and review of infection control logs or hospital laboratory lists. ascertainment of cases was based on laboratory testing ordered by attending healthcare providers for clinical purposes. cases included patients ( ) ≥ years of age, ( ) residing within the eip catchment area, ( ) admitted to a catchment area hospital, and ( ) admitted within days of a positive influenza test either by viral culture, real-time reverse transcription polymerase chain reaction, immunofluorescence antibody staining (indirect or direct), rapid influenza diagnostic test, or any test of unknown type recorded in the medical chart. patients possibly infected with influenza virus during hospitalization ( positive influenza test > days after admission) were excluded as case subjects. demographic, epidemiologic, and clinical information were collected from chart reviews. influenza vaccination status was determined from the medical chart, primary care provider, or via phone interview (of patient or proxy). patients were considered vaccinated for influenza if a vaccine had been administered > weeks before hospitalization, regardless of whether the patient had seasonal vaccine, h n monovalent vaccine (for the pandemic), both seasonal and monovalent vaccine, or unknown vaccine type. if antivirals were administered at any point during the course of illness, a patient was considered treated. age was categorized into groups ( - , - , - , - , and ≥ years). race and ethnicity were determined by chart review or by self-report during patient interviews for vaccination status information. race was categorized into groups (white, black, and other), and ethnicity was categorized as hispanic or non-hispanic. race and ethnicity were analyzed separately. underlying health conditions of interest included asthma, chronic cardiovascular disease (excluding hypertension), chronic metabolic disease, renal disease, chronic lung disease, immunosuppressive disorders (including cancer diagnosis in the months before hospital admission), seizure disorders, history of lymphoma or leukemia, blood disorders, neuromuscular disorders, obesity, and cognitive dysfunction. we combined all underlying chronic disease variables other than cardiovascular disease, chronic metabolic disease, chronic lung disease, renal disease, and asthma into a variable for "other chronic diseases." height and weight were collected during the pandemic but not during the - influenza season. height and weight were used to determine body mass index (bmi), which was used to categorize patients as underweight (bmi < . ), normal weight (bmi . - . ), overweight (bmi . - . ), obese (bmi . - . ), or morbidly obese (bmi ≥ ). the exposure of interest was statin treatment, either before or during hospitalization, which was determined from hospital records. data on statin dose or frequency of administration were not collected. death within days of a positive influenza test was the outcome of interest. mortality after hospital discharge was determined by linkage of hospitalization data with the social security death index (ssdi) by state. linkage was done using registry plus™ link plus (version . ), a probabilistic record linkage program. mortality during hospitalization was determined through chart review and data linkage with ssdi data. this study was submitted for review and approved by the institutional review boards serving the cdc and participating states. propensity scores were used to predict the probability of treatment with statins. the use of propensity scores in observational studies facilitates similar distributions of baseline characteristics between treated and untreated groups, reducing potential treatment selection bias [ ] . logistic regression models were iteratively assessed to determine the balance of covariate proportions between statin treatment groups in the subsequent matched samples. the best and final model was the one that balanced covariates between treatment groups, as determined by standardized differences < . . the final logistic regression model for the - matched sample included age, sex, race, ethnicity, cardiovascular disease, chronic metabolic disease, chronic lung disease, renal disease, asthma, and vaccination status as covariates. the final logistic regression model for the - matched sample included age; sex; race; cardiovascular disease; chronic metabolic disease; chronic lung disease; renal disease; weight category; long-term care residence; vaccination status; and interaction terms for age and race, age and sex, and age and cardiovascular disease. after calculation of propensity scores, a greedy matching algorithm was used to identify untreated patient for each treated patient in the respective matched samples [ ] . the χ test was used to assess differences in characteristics between the statin treatment groups in the unmatched cohort. categorical variables were transformed to indicator variables to facilitate assessment of balance of covariates between statin treatment groups after matching. standardized differences [ ] were used to evaluate measured baseline covariate distributions between statin treatment groups in the matched cohorts. mcnemar's test for matched pairs was used to assess the difference in proportion of deaths between treated and untreated groups. we used cox proportional hazards models with robust standard errors, stratified on matched pairs, to determine the effect of statin treatment on mortality within days of a positive influenza test. we used the method described by rosenbaum [ ] for survival outcomes for determining the sensitivity of point estimates to hidden bias. we conducted statistical analysis using sas software (version . ; sas institute, cary, nc), and openepi (version . . ) was used for post hoc sample size calculation [ ] . table shows demographic and clinical characteristics of treatment groups before matching, for both the - influenza season (statin treatment group n = , nontreatment group n = ) and the pandemic (statin treatment group n = , nontreatment group n = ) cohorts. in the - cohort, the statin treatment group was older, with a greater proportion of males, a greater proportion of whites, and a higher prevalence of chronic medical conditions (with the exception of asthma and "other chronic diseases") compared with the nontreatment group. in the pandemic cohort, the statin treatment group compared with the nontreatment group was older, with a greater proportion of males and whites. the statin treatment group had a higher prevalence of cardiovascular disease, chronic metabolic disease, chronic lung disease, and renal disease, but not of other chronic conditions. the statin treatment group also had a greater proportion of persons considered obese and morbidly obese. influenza vaccination was more prevalent among those in the statin treatment group, for both cohorts. there was no significant difference between the proportion of those treated with antivirals for either cohort. after matching on propensity score (table ) , both the - and pandemic matched samples were balanced on treatment groups. for all covariates, the standardized differences after matching were < . for both cohorts. there were pairs in the - sample. for pairs, the treated case subject died within days, but the untreated case subject did not. there were pairs in which the untreated case subject died within days but the treated subject did not. for pair, both the treated and untreated case subjects died, and for pairs, neither case subject died. the results of mcnemar's test indicate that the -day mortality rates between the treated ( . %) and untreated ( . %) groups were significantly different (p < . ). there were pairs in the - cohort sample. for pairs, the treated case subject died within days but the untreated case subject did not. there were pairs in which the untreated case subject died within days but the treated subject did not. for pairs, both the treated and untreated case subjects died, and for pairs, neither case subject died. the results of mcnemar's test indicate that the -day mortality rates between the treated ( . %) and untreated ( . %) groups were not significantly different (p = . ). cox proportional hazards models with robust standard errors were fit to the matched samples, stratified on matched pairs. the sole predictor variable for the models was statin treatment. we tested post hoc whether logistic regression on the unmatched pandemic cohort would have resulted in a significant point estimate for an effect of statins on mortality. we used a logistic model with backward deletion (and all first-order covariates). because statin treatment was not a covariate selected through stepwise selection, we forced statin treatment into the final model. in a final model that included age, sex, and renal disease as covariates, the adjusted odds ratio (or) for statins was not significant (or = . ; % ci, . - . ). a sensitivity parameter and corresponding bounds were calculated for the observed point estimate from the - matched sample. the results (gamma = . ; maximum p value = . ) indicate that the point estimate is sensitive to hidden bias. an unmeasured confounder that could explain a % difference in the odds of statin treatment between groups could explain the observed association between statin use and mortality. sensitivity analysis for the point estimate for - data was not calculated due to the lack of an observed significant effect. in this analysis, using data from a population-based laboratoryconfirmed influenza hospitalization surveillance platform, we evaluated the effects of statin use over influenza seasons. we found that statins had no statistically significant effect on mortality during the pandemic season, but there was a significant statin effect on reducing mortality during the - b other chronic diseases is a combination of any underlying chronic illnesses mentioned in patient medical records other than cardiovascular disease, chronic metabolic disease, chronic lung disease, renal disease, asthma, and obesity. c any antivirals administered during the course of illness. influenza season. the differential impact of statin treatment on mortality between seasons could be due to differences in circulating strains, because the predominant influenza a virus subtype in - season was h n , whereas influenza a(h n )pdm virus predominated during the pandemic period. age group-specific attack rates among different influenza subtypes can vary, and differences in immune histories by age could have an impact on the different results between the - season and the pandemic. statins have been found to modulate anti-inflammatory effects [ ] ; whether the difference in apparent efficacy of statins between the seasons could be explained by variation in age-specific immune histories or variation in the degree of cytokine dysregulation caused by the different influenza virus subtypes is an area for additional investigation. however, on further examination, the latter association was measurably sensitive to bias and therefore could reflect omissions of covariate measurement rather than an actual relationship between statin treatment and death after influenzaassociated hospitalization. data from the - season was previously analyzed using a multivariable logistic regression model [ ] . results from that analysis showed that after controlling for demographic characteristics, underlying medical conditions, vaccination, and antiviral treatment, the use of statins reduced the odds of death (adjusted or, . ; % ci, . -. ). however, a limitation of observational studies is the lack of random treatment assignment, which can result in sizeable differences in the distribution of covariates between treatment groups. we sought to balance the covariates between the statin-treated and untreated groups by using propensity score analysis. nonetheless, we also found a protective effect of statins on death among laboratoryconfirmed influenza patients hospitalized during the - season. questions persist about the efficacy of statin medications in reducing severe complications of influenza because we showed that our findings could be driven by unmeasured biases. four other studies that looked at statin use and influenza outcomes also found equivocal results. two of them examined the impact of statins in reducing severe disease in adults hospitalized with laboratory-confirmed influenza during the h n pandemic [ , ] . neither found a significant association between use of statins and severe disease (classified as either intensive care unit admission or death), although both were potentially hampered by small sample size. two studies evaluating statin use during multiple influenza seasons in the decade before the pandemic found a protective effect on influenza mortality, although of the studies found only a modest ( % reduction in deaths from pneumonia) effect [ , ] . these latter studies relied entirely on administrative claims data; patients identified with influenza were not laboratory-confirmed, raising concern for misclassification of outcome, and may have been additionally biased by misclassification of exposure, because both studies abstracted data on previous history of statin use but not actual use at the time of the influenza hospitalization. information about whether there is benefit to initiating statin use in patients without other indications for statins at the time of influenza diagnosis would certainly be of clinical and public health interest. in this context, randomized controlled trials (rct) that address initiation of statin treatment in patients with influenza would offer clear advantages. recent rct data have been pessimistic regarding the role of statins in modulating inflammatory responses in infectious disease processes. one rct observed no clinical effect of statins on -day mortality among patients with ventilator-associated pneumonia [ ] ; another showed that statins did not improve clinical outcomes among patients with acute respiratory disease syndrome associated with sepsis [ ] . in contrast, a recent in vitro study showed that statin treatment can protect host cells against influenzainduced inflammation by reducing the production of tumor necrosis factor-α, interleukin- , and interferon-γ, and therefore inhibit influenza a virus replication [ ] . further studies to evaluate the effect of immunomodulatory agents in reducing influenza-related complications may still be warranted, but they may be better suited for settings where these drugs are not used widely. this study has several limitations. we could not determine whether a patient's statin treatment continued throughout the -day follow-up period because we only had medical data for the period of time the patient was hospitalized. the length of exposure to statins before hospitalization was not measured nor was the dose or frequency of statin use before or during hospitalization, which could have a possible effect on the outcome. in addition, identification of death after hospital discharge via data linkage between the ssdi and eip data could result in an underdetection of deaths; the probabilistic linkage algorithm used is highly accurate, but it is not a match-merge of data by, for example, a unique identification number. however, there is no reason to expect that either mortality status would be misclassified or that deaths would be undetected as a result of treatment status or any particular covariate. emerging infections program influenza surveillance sites do not collect detailed data on socioeconomic status or baseline functional status, and data on bmi were not collected during the - influenza season. certainly, an unmeasured covariate such as insurance coverage could hypothetically increase the likelihood of statin treatment prehospitalization while simultaneously reducing the likelihood of death after hospitalization. healthy user bias may certainly apply to the current study as well as most studies cited above [ ] [ ] [ ] [ ] ] . patients being treated with statin medication have been found to have better access to preventive services such as screening services and vaccinations, and therefore they may be healthier at baseline than patients not taking statins [ ] . moreover, those with limited access to care would be more likely to be hospitalized later in the course of illness, and they would have reduced opportunities to respond to medical interventions. during an influenza pandemic, we may have very few tools to prevent and treat influenza virus infection and therefore reduce mortality, because vaccine development can occur very late in the course of the pandemic and antivirals may be in limited quantity and of unknown effectiveness to a novel strain. our study results do not find a definite protective effect of statins on influenzaassociated death. promotion of the use of statins as part of public health pandemic preparedness or for an individual patient's benefit is not warranted based on current available data. influenza illness and hospitalizations averted by influenza vaccination in the united states influenza-associated hospitalizations in the united states estimates of deaths associated with seasonal influenza -united states influenza and the winter increase in mortality in the united states, - cross-reactive antibody responses to the pandemic h n influenza virus global mortality estimates for the influenza pandemic from the glamor project: a modeling study oseltamivir and risk of lower respiratory tract complications in patients with flu symptoms: a meta-analysis of eleven randomized clinical trials outcomes of adults hospitalised with severe influenza antiviral therapy and outcomes of influenza requiring hospitalization in ontario treatment with neuraminidase inhibitors for critically ill patients with influenza a (h n )pdm impact of neuraminidase inhibitor treatment on outcomes of public health importance during the - influenza a(h n ) pandemic: a systematic review and meta-analysis in hospitalized patients patients hospitalized with laboratory-confirmed influenza during the - influenza season: exploring disease severity by virus type and subtype pandemic influenza: a potential role for statins in treatment and prophylaxis how will physicians respond to the next influenza pandemic? beneficial effects of statins on the microcirculation during sepsis: the role of nitric oxide statins in the intensive care unit do statins have a role in preventing or treating sepsis? the effect of statin therapy on infection-related mortality in patients with atherosclerotic diseases prior statin therapy is associated with a decreased rate of severe sepsis statins and sepsis in patients with cardiovascular disease: a population-based cohort analysis statins for the prevention and treatment of infections: a systematic review and meta-analysis pre-admission statin use and inhospital severity of pandemic influenza a(h n ) disease association between use of statins and mortality among patients hospitalized with laboratory-confirmed influenza virus infections: a multistate study influenza and copd mortality protection as pleiotropic, dose-dependent effects of statins influenza morbidity and mortality in elderly patients receiving statins: a cohort study an introduction to propensity score methods for reducing the effects of confounding in observational studies performing a :n case-control match on propensity score observational studies openepi: open source epidemiologic statistics for public health statins as a newly recognized type of immunomodulator effect of immunomodulatory therapies in patients with pandemic influenza a (h n ) complicated by pneumonia effect of statin therapy on mortality in patients with ventilator-associated pneumonia: a randomized clinical trial rosuvastatin for sepsis-associated acute respiratory distress syndrome protective effect of fluvastatin on influenza virus infection association between statins and mortality adherence to lipidlowering therapy and the use of preventive health services: an investigation of the healthy user effect we thank the following personnel: erin parker, mph potential conflicts of interest. w. s. reports personal fees from merck and personal fees from sanofi-pasteur during the conduct of the study; j. m. reports grants from the cdc during the conduct of the study; p. r. reports grants from the cdc during the conduct of the study; and s. m. z. reports grants from the cdc during the conduct of the study. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -rstxyofq authors: tyan, kevin; levin, adriane; avalos-pacheco, alejandra; plana, deborah; rand, eleanor a; yang, helen; maliszewski, laura e; chylek, lily a; atta, lyla; tye, mark a; carmack, mary m; oglesby, n synclaire; burgin, susan; yu, sherry h; leboeuf, nicole r; kemp, jacqueline m title: considerations for the selection and use of disinfectants against sars-cov- in a healthcare setting date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: rstxyofq proper disinfection using adequate disinfecting agents will be necessary for infection control strategies against covid- . however, limited guidance exists on effective surface disinfectants or best practices for their use against sars-cov- . we outlined a process of fully characterizing over products on the epa list n, including ph, method of delivery, indication for equipment sterilization, and purchase availability. we then developed a streamlined set of guidelines to help rapidly evaluate and select suitable disinfectants from list n, including practicality, efficacy, safety, and cost/availability. this resource guides the evaluation of ideal disinfectants amidst practical considerations posed by the covid- pandemic. m a n u s c r i p t there is increasing evidence that rigorous disinfection will be needed to prevent surface transmission of severe acute respiratory virus (sars-cov- ). studies have demonstrated that sars-cov- can remain viable on surfaces for up to hours [ ] , while other human coronaviruses can remain infectious on inanimate surfaces for up to days [ ] . viral shedding from covid- patients can contaminate over % of the surfaces of inside a hospital room [ , ] . one plausible pathway of transmission includes direct deposition of respiratory droplets onto surfaces and re-aerosolization off hospital floors and personal protective equipment (ppe) [ ] . thus, careful and thorough disinfection using proper technique and adequate disinfecting agents must be part of an effective infection control strategy against covid- [ , ] . limited guidance exists on effective surface disinfectants or best practices for disinfectant use against sars-cov- . on march , , the united states environmental protection agency (epa) released list n, a list of commercially available disinfectants that qualify under the epa emerging viral pathogens program for use against sars-cov- [ ] . as of the time of publication, this list includes over unique products encompassing different types of active ingredients. while this list appears extensive, it lacks guidance or discussion of practical concerns that must be taken into consideration when selecting a disinfectant during this pandemic, including efficacy, practicality, safety profile, and availability. as a consequence, healthcare institutions may not be able to dedicate their limited resources to fully understand the scope of available options and their appropriateness in each unique a c c e p t e d m a n u s c r i p t healthcare setting. with dwindling availability of many commercial disinfectants [ ] , a resource is needed to help both healthcare institutions and consumers navigate the list of alternative disinfectants suitable against sars-cov- . considerations that factor into the selection of the ideal disinfectant have previously been discussed [ ] . however, the effects of the covid- pandemic on global supply chains, disinfectant availability, and hospital operations have created new challenges [ ] . in attempting to navigate the extensive catalog of disinfectants on the epa list n, we sought to fill critical data gaps in the listing of each product, including active ingredient concentrations, method of delivery, ph, compatibility for equipment disinfection, and purchase availability (supplemental table ). in order to simplify the process of rapidly evaluating and selecting disinfectants in the context of this pandemic, we offer a contemporaneous set of guidelines (table ) . disinfectants qualify for an emerging viral pathogen claim against sars-cov- if they demonstrate efficacy against a harder-to-kill virus than sars-cov- [ , ] . list n was created on the basis that sars-cov- is an enveloped virus, the subgroup easiest to inactivate compared to hardier large non-enveloped (e.g. adenovirus) and small non-enveloped viruses (e.g. norovirus) [ ] . some products on list n do not have an emerging viral pathogen claim but have been included because they ) demonstrate efficacy against another human coronavirus similar to sars-cov- or ) are epa-approved against select viruses that are harder-to-kill [ ] . a c c e p t e d m a n u s c r i p t crucially, a disinfectant must remain undisturbed and air dry on a surface for a sufficient period of time to inactivate the target pathogen. this contact time is based on efficacy testing submitted to the epa [ , ] . healthcare institutions should take into account the time needed to fully inactivate sars-cov- , as unrealistic contact times (e.g. minutes) may be impossible to adhere to in hospital settings [ ] . hospitals should implement auditing, training, and visual feedback mechanisms that ensure that staff are fully complying with the stated contact times required to disinfect sars-cov- [ , ] . user safety is paramount when selecting disinfectants against sars-cov- . healthcare institutions should prioritize disinfectants that have low toxicity ratings according to the hazardous materials identification system (hmis). furthermore, the ph of the product should be considered, as those in extreme ranges may be unsafe for skin contact or affect environmental safety and disposal requirements [ , ] . ready-to-use (rtu) products may be preferable to concentrated solutions by eliminating the risk of improper dilution or exposure to concentrated disinfectants. finally, the method of application of the disinfectant can impact its safety profile, as disinfectant spray aerosolization has been associated with respiratory irritation and poor asthma control in workers [ , ] . furthermore, studies have established that pre-moistened wipes are equally effective as sprays in reducing bacterial load [ ] , although workers may prefer sprays for more irregular surfaces [ ] . critically, when choosing a spray disinfectant that must be wiped after use, it is important to note that some wipe fabrics may inactivate disinfecting agents (e.g. cotton or cellulose binding of quaternary ammonium compounds) [ ] . to further reduce logistical burden on staff, selected disinfectants should also be compatible with a wide range of surfaces in the hospital. certain disinfectants are compatible only on hard nonporous surfaces whereas others can be applied to soft surfaces like chair cushions or privacy curtains [ ] . some agents, including chlorine bleach (sodium hypochlorite) may also be corrosive to metals and other hospital equipment [ ] and should be implemented sparingly or in conjunction with anti-corrosive agents. a c c e p t e d m a n u s c r i p t the covid- pandemic has caused worldwide shortages of key supplies, including ppe, testing kits, hand sanitizers, and disinfectants. in particular, some of the most popularly used disinfectant products, including pre-moistened wipes, have become difficult to source [ ] . with a disrupted supply chain and large healthcare systems aiming to source new products concurrently, the market for individual disinfectants is unpredictable. hospitals must be prepared with a rank-ordered list of suitable products for their institution based on the aforementioned considerations as well as cost and future availability. the publication of the epa list n was an important step in providing a resource for selecting disinfectants against sars-cov- and can be more easily operationalized in healthcare settings when supplemented with additional data on safety, practicality, and availability. in supplemental table , we curate and simplify relevant information obtained through our research on each product, which entailed locating material safety data sheets (msds) through online databases and manufacturer websites or extracting data from epa registration paperwork. in attempting to better characterize each product on this list, we found that critical details, including ph, compatibility for equipment sterilization, or intended application (household vs. healthcare settings) were difficult to extract or unavailable for many products, thus the resulting database a c c e p t e d m a n u s c r i p t has missing information for several disinfectant products. only a minority of msdss were readily available on consumer-facing websites, with most safety information hidden behind paywalls, requiring product purchase for access, or necessitating burdensome research into epa registration paperwork. this was a major limitation of comprehensive and rapid evaluation of disinfectants, and a new system for making safety data publicly available must be considered in the future. while we also attempted to collect information regarding product cost, vendors, and availability, we found these properties to be overly dynamic to be reliable in a static resource and have omitted this from the final database. given the fluctuating nature of pricing and supply, particularly during the covid- pandemic, we suggest that users curate a rank-ordered list of disinfectants that satisfy the unique considerations of their institution before contacting manufacturers and determining bulk availability and lead times. ultimately, future guidance on disinfectants during times of increased demand must make information on safety, applicability, cost and availability more accessible. the barriers in evaluating and procuring disinfectants against sars-cov- for our healthcare institution compelled us to create this resource as a guide for hospital systems and other end users. we offer a set of important considerations as a framework for addressing institutionspecific needs in the process of selecting the ideal disinfectant to protect patients and staff during this covid- pandemic. efficacy against sars-cov- • does this product have an emerging viral pathogen claim? • what is the wet-contact time required to kill sars-cov- ? safety profile • what is the ph of the product? • does the product have potential for toxicity or irritation? practicality (ease of use, surface compatibility) • what is the method of delivery (pre-moistened wipe, spray, concentrate requiring dilution, etc.)? • can this product be delivered through multiple modalities to allow for flexibility (spray bottle with dry wipe packs vs. saturating wipe rolls in a a c c e p t e d m a n u s c r i p t bucket, etc.)? • what surface types/equipment is the disinfectant compatible with? availability and cost • is this product currently commercially available, and will it remain available for repurchase? • is this product economical for the healthcare institution? 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 greater boston pandemic fabrication team (panfab) c/o harvard-mit center for regulatory science department of dermatology, brigham and women's hospital laboratory of systems pharmacology, department of systems biology computational health informatics program, boston children's hospital deland fellow in health care and society, office of the president, brigham and women's hospital aerosol and surface stability of sars-cov- as compared with sars-cov- persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient aerosol and surface contamination of sars-cov- observed in quarantine and isolation care aerodynamic analysis of sars-cov- in two wuhan hospitals investing in our first line of defense: environmental services workers disinfectants for use against sars-cov disinfectant demand from coronavirus concerns challenges specialty chemical supply chain selection of the ideal disinfectant opening up new supply chains focus on surface disinfection when fighting covid- a novel color additive for bleach wipes indicates surface coverage and contact time to improve thoroughness of cleaning surface disinfection: treatment time (wipes and sprays) versus contact time (liquids) factors in the selection of surface disinfectants for use in a laboratory animal setting the effects of corrosive substances on human bone, teeth, hair, nails, and soft tissue occupational exposure to disinfectants and asthma control in us nurses association of occupational exposure to disinfectants with incidence of chronic obstructive pulmonary disease among us female nurses effectiveness of cleaning-disinfection wipes and sprays against multidrug-resistant outbreak strains disinfectant sprays versus wipes: applications in behavioral health quaternary ammonium disinfectant issues encountered in an environmental services department novel colour additive for bleach disinfectant wipes reduces corrosive damage on stainless steel why clorox wipes are still so hard to find above all we thank the members of the greater boston pandemic fabrication team (panfab) for technical, administrative, and logistic support necessary for the execution of this project.membership found at https://www.panfab.org/the-team-and-the-project/consortium-members. a c c e p t e d m a n u s c r i p t key: cord- -e rc mvu authors: piantadosi, anne; mukerji, shibani s; chitneni, pooja; cho, tracey a; cosimi, lisa a; hung, deborah t; goldberg, marcia b; sabeti, pardis c; kuritzkes, daniel r; grad, yonatan h title: metagenomic sequencing of an echovirus genome from cerebrospinal fluid of a patient with aseptic meningitis and orchitis date: - - journal: open forum infect dis doi: . /ofid/ofx sha: doc_id: cord_uid: e rc mvu enteroviruses cause a wide spectrum of clinical disease. in this study, we describe the case of a young man with orchitis and aseptic meningitis who was diagnosed with enterovirus infection. using unbiased “metagenomic” massively parallel sequencing, we assembled a near-complete viral genome, the first use of this method for full-genome viral sequencing from cerebrospinal fluid. we found that the genome belonged to the subgroup echovirus , which is a common cause of aseptic meningitis but has not been previously reported to cause orchitis. enteroviruses cause a wide spectrum of clinical disease. in this study, we describe the case of a young man with orchitis and aseptic meningitis who was diagnosed with enterovirus infection. using unbiased "metagenomic" massively parallel sequencing, we assembled a near-complete viral genome, the first use of this method for full-genome viral sequencing from cerebrospinal fluid. we found that the genome belonged to the subgroup echovirus , which is a common cause of aseptic meningitis but has not been previously reported to cause orchitis. keywords. enterovirus; meningitis; metagenomics; orchitis. a previously healthy man in his s developed unilateral testicular pain and swelling. four days later, he developed headache and fever. he presented to our institution, where he was febrile to . °f with mild meningismus; testicular swelling and tenderness had resolved. the combination of symptoms raised concern for mumps in the setting of a local outbreak, although parotitis was absent. cerebrospinal fluid (csf) analysis showed total nucleated cells/µl ( % neutrophils, % monocytes, % lymphocytes), glucose of mg/dl (serum glucose of mg/dl), and total protein of mg/dl. he was treated empirically with vancomycin, ceftriaxone, and acyclovir. cerebrospinal fluid enterovirus polymerase chain reaction (pcr) was positive, antimicrobials were discontinued, and the patient recovered fully. mumps serology was positive for immunoglobulin (ig)g and negative for igm, consistent with his reported history of vaccination. a urine culture for mumps performed by the massachusetts department of health state laboratory was negative. cerebrospinal fluid gram stain and culture were negative, as were csf herpes simplex virus and pcr, lyme pcr, and testing for syphilis via the venereal disease research laboratory test. given the relatively unusual presentation of orchitis and meningitis, we performed metagenomic sequencing to obtain additional genomic information about the particular strain of enterovirus and to identify any potential copathogens including mumps virus. we performed metagenomic sequencing and enterovirus genome assembly using methods developed and validated by our group [ , ] . full methods are described in the supplementary appendix. unbiased metagenomic sequencing allows detection of any potential pathogens in a sample. we performed metagenomic analysis of all sequencing reads from this patient's csf and identified enterovirus; no other pathogen, including mumps virus, was found. we assembled a near-full-length enterovirus genome ( base pair [bp], median depth of coverage ×), which included the '-untranslated region (utr) and near-complete coding region, but not the ' end ( bp) of the coding region or the '-utr. by comparing this genome to published enterovirus genomes, we found that this virus belongs to echovirus subgroup ( figure a ), a member of the highly diverse enterovirus b species group, which includes most echoviruses, coxsackie b viruses, and coxsackie a virus [ ] . echovirus has not previously been associated with orchitis, but other enteroviruses have, including echovirus [ ] and coxsackieviruses a and b [ , ] . therefore, we investigated whether the virus we identified was a recombinant between echovirus and a subgroup that is more commonly associated with orchitis, because recombination between enteroviruses occurs frequently [ ] . we first examined the vp gene, which encodes a capsid protein that interacts with host cell receptors and may therefore confer tropism for specific tissue such as the testes. in phylogenetic analysis of the vp gene, our virus again clustered with echovirus , rather than a subgroup more commonly associated with orchitis ( figure b ). in the kb at the ' end of the genome, we observed similarity between our genome and coxsackievirus b (supplementary figure a) but did not observe specific evidence of recombination in this region (supplementary text and supplementary figure b) . echovirus is one of the most common causes of aseptic meningitis worldwide. different lineages of echovirus have been linked to geotemporally distinct outbreaks [ ] [ ] [ ] . this is the first report of echovirus infection associated with orchitis, although it has been reported with other enteroviruses. relatively few infectious agents have been described to present with both orchitis and meningitis (table ) . although it is interesting to speculate that the strain we identified may possess characteristics associated with testicular tropism, we were unable to formally assess this possibility because the virus examined was from csf and not testicular tissue. it is also possible, although unlikely, that the patient experienced distinct infections, first with mumps or another pathogen causing orchitis, and subsequently with enterovirus causing meningitis. our results underscore the utility of metagenomic sequencing in identifying pathogens in csf, an approach that has been used previously to identify viruses in csf based on identification of viral reads and subgenomic contigs [ , ] . metagenomic sequencing has also been used to sequence viral genomes from brain tissue [ , ] , sometimes requiring the use of additional methods such as pcr amplification to obtain full genomes [ , ] . our results extend these methods by demonstrating the first assembly of a viral genome from csf using metagenomic sequencing. therefore, metagenomic sequencing offers the opportunity to aid not only in diagnosis but also in molecular epidemiology of viruses causing central nervous system infection. finally, this case illustrates the importance of maintaining a broad differential diagnosis in the setting of a known viral outbreak, including uncommon presentations of common infections. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. toxoplasma gondii [ ] aspergillus species schistosoma species a epididymitis and orchitis typically present. genomic surveillance elucidates ebola virus origin and transmission during the outbreak enhanced methods for unbiased deep sequencing of lassa and ebola rna viruses from clinical and biological samples evidence for frequent recombination within species human enterovirus b based on complete genomic sequences of all thirty-seven serotypes aseptic meningitis and orchitis associated with echovirus infection a case of coxsackie a virus infection with orchitis index of suspicion molecular epidemiology of echovirus : temporal circulation and prevalence of single lineages widespread circulation of a new echovirus variant causing aseptic meningitis and non-specific viral illness molecular epidemiology of echoviruses and in russia: different properties of genotypes within an enterovirus serotype a variegated squirrel bornavirus associated with fatal human encephalitis acute west nile virus meningoencephalitis diagnosed via metagenomic deep sequencing of cerebrospinal fluid in a renal transplant patient next-generation sequencing in neuropathologic diagnosis of infections of the nervous system human coronavirus oc associated with fatal encephalitis diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing next-generation sequencing for diagnosis and tailored therapy: a case report of astrovirus-associated progressive encephalitis a case of childhood brucellosis with neurological involvement and epididymo-orchitis post-prostate biopsy infection with escherichia coli st leading to epididymo-orchitis and meningitis caused by gram-negative bacilli tuberculous meningitis: pitfalls in diagnosis tuberculoma of the brain with tuberculous adenitis and epididymitis epididymo-orchitis and central nervous system nocardiosis in a bone marrow transplant recipient for acute lymphoblastic leukemia orchitis, parotitis and meningoencephalitis due to lymphocytic-choriomeningitis virus west nile virus encephalitis with myositis and orchitis disseminated toxoplasmosis presenting as symptomatic orchitis and nephrotic syndrome we thank daniel park and simon ye for guidance with computational analyses.financial support. this work was funded by a broadnext gift from the broad institute. a. p. was supported by massachusetts general hospital (training grants t ai and kl tr ). s. s. m. was supported by harvard medical school (t ag ).potential conflicts of interest. all authors: no reported conflicts of interest.all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -z eogm authors: vora, surabhi b; waghmare, alpana; englund, janet a; qu, pingping; gardner, rebecca a; hill, joshua a title: infectious complications following cd chimeric antigen receptor t-cell therapy for children, adolescents, and young adults date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: z eogm background: infectious complications of chimeric antigen receptor (car) t-cell immunotherapy in children and young adults have not been well described. methods: medical records of patients ≤ years old receiving cd car t-cell infusion (cti) at a single institution between and were reviewed. the number of infections per days-at-risk (infection density) in the days preceding and – and – days after cti was calculated. poisson regression and cox analyses were utilized to identify risk factors for infections. results: eighty-three patients received cti during the study period. most patients ( %) had refractory or relapsed acute lymphoblastic leukemia (all). infections occurred in % of patients in the days before cti (infection density, . ) and in % of patients in the first days following cti (infection density, . ). infection density decreased to . in the – days post-cti. most infections were bacteremias ( %) or respiratory viral infections ( %). pre-cti risk factors associated with infection included prior hematopoietic cell transplantation (hct), immunoglobulin g (igg) level < mg/dl, and lymphodepletion other than cyclophosphamide plus fludarabine; post-cti risk factors included higher-severity crs and igg < mg/dl. conclusions: infection rates in children and young adults receiving cd car t-cell therapy increase in the first month and then decline. understanding types and timing of infections and contributing risk factors may help inform prophylactic and monitoring strategies. specific attention should be given to patients with prior hct, severe hypogammaglobulinemia, and severe crs. immunotherapy using chimeric antigen receptor (car) t-cells for hematologic malignancies and other diagnoses is increasing rapidly [ ] . this approach has resulted in high response rates in children with refractory or relapsed (r/r) b-cell acute lymphoblastic leukemia (b-all) [ ] [ ] [ ] . the first commercially available cd car t-cell therapy, tisangenlecleucel (kymriah), was approved by the food and drug administration in [ ] . patients under consideration for car t-cell therapy are at high risk for infections due to extensive prior antitumor therapies. before car t-cell infusion (cti), patients receive lymphodepleting chemotherapy that leads to additional cytopenias. furthermore, cd car-t cells may deplete normal cd b cells in the host, potentially causing prolonged b-cell aplasia and low immunoglobulin g (igg) levels [ , ] . finally, these patients often develop cytokine release syndrome (crs) following cti, which may require treatment with anti-interleukin (il- ) therapies (eg, tocilizumab), steroids, and admission to the intensive care unit (icu), with associated increased risk for immunosuppression and nosocomial infections [ ] [ ] [ ] . the infectious complications of car t-cell therapy have not been well studied in children and young adults. little is known about optimal prophylactic strategies in this setting. two studies have demonstrated a relatively high rate of infections in adult patients after cd cti, especially in the first days [ , ] . patient factors such as underlying all, increased number of prior chemotherapy courses, higher car t-cell doses, and crs were associated with higher infection rates. the majority of early infections were bacterial, whereas respiratory virus infections predominated at later time points. in this study, we examine the epidemiology of and risk factors for infections occurring in the first days after cd cti in children and young adults. this study was approved by the institutional review board at seattle children's hospital. we reviewed medical records of patients aged - years receiving cd car t cells [ ] at our institution between and . the majority of patients remain under our center's care for a minimum of days after therapy, as this is the time frame when the majority of complications are expected [ , ] . each patient's lymphodepletion regimen was determined by the treating physician. bacterial prophylaxis was not routinely prescribed. patients with a history of prior hematopoietic cell transplantation (hct) were routinely started on acyclovir prophylaxis if not already receiving it. the type and duration of fungal prophylaxis were prescribed at the discretion of the treating physician. all patients were prescribed prophylaxis for pneumocystis jirovecii with trimethoprim-sulfamethoxazole or inhaled pentamidine. intravenous immunoglobulin g (ivig) supplementation was recommended for patients with igg levels < mg/dl. empiric antimicrobial therapy was prescribed for fever and neutropenia. further details of the lymphodepleting regimens and supportive care approaches for patients who developed crs are in the supplementary data. we reviewed medical records for infections occuring in the days before and after cti. patients contributed data up to days post-cti; the date of death; the date of loss to follow-up; or the date of receipt of additional antitumor therapies for relapse, repeat cti, or as conditioning for hct, whichever occurred first. absolute neutrophil (anc) and lymphocyte (alc) counts were collected for each patient before lymphodepletion, from all available laboratory data between days and post-cti, and on day (per study protocols) post-cti. igg levels were collected before lymphodepletion and on days and (per study protocols) post-cti. treatment for crs, including use of tociluzimab and/or steroids, was recorded. the primary outcome of interest was infection in the days post-cti. an infection episode was defined as the presence of clinical findings plus corroborating laboratory, radiographic, histopathologic, and/or microbiologic evidence. infections were classified as bacterial (bacteremia or site infection), viral (respiratory or other), or fungal (proven or probable) [ ] . infection onset was defined as the day of initial positive diagnostic test or clinical diagnosis. infections were excluded if they were already present at the time of cti. infection severity was categorized as (mild) if no treatment was required, (moderate) if only oral treatment or minimal supportive care was required, (severe) if intravenous therapy or hospitalization was required, if life threatening, or if fatal [ ] . testing for infection was sent based on provider discretion guided by symptoms, further outlined in the supplementary data. further details pertaining to the assessment of the timing, type, and severity of each infection are also described in the supplementary data. the severity of crs was graded from - as previously described [ ] , and definitions of each grade are shown in supplementary table . descriptive statistics (median, range, percentage) are reported for key variables. we calculated the infection density per days-at-risk based on the number of infections per person-days-at-risk and multiplied by . this was calculated for the days before cti and the - -and - -day periods after cti. the estimates for infection densities are only based on data obtained during the person-days-at risk contributed per patient. we also demonstrate the cumulative incidence of any and each type of infection in the first days after cti, treating death and loss to follow-up as competing risk events. poisson regression was utilized to identify associations between pre-cti factors and infection density within the first days after cti. time-dependent cox proportional hazards models were used to assess the impact of pre-and post-cti factors on the time to first infection within days after cti. for all factors, only data occurring before an infection event were included. for each infection event, the anc and alc values from the day of the event were considered as dichotomous data points (anc < or no, alc < or no). when a value for that day was not available, the most recently available value was used instead. for both poisson and cox regression, variables with a p value of <. in univariate models were considered for multivariate adjusted models. poisson and cox models were evaluated for overfitting or underfitting and schoenfeld residuals, respectively. patients were censored from the study before day post-cti if they died, were lost to close follow-up, or received further lymphodepleting chemotherapy in the setting of relapse, repeat cti, or as conditioning for hct. eighty-three patients received cti during the study period. the median duration of follow-up (range) was ( - ) days. patient and treatment characteristics are described in table . all patients had underlying b-all except for patient with mixed leukemia and with b-cell lymphoma. all patients had relapsed or refractory disease. the median age (range) was ( - ) years. forty-six patients ( %) had previously undergone allogeneic hct, and none were on immunosuppresive therapy or had graft-vs-host disease for at least weeks before cti. before receipt of lymphodepleting chemotherapy, % had an alc < cells/mm , % had an anc < cells/mm , and % had a serum igg < mg/dl. the most common lymphodepletion regimen consisted of fludarabine plus cyclophosphamide ( %). doses of car t cells ranged from . × to × car t cells/kg. details of antimicrobial prophylaxis are outlined in table . at the time of cti, no patient had a positive blood culture within hours or had fever with clinical signs of infection. the majority of patients ( %) experienced neutropenia (anc < cells/mm ) at the time of, or within days of, cti. of these, % for whom complete data were available did not recover from neutropenia (defined as measurements of anc > cells/mm ) by day post-cti. three patients died while still neutropenic in this time period. for the patients who were neutropenic and did recover by day ( %), the median time to recovery was days. severe hypogammaglobulinemia (igg < mg/dl) was identified in % of patients at day (table ) . by day post-cti, % of patients with available data remained neutropenic and % lymphopenic. of patients with igg levels available, % remained hypogammoglubulinemic with a median igg level of mg/dl (irrespective of igg supplementation). forty-eight ( %) patients had an icu admission in the days post-cti. crs occurred in % of patients at a median (range) of ( - ) days after infusion ( table ). the majority of these cases were categorized as grade or ( %), with crs grade or higher occuring in patients ( %). fortythree ( %) patients received treatment for crs with either tocilizumab and/or steroids. forty-five ( %) patients had at least infection in the days before cti, as detailed in supplementary table . forty-eight percent of the infections in this time period were bacterial, and % were viral. nine patients ( %) were being treated for proven or probable fungal infections. the infection density for this time period was . infections per patient-days-at-risk ( figure ). thirty-three patients ( %) had incident infections in the first days post-cti (table ) . twenty infections ( %) were bacterial, including instances of bacteremia. of these episodes of bacteremia, were caused by gram-negative organisms, by gram-positive bacteria, and all occurred within the first days post-cti ( figure ). three of the patients who developed bacteremia had infection with an organism that was identified in the pre-cti period. sixteen patients had viral infections, the majority of which were due to respiratory viruses ( % of total infections). two patients developed herpes zoster, with skin manifestations in both; neither patient was taking acyclovir prophylaxis. one patient with pre-cti probable pulmonary invasive mold infection on mold-active therapy with voriconazole was found to have proven pulmonary infection with cunninghamella on day post-cti. it is unclear whether this represented worsening of previous infection or new infection. the cumulative incidences of infections overall and by infection type are in figure . the infection density during the first days was . infections per days-at-risk ( figure ). forty-eight patients contributed data during this time period, with a median duration of follow-up (range) of ( - ) days. there were viral infections in this time period, which comprised the majority of infections ( %). all were due to respiratory viruses (table ) . five patients had bacterial infections, and there were no fungal infections. the infection density in the - days post-cti decreased to . per days-at-risk ( figure ). table demonstrates the severity of infections. between and days after cti, mild or moderate infections accounted for of total episodes ( %), most of which were viral infections. there were severe infections ( %) and ( %) lifethreatening infections, most of which were bacterial. there were no fatal infections in the first days post-cti. one death occurred on day post-cti due to septic shock with aeromonas hydrophila. the proportion of patients with any infection in the days post-cti stratified by crs grade is shown in figure a . a higher proportion of patients with higher-severity crs had infections; % ( % confidence interval [ci], %- %) had no crs, % had grade ( % ci, %- %), % had grade table . prior hct and igg < mg/dl were associated with increased infection density but did not reach statistical significance in the adjusted model. lymphodepletion with combination cyclophosphamide and fludarabine was associated with significantly decreased infection density (rate ratio, . ; % ci, . - . ) compared with other regimens in the adjusted model. age, sex, refractory vs relapsed b-all status, car t-cell dose, pre-car t-cell infections, and prelymphodepletion neutropenia and lymphopenia were not associated with increased infection density. in a cox proportional hazards model of the impact of preand post-cti variables on time to first infection, prior hct (hazard ratio [hr], . ; % ci, . - . ) and post-cti hypogammaglobulinemia (hr, . ; % ci, . - . ) were associated with increased infection risk in the first days in the adjusted model (table ). this analysis also confirmed the decrease in infection risk with cyclophosphamide and fludarabine lymphodepletion. severe crs was associated with an increased risk for infection but did not reach statistical significance in the adjusted model. this study is the first in-depth description of the frequency, type, severity, and risk factors for infections following cd- car t-cell therapy in children, adolescents, and young adults. overall, of patients ( %) experienced or more infections in the first days after cti. infection density more than doubled in the first days post-cti when compared with the days pre-cti and then decreased in the subsequent - days post-cti. pre-cti hct, lymphodepletion with a regimen other then cyclophosphamide plus fludarabine, and post-cti hypogammaglobulinemia were associated with increased infection. although the overall incidence of any infection in the first month is similar to that found in adults with all following cti [ ] , the infection density of . infections per days-at-risk was higher in our cohort [ ] . as in the adult studies, our patients experienced a predominance of bacterial infections, specifically bacteremias, especially within the first weeks post-cti. we observed a higher incidence of respiratory viral infections compared with findings in adult cti recipients, which may be due to the younger age of our patients. respiratory viral infections are common in pediatric immunocompromised populations [ , ] . one patient ( %) was diagnosed with a proven invasive mold infection on day post-cti while receiving voriconazole for previously diagnosed probable invasive mold infection. this individual had concomitant severe neutropenia and mild crs treated with tocilizumab. it is unclear whether this infection represented new fungal disease or worsening of the previously diagnosed infection. our data suggest that prior hct and hypogammaglobulinemia may be risk factors for infections in the first days post-cti. interestingly, preexisting infection and prelymphodepletion lymphopenia and neutropenia did not significantly influence risk of infection. lymphodepletion with the combination of cyclophosphamide and fludarabine was associated with a decreased incidence of infection in the short term. although this combination regimen has been associated with improved cancer outcomes after cd car t-cell therapy in all [ ] , a relationship with decreased infection has not been previously demonstrated. in our cohort, those patients who received car t-cell therapy more recently were more likely to have received this combination lymphodepletion. these patients may also have been more likely to have received antibacterial prophylaxis or have received car t-cell therapy earlier in their all disease process. in addition, cyclophosphamide dosing of g/m may have caused more bone marrow suppression than the combination conditioning regimen with a lower cyclophosphamide dose ( . g/m ). unlike previous studies, we did not demonstrate a link between higher car t-cell doses and infection. however, our dose range was narrower than those used in previous studies in adult patients. prior studies in adult car t-cell recipients with lymphoma, chronic lymphocytic leukemia (cll), and all demonstrated that severe crs (grade or higher) was associated with increased infections [ , ] . in our patients with all, we found a similar association, but this did not reach statistical significance. however, we had fewer patients with severe crs than in other studies, which may have limited our ability to identify a clear link with infection. the low rates of crs in this cohort may be related to the different car t-cell product and/or an early intervention strategy for crs [ ] . neutropenia is well known to be associated with increased risk of bacterial infections [ ] . in a study of adult cti recipients, the median time to neutrophil recovery was days, but prolonged cytopenias have been demonstrated previously, even in patients with mrd-negative remission after car t-cell therapy [ , , , ] . in our study, almost half of the pediatric patients remained neutropenic at day , with persistent neutropenia through day in % of patients. given that % of bacterial infections in the first days occurred during neutropenia [ ] , this has important implications for the longer-term management of patients with persistent cytopenias. for patients in whom records were available for the - day period post-cti, infection rates dropped to a rate even lower than in the pre-cti period. this is despite the fact that sicker patients were less likely to return to their home centers after the first month and therefore were more likely to be included in our analysis. one infection-related death occurred on day due to multiorgan failure attributed to bacterial sepsis. the infection density in the - -day time period in this study was similar to that found beyond days in adult cti recipients [ ] . persistent b-cell aplasia is a known effect of cd car t-cell therapy and indeed can serve as a proxy of persistence of car t cells themselves [ ] . we found that % of patients had igg levels of < mg/dl by days post-cti, and severe hypogammaglobulinemia was associated with increased infection risk. persistent hypogammoglobulinemia is also a common feature after cti in adults [ , , ] . further study of the duration and extent of these deficits could influence infection prevention strategies such as vaccination and more standardized administration of ivig supplementation. standardization of antimicrobial prophylaxis in patients receiving cti may help prevent infections. specifically, we identified patients who developed herpes zoster in the first month after cti, both of whom had not received antiviral prophylaxis. we have now instituted a policy of antiviral prophylaxis with acyclovir for all patients starting at lymphodepletion and continuing for at least days. we are also instituting standard appoaches to antibiotic prophylaxis during neutropenia in patients who are expected to have a prolonged duration (> days) of anc ≤ /mm . ensuring that prophylaxis covers previously identified infections is an important consideration. indeed, of the patients with bacteremia in the - -day post-cti period had preceding bacteremia with the same organism. although there was only episode of invasive fungal disease, our standard approach to antifungal prophylaxis has also evolved. fluconazole is given to all patients during neutropenia; for patients with a history of mold infection, we consider starting or continuing a mold-active azole. the optimal type and duration of prophylactic regimens need further study [ ] . this study has limitations given the retrospective design and use of data from a single center. analyses of infection events beyond days after cti included fewer patients due to loss to follow-up after patients returned to their primary oncologists. this may have resulted in biasing analyses during this time period toward sicker patients. our patients received variable antimicrobial prophylaxis regimens, and our analysis was not powered to perform risk factor analysis for each type of infection individually; risks may vary for viral, bacterial, and fungal infections. it is possible that patients with lymphopenia and neutropenia were more likely to receive antimicrobial prophylaxis, which may have altered our ability to detect an association between these factors and infection outcomes. assigning causality for the infections in the early period after cti is difficult. many of the infections may not be directly attributable to the product itself given the underlying risk factors, the conditioning lymphodepleting chemotherapy, and the development and treatment of crs. in fact, the infection characteristics in adult patients were found to be similar to all patients receiving salvage chemotherapy [ ] . in addition, these data may not be generalizable to car t-cell treatments for other hematologic or solid malignancies. finally, the use of different car t-cell constructs or concurrent antitumor therapies could likely affect infection risk as well. increasing use of car t-cell therapy for the treatment of malignancies is leading to improvements in survival for high-risk children with all, while also posing risks for infections, particularly during the early period after cti. our results suggest that viral, bacterial, and fungal prophylaxis and lymphodepletion regimens need to be carefully considered in the setting of car t-cell therapy. patients with previous hct, hypogammaglobulinemia, and severe crs may be at highest risk. further study of patients with standardized prophylactic regimens and long-term follow-up will be useful for optimizing treatment guidelines for these high-risk children. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. chimeric antigen receptor therapy intent-to-treat leukemia remission by cd car t cells of defined formulation and dose in children and young adults tisagenlecleucel in children and young adults with b-cell lymphoblastic leukemia chimeric antigen receptor t cells for sustained remissions in leukemia fda approval brings first gene therapy to the united states car-t -and a side order of igg, to go? -immunoglobulin replacement in patients receiving car-t cell therapy late events after treatment with cd -targeted chimeric antigen receptor modified t cells recent advances in car t-cell toxicity: mechanisms, manifestations and management pediatric acute lung injury and sepsis investigators (palisi) network. management guidelines for paediatric patients receiving chimeric antigen receptor t cell therapy inflammatory and infectious syndromes associated with cancer immunotherapies infectious complications of cd -targeted chimeric antigen receptor-modified t-cell immunotherapy cytokine release syndrome grade as a predictive marker for infections in patients with relapsed or refractory b-cell acute lymphoblastic leukemia treated with chimeric antigen receptor t cells revision and update of the consensus definitions of invasive fungal disease from the european organization for research and treatment of cancer and the mycoses study group education and research consortium blood and marrow transplant clinical trials network trial . infections after transplantation of bone marrow or peripheral blood stem cells from unrelated donors current concepts in the diagnosis and management of cytokine release syndrome cytomegalovirus in pediatric hematopoietic stem cell transplantation: a case-based panel discussion of current challenges a multicenter consortium to define the epidemiology and outcomes of inpatient respiratory viral infections in pediatric hematopoietic stem cell transplant recipients cd car-t cells of defined cd +:cd + composition in adult b cell all patients preemptive mitigation of cd car t-cell cytokine release syndrome without attenuation of antileukemic efficacy meta-analysis: antibiotic prophylaxis reduces mortality in neutropenic patients clinical utilization of chimeric antigen receptor t cells in b cell acute lymphoblastic leukemia: an expert opinion from the european society for blood and marrow transplantation and the american society for blood and marrow transplantation late events after treatment with cd -targeted chimeric antigen receptor modified t cells financial support. this key: cord- -zhlvvuj authors: nordén, rickard; magnusson, jesper; lundin, anna; tang, ka-wei; nilsson, staffan; lindh, magnus; andersson, lars-magnus; riise, gerdt c; westin, johan title: quantification of torque teno virus and epstein-barr virus is of limited value for predicting the net state of immunosuppression after lung transplantation date: - - journal: open forum infect dis doi: . /ofid/ofy sha: doc_id: cord_uid: zhlvvuj background: major hurdles for survival after lung transplantation are rejections and infectious complications. adequate methods for monitoring immune suppression status are lacking. here, we evaluated quantification of torque teno virus (ttv) and epstein-barr virus (ebv) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. methods: this prospective single-center study included patients followed for years after transplantation. bacterial infections, fungal infections, viral respiratory infections (vrti), cytomegalovirus (cmv) viremia, and acute rejections, as well as ttv and ebv levels, were monitored. results: the levels of torque teno virus dna increased rapidly after transplantation, likely due to immunosuppressive treatment. a modest increase in levels of epstein-barr virus dna was also observed after transplantation. there were no associations between either ttv or ebv and infectious events or acute rejection, respectively, during follow-up. when tacrolimus was the main immunosuppressive treatment, ttv dna levels were significantly elevated – months after transplantation as compared with cyclosporine treatment. conclusions: although replication of ttv, but not ebv, appears to reflect the functionality of the immune system, depending on the type of immunosuppressive treatment, quantification of ttv or ebv as biomarkers has limited potential for defining the net state of immune suppression. for patients with end-stage lung disease, limited life expectancy, and otherwise acceptable physical condition, lung transplantation may be a life-saving therapeutic option. the -year survival rate is only approximately % in most centers, and major limiting factors for the outcome of lung transplantation are the frequent occurrence of infectious complications and rejection of the transplanted organ [ ] . standard immunosuppression, to prevent graft rejection, consists of a combination of immunosuppressive drugs that subvert b and t cells [ ] [ ] [ ] . currently, there is a lack of an easy-to-use marker that accurately predicts the net effect of the combined immunosuppression. such a biomarker would be an important tool in the management of patients with compromised immune function to identify overor underimmunosuppression and evaluate the risk of infectious complications and acute rejections. viruses are often only viewed as pathogenic entities, but there are several examples of viruses that are frequently found in healthy individuals without causing obvious disease [ , ] . torque teno virus (ttv) is a human dna virus that causes asymptomatic viremia with a high prevalence in the general population [ ] [ ] [ ] [ ] [ ] [ ] [ ] . cell-mediated immunity is considered important in controlling ttv infection [ ] [ ] [ ] [ ] . accordingly, serum levels of ttv-dna increase dramatically in patients who have undergone solid organ transplantation, presumably as a result of immunosuppression [ , , ] . epstein-barr virus (ebv) is another dna virus, commonly acquired early in life, with a high prevalence in us adults [ ] , that establishes latent infection in memory b cells [ , ] . the levels of ebv often increase in blood after immunosuppressive treatment, and ebv can cause post-transplant lymphoproliferative disorder (ptld) when the immune system is repressed. hence, both ttv and ebv have previously been suggested as surrogate markers of the net state of immunosuppression [ , , ] . the aim of the present study was to evaluate levels of ttv and ebv in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. all patients over the age of years who received a single or double lung transplant, who survived the initial postoperative intensive care period and remained in gothenburg during the follow-up period, between january , , and april , , at the sahlgrenska university hospital transplant centre, gothenburg, sweden, were asked to participate in this prospective single-center cohort study. all included subjects underwent follow-up (fu) visits at , , , . , , , , , and months after transplantation. at every fu visit, whole blood, serum, and nasopharyngeal samples (nph) were collected. protocol bronchoscopies were performed at , , and months post-transplantation and when indicated based on clinical presentation. bronchoalveolar lavage (bal) samples were collected at every bronchoscopy. all bal samples underwent direct microscopy for early detection of aspergillus hyphae and were cultured for bacteria and fungi and tested for legionella pneumophila, pneumocystis jirovecii, and human cytomegalovirus (cmv) using real-time polymerase chain reaction (pcr). bal samples from patients with cystic fibrosis were routinely cultured for mycobacterium tuberculosis and atypical mycobacteria. bacterial and fungal culture testing from blood, urine, and sputum was performed upon suspicion of infection. nph and bal samples from every fu visit, as well as additional nph samples obtained upon suspicion of airway infection between scheduled fu visits, were analyzed by multiplex real-time pcr for detection of airway pathogens. serum samples obtained at pretransplant evaluation were used for ttv-dna and ebv-dna quantification. for quantification of ttv and ebv during fu, serum and whole blood samples were used, respectively. induction therapy consisted of rabbit antithymocyte globulin, which was given for - consecutive days together with methylprednisolone intravenously. post-transplantation immunosuppression included prednisone . mg/kg/d and mycophenolate mofetil (mmf) g/d. the patients then received either oral cyclosporine (csa; - mg/kg), adjusted to maintain a serum level of - ng/ml, or tacrolimus (tac; . mg/kg) given orally divided in doses daily, adjusted to maintain a serum level of - ng/ml. the choice between csa and tac was made based on clinical presentation. patients previously treated with tac and patients with cystic fibrosis were given tac. there was also a preference for tac if the recipient was younger. the dosage of immunosuppression was gradually lowered during fu. further changes in immunosuppressive therapy were based on clinical presentation. four patients, who either underwent retransplantation or had previous immunosuppressive treatment due to autoimmune conditions, were given nonstandard immunosuppression therapy based on previous exposure to immunosuppressive drugs. all patients received a combination of mg of sulfametoxazol and mg of trimetoprim thrice weekly to prevent pneumocystis jirovecii infection. patients seropositive for cmv at the pretransplant evaluation were given valganciclovir at a dose of mg daily for months. patients seronegative for cmv pretransplant while the organ donor tested positive (ie, cmv mismatches) were given the same treatment for months. bacterial infection was defined as a positive bacterial culture in conjunction with symptoms of clinical infection or, in the absence of positive culture, symptoms consistent with bacterial infection that was treated with antibiotics. fungal infection was defined as significant presence of fungi in culture from a sterile location in conjunction with symptoms of infection according to the european organization for research and treatment of cancer (eortc) criteria [ ] . vrti or mycoplasma pneumoniae infection was defined as detection of a pathogen by multiplex real-time pcr in nph or bal. cmv viremia was defined as elevated levels of cmv-dna that prompted antiviral therapy. cmv-seronegative recipients were considered to have viremia if cmv-dna was detected, whereas recipients seropositive for cmv prior to transplantation where considered to have cmv viremia only if the level was above . log ( ) copies/ml. to distinguish milder infections from more severe infectious events, a subgroup of events requiring initial intravenous antimicrobial (antibacterial, antiviral, or antifungal) therapy were defined as severe. acute rejection was defined as either a lung biopsy showing rejection of ishlt grade a or higher [ ] or, in the absence of a biopsy, physical (increased need for oxygen) and radiological findings (progressive infiltrate without signs of infection) consistent with acute rejection followed by a prompt response to high-dose ( g/d for consecutive days) corticosteroid therapy (methylprednisolone). nucleic acid isolation was performed with a magna pure lc total nucleic acid or dna isolation kit for serum (ttv) or whole blood (ebv and cmv) using a standardized protocol, according to the instructions (roche diagnostics, mannheim, germany). input/output volume was set to / µl, and the sample was eluted in extraction buffer. the ttv-dna levels were determined using a real-time pcr system (applied biosystems, foster city, ca). each pcr reaction contained µl of extracted total nucleic acid, µl of x universal master mix (applied biosystems, foster city, ca), . µl and µm of forward and reverse primer, respectively, . µl and µm of bhq hydrolysis probe, and µl of rnase-free h o. the reaction conditions were °c for minutes and °c for minutes prior to cycles at °c for seconds and °c for seconds. the assay range was determined by serial dilution of plasmids with an insert of a synthesized sequence matching the ttv pcr product, and quantification was obtained from a plot of ct values. cmv-and ebv-dna levels were determined using a method described previously with minor modifications [ ] . all primer and probe sequences are listed in supplementary table . for ebv and cmv quantification, a control sample consisting of unrelated phocine herpesvirus (phhv- ) was included prior to nucleic acid extraction. ttv load was quantified on the qx droplet digital pcr system using the ddpcr supermix for probes (no dutp; bio-rad, hercules, ca). primer and probe concentrations in the -µl final reaction were and nm, respectively. the pcr conditions were °c for minutes followed by °c for minutes, then seconds at °c and minute at °c for a total of cycles, and finally a step at °c for minutes. after overnight incubation at °c, the droplet fluorescence signal was determined. data analysis was done using bio-rad quanta soft analysis software. isolated dna and rna were analyzed using a multiplex real-time pcr system designed to detect adenovirus, bocavirus, chlamydophila pneumoniae, human coronavirus (nl , hku , oc and e), human enterovirus, human metapneumovirus, human rhinovirus, influenza a virus, influenza b virus, mycoplasma pneumoniae, parainfluenzavirus ( , , and ), and respiratory syncytial virus. the pcr settings and a list of primers and probes have been described previously [ ] . comparisons on group level for numerical variables were performed using the mann-whitney u test. pearson's correlation and linear regression were used to evaluate the relationship between the real-time pcr and ddpcr measurements. cox regression with ttv, ebv, and both as time-dependent covariates was used to analyze the relationship between the biomarkers and the outcomes vrti, fungal infection, bacterial infection, cmv viremia, or any infectious event. each patient was treated as a cluster to handle multiple infections occurring in a single individual. univariable logistic regression was used in each of periods, q ( - months), q ( - ), q ( ) ( ) ( ) ( ) ( ) ( ) ( ) , and q ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) , with the outcomes vrti, fungal infection, bacterial infection, cmv viremia infection, or acute rejection and the predictors age, treatment, cmv mismatch, log ttv (beginning of period), or log ebv (beginning of the period). a p value <. was considered significant. r software, version . . (r core team, , r foundation for statistical computing, vienna, austria; http://www.r-project.org/), was used for all statistical analyses except for pearson's correlation analysis, which was performed using graphpad prism software (graphpad software inc., san diego, ca). the study was approved by the regional ethical review board in gothenburg (dnr: - ), and all subjects provided written and oral consent to participate. in total, lung transplant recipients were included in the study, of which ( %) were still alive months after transplantation. detailed patient description is outlined in table . blood-, bal-, and nasopharyngeal samples (nph) were collected longitudinally at follow-up (fu) visits until months post-lung transplantation (ltx; n = ), including pretransplant samples. the total nucleic acid content was isolated from serum or whole blood samples and analyzed for ttv-, ebv-, and cmv-dna load by real-time pcr. the total nucleic acid content was isolated from the nph and bal samples and analyzed for respiratory pathogens using multiplex real-time pcr. a majority of the patients had detectable ttv-dna levels before transplantation (pre-ltx), and the levels subsequently increased until a peak was reached at months post-ltx, after which the levels gradually decreased (figure ). the mean ttv-dna levels for the respective time periods were . log - months post-ltx, . log - months post-ltx, . log - months post-ltx, and . log - months post-ltx, respectively. conversely, a majority of the patients had no detectable ebv-dna prior to transplantation as determined in serum. at month post-ltx, a peak in mean ebv-dna levels was observed, which decreased already months post-ltx and thereafter remained at a relatively constant level, determined in whole blood (figure ). the mean ebv-dna levels for the respective time periods were . log - months post-ltx, . log - months post-ltx, . log - months post-ltx, and . log - months post-ltx, respectively. overall, fewer patients had detectable levels of ebv-dna compared with ttv-dna ( figure ). although the individual ttv-dna levels varied, a majority of the patients had detectable levels across the entire fu period. in comparison, only a minority of the patients had detectable levels of ebv-dna over a longer consecutive period, and a large fraction had ebv-dna levels below the level of quantification (loq) at any given time point during fu (figure ). three patients developed suspected ptld. no case was biopsy-verified, and all were reversed upon modification of immunosuppression. detailed individual ttvand ebv-dna level kinetics for each patient, including information regarding all infectious events and acute rejections, are displayed in supplementary figure . comparison of ttv-and ebv-dna levels in lung transplant recipients who received either tacrolimus-or cyclosporinebased therapy revealed that cyclosporine-treated patients had significantly lower ttv-dna levels in serum at month post-ltx and onwards, compared with the tacrolimustreated patients (figure ). there was no significant difference in ebv-dna levels in whole blood between tacrolimus-and cyclosporine-treated patients at any time point during fu (figure ). the fu was divided into periods, denoted q through q , defined as - (q ), - (q ), - (q ), and - (q ) months after transplantation. the periodic intervals were chosen to distinguish the initial phase of intensive immunosuppression from the later periods when immunosuppressive therapy was gradually lowered. viral infections (vrti) were more common during the first months, while bacterial and fungal infections were evenly distributed throughout the period and cmv viremia occurred at a higher frequency - months after ltx after discontinuation of prophylactic ganciclovir treatment ( table ) . events of acute rejections were most common during the first postoperative months and then decreased over time ( figure ). all but episodes of acute rejections were biopsy-verified. the frequency of infectious events ( figure and table ) was compared with the mean ttv-dna or ebv-dna levels during each period (q -q ) and the during the total fu period, respectively. no statistically significant association was found. with logistic regression, log ttv-dna or log ebv-dna levels in the beginning of the period did not predict any infectious event in any of the periods (supplementary table ). next, we performed a cox regression analysis to establish if ttv-or ebv-dna levels were associated with either viral table ). no significant associations were found using this criterion. when comparing other factors relevant to infections and acute rejection, using logistic regression, we found that age, cmv mismatch, and dominant immunosuppressive treatment did not predict outcome in any of the periods denoted q through q (supplementary table ). most acute rejection events (ars) occurred within the first months post-ltx (figure ). logistic regression with initial ttv-dna or ebv-dna for each period, respectively, did not predict whether an acute rejection event would occur during that period (data not shown). previous studies [ , ] have described higher mean ttv-dna levels in lung transplant patients than reported here. in order to verify the real-time pcr results, ttv-dna levels of patients with mean ttv-dna levels above log in period q were assessed by digital droplet pcr (ddpcr). the ttv-dna level was underestimated by more than log by real-time pcr in samples, and overall the levels obtained by realtime pcr correlated well with the results obtained by ddpcr (pearson r = . , p = . ) (supplementary table ). ttv and ebv has been proposed as biomarkers reflecting the functionality of the immune system after ltx. in this prospective study, evaluating serial samples for ttv and ebv and carefully recording infectious and rejection events during an fu period of months, we found no associations between the biomarkers and the risk of complications. we found that ttv-dna levels increased rapidly; month after ltx, the levels were already markedly elevated, presumably due to ablation of the functional effector cells of the immune system that normally control the ttv infection [ , ] . at months post-ltx, the mean ttv-dna level peaked and then gradually declined, reflecting the gradual moderation of immunosuppressive therapy. interestingly, the ttv-dna level was lower in patients who received cyclosporine treatment, possibly mirroring a different immune modulatory mechanism for cyclosporine compared with tacrolimus. görzer et al. [ ] previously suggested that this might be due to cyclosporine being less efficient as an immunosuppressant. however, we found no association between type of immunosuppressive regimen and acute rejection or other events that would indicate a difference in net immunosuppressive effect. recently, ttv-dna has been associated with chronic lung allograft dysfunction after lung transplantation [ ] , but in our study this was not included as an outcome. it is possible that the observed higher mean ttv-dna levels in other studies could be explained by differences in induction therapy and distribution of respective immunosuppressive regimen. for example, in the study by görzer et al. [ ] , the type of induction therapy was not defined and only % of the patients were treated with cyclosporine. there is some evidence that ttv replication is dependent on the type of induction therapy that appears to reflect changes in lymphocyte concentration; however, the duration is brief, after which the levels of ttv recover [ ] . in the present study, ttv viral load was determined in serum samples, whereas plasma was used in previous studies [ , ] . however, to our knowledge, there are no apparent reasons for variations in ttv-dna load, depending on whether plasma or serum is being used for analysis. to compare results regarding ttv levels between different transplantation centers, it is vital to reliably quantify the concentrations of ttv-dna in a standardized manner. here it was shown that the real-time pcr method was adequate as compared with the ddpcr method, which is considered a more reliable method for accurate quantification [ ] . nonetheless, real-time pcr is prone to interlaboratory differences, and utilization of ddpcr for quantification has been suggested to circumvent this problem, facilitating direct comparison of results between centers [ , ] . digital droplet pcr depends on partitioning of each master mix followed by end point pcr. quantitation is determined using poisson statistics to generate a result that is not dependent on a relation to a standard curve and should therefore exhibit lower variability between laboratories. however, the ddpcr assays still depend on amplification of a specific target sequence, and depending on the design of the primer and probe, the targeted sequence can vary. recent work has shown that viral dna in plasma samples is to a large extent free and not associated with viral particles and is also subjected to various degrees of degradation, influencing the results, depending on the amplicon length determined by the pcr-assay design [ ] . thus, standardization of the entire assay including primer and probe design, use of international standards, and assessment of the commutability of reference material is needed before a direct comparison of interlaboratory results can be made with absolute confidence, even with the use of ddpcr [ , ] . it remains to be clarified in which cell types ttv replication occurs, but cd + t cells and cd + + t cells appear to be important for controlling the infection, whereas ebv resides within the b-cell pool and is controlled by cd + and cd + t cells [ , , , , , [ ] [ ] [ ] [ ] . in this work, we show that the choice of calcineurin inhibitor affects the ttv-but not the ebv-dna levels, possibly reflecting separate mechanisms for viral replication rather than merely ablation of the t-cell pool. as the choice of immunosuppressive regimen was made at the discretion of the treating physician, these findings should be interpreted with caution but warrant further investigation. in this study, infectious events were defined as symptoms prompting antimicrobial therapy also in cases without a positive culture (bacterial and fungal infections) or simply detection of a potential pathogen by pcr (vrti, cmv). attempting to focus on more severe infectious events, subgroup analysis of events requiring intravenous therapy was made. also, this analysis failed to reveal any significant association between ttv-or ebv-dna levels and infectious events. however, no proper validated scoring system for grading of the severity of infectious complications was used in this study, and we cannot exclude that our definitions cause underestimation of severe complications. further studies using proper grading of events are needed. ebv has previously been suggested as a surrogate marker for immunosuppression as an association between elevated ebv-dna levels and reduced incidence of acute rejection of lung transplants was observed [ ] . in addition, ebv-dna was safely used as a trigger for reduction of immunosuppression late after lung transplantation and was found to be associated with a shorter time to development of infectious complications or solid tumors, but not ptld [ , ] . we found no association between ebv-dna and acute rejection at any time during fu. a direct comparison could, however, be hampered by the fact that ebv-dna was analyzed in this study, and ebv-encoded rna in an earlier study [ ] . in the present study, mean ebv-dna levels did not increase as markedly as ttv-dna levels after transplantation, even though ebv-specific t cells most likely are subverted by immunosuppressive therapy [ ] . the seroprevalence pre-ltx and number of patients positive for ebv-dna at any time during fu were comparable to previous studies [ , , ] . one possible caveat when determining ebv dna load is the use of valgangciclovir for preventing reactivation or primary infection of cmv. all patients received months of valgangciclovir treatment initially after ltx; there are a few studies showing that valgangciclovir treatment reduces ebv load, which may have affected the results in this study [ , ] . in conclusion, ttv-but not ebv-dna load appears to reflect the function of the immune system after lung transplantation, depending on the type of immunosuppressive treatment. however, we found no association between either ttv-or ebv-dna load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression. further studies are warranted to define the effect of immunomodulation on ttv and ebv replication in relation to various immunosuppressive regimens. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. international society for heart and lung transplantation. the registry of the international society for heart and lung transplantation: thirty-fourth adult lung and heart-lung transplantation report- ; focus theme: allograft ischemic time purine metabolism and immunosuppressive effects of mycophenolate mofetil (mmf) cyclosporine: a review mode of action of tacrolimus (fk ): molecular and cellular mechanisms diagnostic performance of five assays for anti-hepatitis e virus igg and igm in a large cohort study persistence of dna sequences of bk virus and jc virus in normal human tissues and in diseased tissues tt virus infection in french hemodialysis patients: study of prevalence and risk factors human anelloviruses: an update of molecular, epidemiological and clinical aspects a novel dna virus (ttv) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology classification of ttv and related viruses (anelloviruses) circular genomes related to anelloviruses identified in human and animal samples by using a combined rolling-circle amplification/sequence-independent single primer amplification approach history of discoveries and pathogenicity of tt viruses torquetenovirus: the human virome from bench to bedside effect of immune modulation on tt virus (ttv) and ttv-like-mini-virus (tlmv) viremia role of hematopoietic cells in the maintenance of chronic human torquetenovirus plasma viremia plasma dna levels of torque teno virus and immunosuppression after lung transplantation prevalence and prognostic significance of infection with tt virus in patients infected with human immunodeficiency virus temporal response of the human virome to immunosuppression and antiviral therapy torque teno virus in children who underwent orthotopic liver transplantation: new insights about a common pathogen age-specific prevalence of epstein-barr virus infection among individuals aged - years in the united states and factors affecting its acquisition ebv persistence in memory b cells in vivo b cell activation and the establishment of epstein-barr virus latency association between elevated whole blood epstein-barr virus (ebv)-encoded rna ebv polymerase chain reaction and reduced incidence of acute lung allograft rejection epstein-barr virus-dna load monitoring late after lung transplantation: a surrogate marker of the degree of immunosuppression and a safe guide to reduce immunosuppression european organization for research and treatment of cancer/invasive fungal infections cooperative group; national institute of allergy and infectious diseases mycoses study group (eortc/ msg) consensus group. revised definitions of invasive fungal disease from the european organization for research and treatment of cancer/invasive fungal infections cooperative group and the national institute of allergy and infectious diseases mycoses study group (eortc/msg) consensus group revision of the working formulation for the standardization of nomenclature in the diagnosis of lung rejection comparison of serum and whole blood levels of cytomegalovirus and epstein-barr virus dna comparison of the filmarray assay and in-house real-time pcr for detection of respiratory infection association between plasma torque teno virus level and chronic lung allograft dysfunction after lung transplantation short-term kinetics of torque teno virus viraemia after induction immunosuppression confirm t lymphocytes as the main replication-competent cells pre-transplant plasma torque teno virus load and increase dynamics after lung transplantation quantification of hev rna by droplet digital pcr a miqe-compliant real-time pcr assay for aspergillus detection absolute quantification by droplet digital pcr versus analog real-time pcr determination of the biological form of human cytomegalovirus dna in the plasma of solid-organ transplant recipients quantitative assessment of commutability for clinical viral load testing using a digital pcr-based reference standard are we there yet? impact of the first international standard for cytomegalovirus dna on the harmonization of results reported on plasma samples dendritic cells cross-present latency gene products from epstein-barr virus-transformed b cells and expand tumor-reactive cd (+) killer t cells human cd (+) t lymphocytes consistently respond to the latent epstein-barr virus nuclear antigen ebna cd + t lymphocytes and functional immune deficiency changes in cd + + t lymphocyte expansions after autologous hematopoietic stem cell transplantation correlate with changes in torquetenovirus viremia epstein-barr virus dnaemia is an early surrogate marker of the net state of immunosuppresion in solid organ transplant recipients human cytotoxic t lymphocyte responses to epstein-barr virus infection detection of epstein-barr virus dna in peripheral blood is associated with the development of bronchiolitis obliterans syndrome after lung transplantation efficacy and safety of valganciclovir in liver-transplanted children infected with epstein-barr virus valganciclovir for the suppression of epstein-barr virus replication financial support. this project was supported by funding from stiftelsen professor lars-erik gelins minnesfond, fou laboratoriemedicin, sahlgrenska university hospital, the swedish heart-lung foundation, the region västra götaland research funds (vgfoureg- , vgfoureg- ), regional alf funds (alfgbg- , alfgbg- ), and region halland. potential conflicts of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- - hmzgwrw authors: izzy, saef; tahir, zabreen; cote, david j; al jarrah, ali; roberts, matthew blake; turbett, sarah; kadar, aran; smirnakis, stelios m; feske, steven k; zafonte, ross; fishman, jay a; el khoury, joseph title: characteristics and outcomes of latinx patients with covid- in comparison to other ethnic and racial groups date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: hmzgwrw background: there is limited understating of the impact of covid- on the latinx population. we hypothesized that latinx patients would be more likely to be hospitalized and admitted to the icu than white patients. methods: we analyzed all patients with covid- in massachusetts hospitals between february and april , . we examined the association between race, ethnicity, age, reported comorbidities, and hospitalization and intensive care unit (icu) admission using multivariable regression. results: of covid- patients, % were hospitalized; % required icu and . % died. % of patients were white, % latinx, % african american, and % asian american. ethnicity and race were significantly associated with hospitalization. more latinx and african american patients in the younger age groups were hospitalized than whites. latinx and african americans disproportionally required icu, with % of hospitalized latinx patients requiring icu compared to % of african americans, % of asian americans, and % of whites (p& . ). within each ethnic and racial group, age and male gender were independently predictive of hospitalization. previously reported pre-existing comorbidities contributed to the need for hospitalization in all racial and ethnic groups (p& . ). however, the observed disparities were less likely related to reported comorbidities, with latinx and african american patients being admitted at twice the rate of whites, regardless of such comorbidities. conclusions: latinx and african american patients with covid- have higher rates of hospitalization and icu admission than white patients. the etiologies of such disparities are likely multifactorial and cannot be explained only by reported comorbidities. the health, societal, and economic impacts of coronavirus disease (covid- ) have been felt worldwide, with nearly million confirmed infections leading to more than , deaths by early july , with numbers continuing to grow. [ ] [ ] [ ] studies from china, italy, spain and the united states have identified several factors associated with symptomatic infection and hospitalization, with or without admission to intensive care units (icu). [ ] [ ] [ ] [ ] [ ] [ ] older age has been shown to significantly increase the risk for hospitalization and death. , hypertension, heart disease, obesity, and diabetes are common comorbidities associated with hospitalization in covid- patients. , , , most of these published reports either describe the disease in relatively homogenous ethnic and racial populations, or they do not compare covid- infected patients who did and did not require hospitalization. in the united states, where a racially and ethnically diverse population has been exposed to infection in the setting of known racial and ethnic health disparities, several news reports have suggested that ethnic and racial minorities, especially latinx and non-latin african american individuals, may bear a higher burden of disease during the covid- pandemic. [ ] [ ] [ ] [ ] [ ] these reports also propose that such disparities are due to higher rates of pre-existing comorbidities in latinx and non-latin african american patients. other than these limited reports, the association between ethnicity and, race, and reported pre-existing comorbidities as risk factors for hospitalization and icu admission in covid- patients, has yet to be examined in a large, ethnically and racially diverse population. in this paper, we hypothesized that there are ethnicity and race-related disparities in hospitalization and icu admission for covid- patients regardless of age and reported pre-existing comorbidities. we used medical records available from the largest not-for-profit healthcare system in massachusetts to examine the association between age, race and ethnicity, reported preexisting comorbidities, and the need for hospitalization and icu admission in a large study population of covid- positive patients. mass general brigham is a not-for-profit healthcare system affiliated with harvard medical school that comprises m a n u s c r i p t the design of the study was approved by the mass general brigham institutional review board (irb) who deemed that the study does not include factors necessitating patient consent. we used data reporting functions available through the electronic health record (epic systems, verona, wi) shared by all mass general brigham healthcare system institutions. we collected data on all patients years or older who tested positive for covid- during an inpatient, outpatient, or emergency room visit between february , and april , . we revisited the records on april , to collect follow up data on mortality and other outcomes. patients who presented to mass general brigham institutions with symptoms of fever, cough, sore throat, fatigue, muscle aches, new anosmia, who were exposed to someone who tested positive for covid- , or if referred by a healthcare provider were tested per specified testing criteria/guidelines set forth by the institution. patients were diagnosed as infected with covid- if sars-cov- rna was detected in upper or lower respiratory specimens by nucleic acid testing (nat) assays designated for emergency use authorization (eua) by the food and drug administration (fda) and in accordance with the centers for disease control and prevention (cdc) guidelines. , each assay targets at least one sars-cov- gene region; positive results are reported for each assay as defined by the manufacturer or reference laboratory. hospitalization at any time during the course of the illness and admission to an icu at any time during hospitalization were primary endpoints. patients who were discharged home initially but were admitted later were categorized as hospitalized patients. patients hospitalized for longer than the follow up period were censored for study outcomes. we extracted the following covariates from the electronic health records for all patients: age, gender, patient-reported race (white, african american, asian american or pacific islander, other, or unknown), patient-reported ethnicity (latin or non-latin), smoking status, and the presence of recorded metabolic diseases including obesity (as measured by body mass index [bmi]), diabetes mellitus, and hyperlipidemia. the presence of organ-specific disease included hypertension, coronary heart disease, congestive heart failure, chronic obstructive pulmonary disease, asthma, m a n u s c r i p t interstitial lung disease, cerebrovascular disease, chronic kidney disease, end stage renal disease, malignancy including hematologic malignancy (lymphoma, leukemia), hiv, and history of organ or bone marrow transplantation. missing data were imputed by multiple imputation using the amelia package in r. the multiple-imputation models used all baseline data. bmi and smoking status for all patients were also imputed by multiple-imputation models using r, and imputations were carried out in total under the assumption that data were missing at random. data for median household income and population density were obtained from census data reported by the census bureau for the state of ma, and were linked to patient by zip code of reported residential address. because immunocompromised patients generally demonstrate increased susceptibility to respiratory viral infections, we analysed our study population of patients for history of solid organ transplantation (sot), lymphoma, leukemia or hiv to assess whether these factors were associated with hospitalization or icu admission. as appropriate, descriptive analyses of variables are presented as proportions or medians with interquartile range (iqr) for all endpoints (not hospitalized, hospitalized, admitted to icu). categorical data were compared using chi-squared tests, while t-test was used for continuous variables to identify univariable associations. multivariable logistic regression models were constructed to identify factors associated with hospitalization and icu admission. we tested our assumption that data were missing at random by constructing logistic regression models for missingness using all of the variables included in multiple imputations. we further examined the association between racial and ethnic background and hospital admission by comparing proportions of endpoints for each -year age interval from to . we also examined the association between racial and ethnic background, pre-existing comorbidities, and hospitalization or icu admission by stratifying by number of baseline comorbidities ( vs. ≥ ) and race and ethnicity. we further performed a sensitivity analysis with adjustment for socioeconomic status as a predictor for hospitalization/icu admission for patients from massachusetts state with median household income data available. patients with median household income less than th percentile ($ , ) were classified to have low ses as a dichotomous variable. statistical significance was defined as p< . for all analyses, and all statistical analysis was completed using r v . . . we graphed the geographic representation of the confirmed covid patients during our study using microsoft excel version . . a total of , patients were diagnosed with laboratory confirmed covid- in the time frame of the study and were included in our analysis (figure ) . out of the total study population, , ( . %) were hospitalized. overall, hospitalized patients were more likely to be male ( % vs. %, p< . ) and older (median vs. years, p< . ) compared to non-hospitalized patients. hospitalized patients were also more likely to be obese ( % vs. % bmi - kg/m , p< . ), with on average more cardiovascular and pulmonary risk factors, and more comorbid conditions compared to non-hospitalized patients ( table ) . the most common comorbidities in the hospitalized study population were hypertension ( %), hyperlipidemia ( %), diabetes ( %), and obstructive lung disease ( %). the mortality rate was higher in hospitalized compared to nonhospitalized patients ( % vs. . %, p< . ). our test of the missing at random assumption demonstrated significant predictors of missingness for all variables for which imputation was conducted. among the total covid- positive patient study population, , ( %) were white, , were latinx ( %), were african american ( %) and were asian american ( %). ethnicity and race were significantly associated with the rate of hospitalization. latinx and african american patients were more likely to be admitted to the hospital than white patients ( . % and . %, respectively, vs. . % for white patients). overall latinx, african american, and asian american hospitalized patients were younger compared to white patients (median age , and , vs. respectively, p< . , table ). subgroup analyses of the ages between - at -year intervals showed that in each age group, latinx and african american patients were more likely to be admitted as a result of covid- compared to white patients (p< . for each comparison, figure ). for example, among those - and - years old, latinx and african american patients were admitted to the hospital at the rates of ( % and % vs. %, and % and % vs. %, in comparison to. white patients respectively, p< . for each comparison). we observed similar, among those aged > (supplementary table ) . with regard to reported comorbidities, hospitalized latinx patients were more likely to be obese in the range of - kg/m ( % compared to % among white and % among african american patients, p< . ). however, the proportions of white, latinx and african american patients who were in range of > kg/m were similar. white patients had higher rates of reported hyperlipidemia, hypertension, obstructive lung disease, coronary artery disease, congestive heart m a n u s c r i p t failure, chronic kidney disease and malignancy compared with other groups (p< . , table , supplementary table ) . when stratified by baseline reported comorbidities, latinx and african american patients were admitted at twice the rate of whites, regardless of whether they had reported preexisting comorbidities (p< . , table ). compared to non-hospitalized patients, univariable logistic regression stratified by race identified pre-existing comorbidities including metabolic, cardiovascular, cerebrovascular, pulmonary and kidney disease as predictors for hospitalization in all racial and ethnic groups (p< . , supplementary table ). most of these predictors remained significant after adjustment for socioeconomic status (supplementary table ). based on patients' zip-code data, % of all the patients who tested positive lived in zip codes with median income between $ , -$ , , of which % were hospitalized. a higher proportion of hospitalized latinx and african american patients lived in those zip codes ( % and % respectively, compared to % of white patients, figure a, supplementary table ) . interestingly, smaller proportions of patients living in zip codes with income <$ , were hospitalized (supplementary table ). in addition, residence in a zip-code with greater density of living per household was corelated with a higher likelihood of hospitalization (figure b, supplementary table ). in our study population, % of admitted patients were from areas residence with population density > , /square mile. a history of solid organ transplantation was associated with a significantly increased risk for hospitalization (p< . ). of the transplant patients who were covid- positive ( kidney recipients, three liver recipients, four heart recipients, two lung recipients and one heart/lung recipient) seventeen ( %) were admitted. in contrast, hiv, lymphoma or a history of leukemia were not associated with increased risk for hospitalization or icu admission (supplementary table ). a possible difference between sot patients and those with hiv or a history of lymphoma or leukemia, is that sot patients were universally immunosuppressed at the time of infection while the degree of immune impairment for other groups was likely more heterogeneous. m a n u s c r i p t latinx and african american patients disproportionally required admission to the icu compared to white patients. overall, % of hospitalized latinx patients required admission to the icu compared to % of african american patients, % of asian american patients and % of white patients (p< . , table ). the presence of reported metabolic or organ-specific comorbidities was not significantly associated with need for icu admission (supplementary table ) . in multivariable regression analysis, age greater than years old (or= . , %ci: . - . for latinx, or= . , %ci: . - . for african american patients) and obesity with bmi > kg/m (or= . , %ci: . - . for latinx patients), and diabetes (or= . , %ci: . - . for african american patients) were identified as significant predictors of icu admission ( table ). in addition to these predictors, low median household income was as a significant predictor for icu admission in white patients (or= . , % ci: . - . ) after adjustment for socioeconomic status (supplementary table ). in spite of aggressive efforts by the medical and public health communities worldwide, understanding of the overall impact of the covid- pandemic remains limited. based on data from china, italy, and spain, and preliminary data from the united states, patients who are years or older are more vulnerable to covid- , with higher morbidity and mortality. [ ] [ ] [ ] [ ] [ ] [ ] furthermore, patients with other comorbidities, such as cardiovascular disease and hypertension, are more likely to be hospitalized and die from the infection. , , , this evidence mostly derives from studies performed in racially and ethnically homogeneous populations. , the impact of the disease in an ethnically and racially diverse population has not been fully explored. anecdotal and news reports and a report from the uk suggest that racial and ethnic minorities may be more likely to contract covid- , and more likely to suffer poor outcomes as a result of infection. [ ] [ ] [ ] [ ] [ ] price-haywood et al. and others showed that the majority of patients hospitalized with covid- and of those who died in a louisiana study population were african american. , our firsthand clinical experience with covid- patients indicate that in addition to african american patients, a higher percentage of covid- latinx patients required hospitalization and critical care admission. to examine this issue, we investigated the impact of covid- on the patient population covered by our group of hospitals, which serve a diverse and broad population of eastern massachusetts similar to the racial and ethnic compositions of many large metropolitan areas of the united states. we confirmed that age, male gender and obesity are indeed important risk factors m a n u s c r i p t for worse outcomes after covid- infection, and that the presence of reported comorbid medical conditions is an important contributing factor to hospitalization among all ethnic and racial groups. three additional important findings emerged from our study. first, analysis of our large study population confirmed our firsthand clinical experience and showed indeed that latinx and african american patients are at higher risk of being hospitalized and admitted to icu level of care with covid- , than white patients. a second important finding is that the differences observed between latinx and african american vs. white patients occur at all age groups and are not only limited to the "higher risk" older age groups identified in prior studies. a third important finding is that the observed disparities appear to be less likely related to reported pre-existing medical comorbidities, since latinx and african american patients who tested positive for covid- were admitted at twice the rate of whites, regardless of whether they had reported comorbidities or not. in addition, the proportion of white patients who had reported comorbidities such as hyperlipidemia, hypertension, obstructive lung disease, coronary heart disease, cerebrovascular disease was at least as great as the proportions of latinx and african american patients who have these comorbidities. the underlying etiology of such disparity in hospitalization from covid between latinx and african american vs. white patients is likely multifactorial. first, patients from these historically disadvantaged racial and ethnic groups may be less likely to be insured than white patients. immigration status could also play another role in restricting access of racial and ethnic minority patients to health insurance coverage and increase their challenges in finding a source of care to get tested or accessing covid related treatments. therefore, they may have presented at a later, more severe phase of the disease and therefore required hospitalization. in support of this, when we analyzed the zip-code of residence of these patients we found a close correlation between residence in a zip code of low median income and greater density of living in the same household with higher rate of hospitalization. in general, lower income patients tend to defer seeking healthcare for fear of financial burden and/or limited health care access and quality. second, it is possible that latinx and african american patients with covid have a higher severity of reported comorbidities. our data do not show that such disparities in hospitalization can be explained by the presence of reported comorbidities. however, there are limitations to our interpretation of these data. because our findings are based on reported data in the medical records, they do not take into account the severity of the preexisting conditions, which is difficult to quantify in such a large study population. it is likely that the severity of certain underlying comorbidities is higher in ethnic and racial minorities than in white patients, perhaps due to previously described healthcare disparities, , or to issues with medication use and adherence. [ ] [ ] [ ] third, other issues of stress and allostatic load that could impact health, which were out of the scope of our observational study may also be contributing factors to the observed disparities and require further investigation. , these include crowded housing conditions as we alluded above, or the type of employment where exposure to covid could possibly be more common. our study has several possible limitations. first, this is a registry database study from a single mixed health system (with primary and tertiary institution) using structured data captured in the a c c e p t e d m a n u s c r i p t electronic medical record. this study may also underrepresent covid patients who do not seek medical attention or have whose medical data are stored at other facilities. however, the strengths of this study include a large, diverse study population of covid- positive patients from a wide geographic region that allowed us to analyze a large number of latinx, african american, asian american in addition to white patients. we were also able to collect detailed sets of variables on each patient, including factors that predict hospitalization and icu-level care, which allows for multivariable adjustment. follow up identified a number of outcome events, including deaths and icu-level admissions. while we acknowledge the limitations of our study, reporting data based on societal understanding of race and ethnicity, using patient self-reported race and ethnicity, is an important step in highlighting existing disparities in covid- treatment and try to mitigate contributing factors for the future. , our findings also could have immediate policy implications, since it would be crucial to target the most vulnerable groups when testing or vaccination strategies are devised to limit further spread of covid- and minimize its impact. this is especially relevant with the new surge in the numbers of covid cases in states where latinx patients constitute a significant portion of the population such as florida and texas. m a n u s c r i p t table and figure legends table . characteristics of all covid- positive patients in the mass general brigham healthcare system. table . baseline characteristics by race and ethnicity among admitted covid- patients. table . rate of hospitalization among all covid- patients by baseline comorbidities and race and ethnicity. *the household income and population density reported are obtained from county-level census data. dr. ross zafonte serves on the scientific advisory board of oxeia biopharma, biodirection, elminda, and myomo. he also evaluates patients in the mgh brain and body-trust program which is funded by the nfl players association. the remaining authors declare no conflict of interests. m a n u s c r i p t iqr=interquartile range, copd=chronic obstructive pulmonary disease, chf=congestive heart failure, ckd=chronic kidney disease, esrd=end stage renal disease *missing for % of population **missing for % of population m a n u s c r i p t epidemiology of covid- in a long-term care facility in king county presenting characteristics, comorbidities, and outcomes among patients hospitalized with covid- in the an interactive web-based dashboard to track covid- in real time early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china the resilience of the spanish health system against the covid- pandemic coronavirus disease (covid- ) in italy facing covid- in italy -ethics, logistics, and therapeutics on the epidemic's front line critical care utilization for the covid- outbreak in lombardy, italy: early experience and forecast during an emergency response 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 severe outcomes among patients with coronavirus disease (covid- ) -united states does comorbidity increase the risk of patients with covid- : evidence from meta-analysis epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study the changing racial and ethnic composition of the us population: emerging american identities african american covid- mortality: a sentinel event covid- and african americans kills-latinxs-and-african americans-in-new-york-city.) . interim guidelines for collecting, handling, and testing clinical specimens from persons for coronavirus disease (covid- ) income statistics and demographics for states, counties, cities and zip codes 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 hospitalization and mortality among african american patients and white patients with covid- . nejm . . population health statistics: race and ethnicity reports socioeconomic disparities in health in the united states: what the patterns tell us mechanisms for racial and ethnic disparities in glycemic control in middle-aged and older americans in the health and retirement study contribution of major diseases to disparities in mortality racial and ethnic disparities in medication adherence among privately insured patients in the united states socioeconomic status and nonadherence to antihypertensive drugs: a systematic review and meta-analysis race/ethnicity, disability, and medication adherence among medicare beneficiaries with heart failure allostatic load burden and racial disparities in mortality protective and damaging effects of stress mediators obesity as a predictor for a poor prognosis of covid- : a systematic review commentary: obesity: the "achilles heel" for covid- ? racial health disparities and covid- -caution and context covid- and racial/ethnic disparities a c c e p t e d m a n u s c r i p t key: cord- -mnou j authors: wang, yaping; liao, baolin; guo, yan; li, feng; lei, chunliang; zhang, fuchun; cai, weiping; hong, wenxin; zeng, yu; qiu, shuang; wang, jian; li, yueping; deng, xilong; li, jianping; xiao, guangming; guo, fengxia; lai, xunxi; liang, zhiwei; wen, xueliang; li, pinghong; jiao, qian; xiang, fangfei; wang, yong; ma, chenghui; xie, zhiwei; lin, weiyin; wu, yanrong; tang, xiaoping; li, linghua; guan, yujuan title: clinical characteristics of patients infected with the novel coronavirus (sars-cov- ) in guangzhou, china date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: mnou j background: the clinical manifestations and factors associated with the severity of severe acute respiratory syndrome coronavirus (sars-cov- ) infections outside of wuhan are not clearly understood. methods: all laboratory-confirmed cases with sars-cov- infection who were hospitalized and monitored in guangzhou eighth people’s hospital were recruited from january to february . results: a total of patients were included in this study. the median patient age was years, and . % had exposure to wuhan. the median virus incubation period was days. fever ( . %) and dry cough ( . %) were the most common symptoms. a decreased albumin level was found in . % of patients, lymphopenia in . %, and pneumonia based on chest computed tomography in %. approximately % of patients (n = ) had severe disease, and there were no deaths. compared with patients with nonsevere disease, those with severe disease were older, had a higher frequency of coexisting conditions and pneumonia, and had a shorter incubation period (all p < . ). there were no differences between patients who likely contacted the virus in wuhan and those who had no exposure to wuhan. multivariate logistic regression analysis indicated that older age, male sex, and decreased albumin level were independently associated with disease severity. conclusions: most of the patients infected with sars-cov- in guangzhou, china are not severe cases and patients with older age, male, and decreased albumin level were more likely to develop into severe ones. in december , cases of unexplained pneumonia related to the huanan seafood market began appearing in wuhan, hubei province, china [ ] . it was subsequently determined that the pathogen was a novel coronavirus, and the gene sequence was closely related (with % identity) to bat-derived severe acute respiratory syndrome (sars)-like coronaviruses [ ] . the virus is the seventh member of the known coronavirus family that is able to infect humans [ ] . as the virus is similar to sars coronavirus (sars-cov), which is a member of the subgenus sarbecovirus (beta-cov lineage b) [ ] , it was subsequently renamed sars-cov- . the pneumonia caused by the virus was named coronavirus disease (covid- ) . the outbreak of sars-cov- infection has become a global health concern. as of may , , there were documented cases in china and deaths due to the disease (http:// my-h news.app.xinhuanet.com/h activity/yiqingchaxun/ index.html). although the number of infected persons has increased rapidly, clinical investigations of patients, especially those outside of wuhan, are lacking. chen et al. [ ] studied the clinical features of patients with covid- and found that sars-cov- was more likely to infect older men with comorbidities and to lead to acute respiratory distress syndrome (ards). several recent studies [ , ] have indicated that the rapid spread of the virus is due to human-to-human transmission and have found evidence of familial cluster cases. wang et al. [ ] studied hospitalized patients with covid- in wuhan: % of the patients were suspected to have been infected by in-hospital transmission of sars-cov- , % of the patients required treatment in the intensive care unit (icu), and the mortality rate was . %. as of may , , guangdong province, china, has the most confirmed cases outside of hubei (http://wsjkw.gd.gov.cn/ xxgzbdfk/content/post_ .html). guangzhou is the economic and health care center of guangdong province and is one of the most popular cities for migrant workers. the guangzhou eighth people's hospital is the major center for the care of patients with new emerging infectious disease in guangdong. thus, the purpose of this study was to examine the epidemiological, clinical, and laboratory characteristics of patients with sars-cov- infections in guangzhou. the records of patients with covid- diagnosed by the guangdong center for disease control (cdc) who were admitted to the guangzhou eighth people's hospital from january , , to february , , were retrospectively reviewed. the study was approved by guangzhou eighth people's hospital ethics committee, and written informed consent was obtained from patients involved before enrollment when data were collected retrospectively. for the analyses, patients were divided into those with severe disease and those with nonsevere disease based on world health organization (who) interim guidance [ ] . patients were also divided into an "imported" group and a local group. imported group patients were those who had been to wuhan within days or who were residents of wuhan before admission, and the local group included patients who had not left guangdong during the past month. the incubation period was defined as the duration of time from the contact with the source of transmission to the onset of symptoms. fitness for discharge was based on abatement of fever for at least days, with improvement of chest computed tomography (ct) findings and viral clearance in upper respiratory tract nasopharyngeal samples. data were obtained from the patient medical records database and included demographic and epidemiological characteristics, clinical symptoms and signs, and laboratory test and radiographic imaging results. the laboratory test results collected included complete blood cell count (cbc), tests of coagulation function and liver and kidney function, electrolyte levels, c-reactive protein (crp), procalcitonin (pct), lactate dehydrogenase (ldh), and creatine kinase (ck). the primary radiographic assessment was chest ct. if there were missing data or clarifications were needed, the information was obtained by communicating directly with the patient, the attending doctor, or other data providers. all data used in the analyses were checked by doctors. the end points included the rate of severe infections, complications, the need for icu admission, the need for mechanical ventilation, and death. these end points were not applied to a fixed time range (ie, within days) as clinical observations were still in progress. all patients who were transferred to the guangzhou eighth people's hospital were diagnosed by a throat swab nucleic acid test administered by the guangdong cdc. on admission, respiratory samples were taken to determine viral load by a reverse transcription polymerase chain reaction (rt-pcr) assay. in brief, upper respiratory throat swab samples were collected from all patients after admission, and the samples were stored in virus medium. an rna isolation kit (da an gene co., ltd, guangzhou, china) was used to extract viral rna from the samples. rt-pcr was performed using the rna detection kit for sars-cov- (da an gene co., ltd). the orf ab and n genes of sars-cov- were the amplification target regions. the receiver operating characteristics (roc) curve method was used to determine the internal standard reference cycle threshold (ct) value, which was determined to be . if the ct value was ≤ , the sample was considered positive; if the value was > , the sample was considered negative. as all the continuous variables in this study were not normally distributed, continuous variables were presented as median and interquartile range (iqr). categorical variables were described as numbers and percentages. the wilcoxon-mann-whitney u test was used to test differences between groups for continuous variables, as they did not follow a normal distribution. the chi-square test was used to examine differences of categorical variables. variables with a p value <. in bivariate analysis were included in the multivariate logistic regression analysis. forward stepwise binary logistic regression was used for multivariate analysis. variables with a p value <. were retained in the final regression model. spss, version . (ibm corp., armonk, new york, us), was used for data analysis. a total of patients with laboratory-confirmed sars-cov- infections were included in the analysis. the median age of the patients (iqr) was ( - ) years, . % were at least years old, . % were males, and . % had at least coexisting medical condition. none of the patients described exposure to the huanan seafood market, and none of the patients were health care workers. based on the who definition [ ] , ( . %) patients had nonsevere disease and ( . %) patients had severe disease. compared with the nonsevere group, patients with severe disease were older and had a much higher frequency of coexisting medical conditions. additionally, the frequency of imported cases was higher in the severe group than in the nonsevere group ( . % vs . %; p = . ) ( table ). the median incubation time for all patients was days; however, the incubation time was significantly shorter in the severe group than in the nonsevere group ( days vs days; p = . ). the median interval between hospital admission and symptom onset was days, but it was significantly longer in the severe group than in the nonsevere group ( days vs days; p = . ). in all patients, the most common symptoms at the onset of illness were fever ( . %), dry cough ( %), sputum production ( . %), and sore throat ( . %). diarrhea was rare, with only . % of patients reporting this symptom. compared with the nonsevere group, the frequencies of fever, dry cough, sputum production, fatigue, and shortness of breath were much higher in the severe group (table ) . patients were also divided into imported and local disease groups by epidemiological history. there were no significant differences in the parameters described above between the groups; however, family cluster infections were more common in the local group (supplementary table ). at admission, leukopenia was found in . % of patients, neutropenia in . %, and lymphopenia in . % (table ). other routine blood indices were within the normal ranges. however, the percentages of patients with increased leukocytes and neutrophils and lower levels of lymphocytes were greater in the severe group than in the nonsevere group. in addition, ldh, ck, and aspartate aminotransferase (ast) levels on admission (iqr) were higher in the severe group than in the nonsevere group: incubation period, d ( - ) ( - ) ( ) ( ) ( ) ( ) . interval between admission to hospital and symptom onset, d ( - ) ( - ) ( - . ) . data are presented as median (interquartile range) and no. (%). p values denote the comparison between the nonsevere group and the severe group. a hepatitis b infection denotes that hepatitis b surface antigen tested positive, with or without elevated alanine or aspartate aminotransferase levels. b cancers refers to any malignancy. all cases were stable disease. albumin (alb) level was decreased in . % of all patients, and more patients in the severe group had decreased alb levels than in the nonsevere group ( . % vs . %; p < . ). among all patients, univariate analysis indicated that age, sex, imported disease, incubation period, interval between hospital admission and symptom onset, any coexisting medical condition, leukocyte count, neutrophil count, lymphocyte count, pct, ldh, ck, alb, ast, and d-dimer were associated with disease severity. thus, these variables were included in the multivariate logistic regression. the multivariate analysis indicated that age - years (reference, - years), male sex, and decreased alb level were independently associated with disease severity (table ) . on admission, ( %) patients in the nonsevere group had no abnormalities on chest ct scan, whereas all patients in the severe group had pneumonia. bilateral pneumonia ( . %) and multiple small patchy shadows and ground-glass shadows ( . %) were the most common findings (table ) . pneumonia was defined as appearance of symptoms of fever, coughing, or dyspnea and chest ct showing multiple small patchy shadows and interstitial changes in or both lungs at an early stage, which then progressed to multiple ground-glass shadows and infiltration shadows on both lungs. compared with the nonsevere group, the severe group was more likely to have bilateral involvement ( . % vs . %; p < . ) and pleural effusion ( . % vs . %; p = . ). chest ct scan patterns were similar between the imported and local disease groups (supplementary table ). upper respiratory throat swab samples were collected from all patients at admission, and specimens were positive for the orf ab gene, with a median ct value of . of these patients, . % had higher viral loads (ct values < ), whereas . % had low viral loads (ct values, to ). a total of specimens were positive for the n gene, with a median ct value of , and . % of the specimens had higher viral loads. the levels of viral rna were not different between the severe and nonsevere groups. there was no significant difference in viral load between imported and local disease cases (supplementary table ). during hospitalization, the most common complication was pneumonia ( %), followed by ards ( . %) and disseminated intravascular coagulation (dic; . %). the rates of all complications were higher in patients with severe disease than in those with nonsevere disease. a total of patients ( . %) received empiric antibiotic treatment, ( . %) received antiviral therapy, ( . %) received systemic corticosteroid treatment, and ( . %) received immunoglobulin therapy. additionally, patients ( . %) were administered antifungal medications (table ). approximately half of the patients ( . %) received oxygen, and . % of patients required noninvasive ventilation. eleven patients ( . %) required invasive mechanical ventilation, and of the patients received extracorporeal membrane oxygenation (ecmo) and continuous renal replacement therapy (crrt) as salvage therapy. as expected, these treatments were used in significantly more patients with severe disease as compared with those with nonsevere disease (noninvasive ventilation: . % vs . %; p < . ; invasive mechanical ventilation: . % vs %; p < . ; ecmo: . % vs %; p < . ; crrt: . % vs %; p < . ) because application of these treatments was included in the who's definition of severe disease. as of february , , patients ( . %) were still hospitalized. a total of patients ( . %) had been discharged, and patients ( . %) had been transferred to another hospital due to serious illness. as of february , no patient had died (table ). we investigated the epidemiological, clinical, and laboratory characteristics of patients with covid- in guangzhou, guangdong, the most affected province outside of hubei. this is the largest sample size outside wuhan, the center of the epidemic as we know it so far. the most common symptoms were fever and dry cough, and ~ % of the patients had severe disease. there were no health care workers in the patient sample, no cases of in-hospital infection, and no deaths at the time this report was prepared. many studies [ , ] regarding sars-cov- have been published recently. in contrast to studies from the city of wuhan and zhejiang province, in which most patients were males, slightly more than half of our patients were females ( . %). furthermore, the patients in the present study had milder disease with respect to a lower frequency of symptoms such as fever, dry cough, and shortness of breath. the rates of severe cases and mortality in guangzhou were much lower than reported in wuhan ( . % and %, respectively), which is similar to the rates reported in zhejiang [ ] . the rate of gastrointestinal symptoms was low in our study, which is consistent with early reports from wuhan but is contradictory to a recent us study that reported a gastrointestinal symptom rate of % [ ] . this discrepancy may be attributed to the difference in clinical characteristics between populations or to a change in the virus. however, further studies should be conducted to investigate this issue. the number of infected patients increased sharply in a short period and medical resources were in short supply, which delayed diagnosis and treatment for many patients. in addition, early diagnosis, isolation, and treatment in guangzhou might have collectively contributed to the marked reduction in the mortality rate. to further evaluate the relationship between source of infection and disease severity, patients were divided into an imported group and a local group based on epidemiological history. clinical characteristics and laboratory test results were similar between the groups, but the proportion of imported cases was higher in the severe group ( %). however, this association was not significant in the multiple logistic regression. sars-cov viral particles damage the cytoplasmic component of lymphocytes, which results in lymphocyte apoptosis. thus, patients infected with sars-cov are likely to exhibit lymphopenia. a prior study reported that % of patients with nonsevere sars-cov infections had mild lymphopenia [ ] . lymphopenia is a prominent feature of severe middle east respiratory syndrome (mers) infection [ ] , and it is common in patients with severe sars-cov infection [ ] . in our study, % of patients with severe infections had some degree of lymphopenia. this suggests that lymphopenia in sars-cov- infections may be related to the severity of the disease. patients who are older and those with multiple underlying diseases are more likely to develop severe disease [ ] . another study demonstrated that patients treated in the icu were more likely to be older and to have underlying comorbidities, dyspnea, and anorexia than patients who did not require icu admission [ ] . this is consistent with the results of our study. studies of other viral diseases, such as rabies, have indicated that the incubation period of viral diseases is significantly related to the severity of the disease. shorter incubation periods are associated with more serious disease, and this is related to the number of cells initially infected by the virus. however, no studies have examined the relationship between the incubation period of covid- and disease severity so far. we found that the incubation period was shorter in patients with severe disease, which suggests that the incubation period of covid- may be related to disease severity. in addition, patients with bilateral pneumonia diagnosed on admission by ct were more likely to develop severe disease [ ] . so it is important to process chest ct scans soon after admission. multivariate logistic regression analysis indicated that older age, male sex, and lower albumin level were independently associated with severe sars-cov- infection. alb is synthesized by hepatocytes and is the most abundant protein in plasma. gatta et al. [ ] reported that hypoalbuminemia was one of the most important factors affecting the prognosis of patients with sepsis. peires et al. [ ] showed that a decrease of alb level in patients with sepsis indicated worsening of the disease and poor prognosis. the mechanism of alb reduction due to sepsis is considered to be due to the excessive inflammatory reaction of the body. the inflammatory reaction leads to the release of oxygen free radicals and prostaglandins from kupffer cells, which can inhibit the synthesis of alb by the liver and promote the consumption and decomposition of protein, thus leading to hypoalbuminemia. so it is important to evaluate alb levels dynamically in these patients. rt-pcr analysis of respiratory or fecal samples, together with serological testing, can confirm the diagnosis of sars-cov infection in most sars patients. however, the sensitivity of detecting viral rna is reported to be . % in nasal swabs, . % in throat swabs, and . % in sputum samples [ ] . testing multiple nasopharyngeal and fecal samples increases the sensitivity of detecting viral rna [ ] , and no significant correlation between viral load and severity of sars-cov- infection has been noted. considering that ct values were comparable between the severe group and the nonsevere group, the progression of sars-cov- respiratory failure might not be due to uncontrolled viral replication, but might be related to immunopathological damage. this study has several limitations. first, the definition of the incubation period should be the time from when the pathogen invades the body to the earliest onset of clinical symptoms. the uncertainty of the exact dates (recall bias) might have inevitably affected the assessment of incubation period. in addition, by the deadline for data collection of this study (february , ), patients ( . %) were still hospitalized. at the time of manuscript submission, the onset time in some patients may have been shorter than the observation period of days, during which these patients could have developed severe disease, resulting in deviation of clinical observation characteristics. at present, there are no further follow-up data for these patients due to the urgent need for information that may guide clinical decision-making. future study with longer follow-up periods should be conducted to validate the findings of this study. the exposure history was recorded based on patient self-report at admission; all the patients were sober and able to answer questions. therefore, there may inevitably be a certain degree of subjectivity in the exposure history of the patients. we also found that < % of patients did not know where they were infected, so there may be other unknown potential exposure. moreover, viral load from other specimens is a potentially useful marker of disease severity; however, only throat swabs were available in the present study. most of the patients infected with sars-cov- in guangzhou, china were not severe cases, with relatively lower severe ration than that reported in wuhan, and this may be due to earlier diagnosis and treatment. moreover, patients with older age, male, and decreased albumin level were more likely to develop into severe ones. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. china novel coronavirus investigating and research team. a novel coronavirus from patients with pneumonia in china genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding composition and divergence of coronavirus spike proteins and host ace receptors predict potential intermediate hosts of sars-cov- evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster clinical characteristics of coronavirus disease in china clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china clinical management of severe acute respiratory infection when novel coronavirus ( -ncov) infection is suspected clinical features of patients infected with novel coronavirus in wuhan, china clinical findings in a group of patients infected with the novel coronavirus (sars-cov- ) outside of wuhan, china: retrospective case series gastrointestinal symptoms and covid- : case-control study from the united states multiple organ infection and the pathogenesis of sars t-cell immunity of sars-cov: implications for vaccine development against mers-cov clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study imaging features of novel coronavirus pneumonia coronavirus as a possible cause of severe acute respiratory syndrome quantitative detection and viral load analysis of sars-cov- in infected patients sars-cov- viral load in upper respiratory specimens of infected patients financial support. this key: cord- -prock co authors: kalligeros, markos; tashima, karen t; mylona, evangelia k; rybak, natasha; flanigan, timothy p; farmakiotis, dimitrios; beckwith, curt g; sanchez, martha; neill, marguerite; johnson, jennie e; garland, joseph m; aung, su; byrd, katrina m; o’brien, thomas; pandita, aakriti; aridi, jad; macias gil, raul; larkin, jerome; shehadeh, fadi; mylonakis, eleftherios title: remdesivir use compared to supportive care in hospitalized patients with severe covid- : a single-center experience date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: prock co background: the us food and drug administration issued an emergency use authorization for remdesivir use in patients with severe covid- . methods: we utilized data from two quaternary, acute care hospitals. the outcomes of interest were the impact of remdesivir on in-hospital death by day as well as time to recovery, clinical improvement, and discharge. we utilized cox proportional hazards models and stratified log-rank tests. results: patients were included in the study. median age was years; . % were male; / patients ( . %) who received supportive care and / patients ( . %) who received remdesivir died. the unadjusted risk for -day in-hospital death was lower for patients who received remdesivir compared to patients who received supportive care (hr . ; % ci: . - . ). although this trend remained the same after adjusting for age, sex, race and oxygen requirements on admission (ahr . ; % ci: . - . ), as well as chronic comorbidities and use of corticosteroids (ahr . ; % ci: . - . ), it did not reach statistical significance. the use of remdesivir was not associated with an increased risk of acute kidney injury (aki) and liver test abnormalities. although not statistically significant, the rate ratios for time to recovery, clinical improvement, and discharge were higher in women and black or african american patients. conclusion: patients on remdesivir had lower, albeit not significant, all-cause in hospital mortality, and the use of remdesivir did not increase the risk for aki. promising signals from this study need to be confirmed by future placebo-controlled randomized clinical trials. the development of safe and effective therapeutic agents against severe acute respiratory syndrome coronavirus (sars-cov- ) is a top priority in the battle against the covid- pandemic. remdesivir, also known as gs- , is an intracellularly metabolized nucleotide prodrug that inhibits viral rna polymerases and has a broad spectrum of antiviral activity, which includes corona-and flaviviruses [ ] . animal studies have shown remdesivir to be efficacious against sars-cov- and middle east respiratory syndrome (mers)-cov [ , ] . during the early days of the covid- pandemic, it was among the first drugs to show in vitro activity against sars-cov- [ ] . despite high expectations for remdesivir in treating covid- [ , ] , the results from the first randomized placebo-controlled trial from china were inconclusive [ ] . however, results of a larger scale multicenter trial conducted by the national institute of allergy and infectious diseases, showed a significant clinical benefit in terms of time to recovery [ ] . subsequently, the us food and drug administration (fda) issued an emergency use authorization for remdesivir use in patients with severe covid- [ ] . in march , our institution became part of a multicenter open-label, phase- clinical trial that studied the use of remdesivir in patients with severe covid- . for this study, we analyzed data from patients who participated in the aforementioned trial, and compared them to patients with severe covid- who received supportive care at our institution to investigate the efficacy and safety of remdesivir in patients with severe covid- . a c c e p t e d m a n u s c r i p t we utilized data from two quaternary, acute care hospitals, rhode island hospital (rih) and the miriam hospital (tmh), located in providence, rhode island, usa, which function as a single academic medical center. all consecutive hospitalized patients from february th to may th , who had a positive pcr nasopharyngeal or oropharyngeal sars-cov- swab were screened for potential study inclusion. the institutional review board of rih and tmh approved this observational study. starting on march th, both rih and tmh became part of a phase , multi-center, open-labeled clinical trial (nct ) [ ] . all patients hospitalized with pcr confirmed covid- were evaluated by infectious disease specialists in both hospitals for potential trial inclusion. to be considered eligible for trial inclusion, patients had to meet the following criteria: ) currently hospitalized, aged ≥ years, ) sars-cov- infection confirmed by pcr test ≤ days before trial enrollment ) spo ≤ % on room air or requiring supplemental oxygen at screening ) presence of radiographic evidence of pulmonary infiltrates. in addition, patients who met any of the following clinical exclusion criteria were not considered eligible: ) alt or ast > times of the upper normal limit (unl), ) creatinine clearance < ml/min using the cockcroft-gault equation, ) pregnant or breastfeeding. trial participants received remdesivir intravenously (iv) as a -mg loading dose on day , followed by a daily -mg maintenance dose on days through or until hospital discharge, death, or meeting criteria for study drug hold or discontinuation (serious adverse event related to rdv, alt > xunl, alt > xunl and total bilirubin > xunl, creatinine clearance < ml/min). patients who were discharged before day were followed-up with a post-discharge follow-up phone call on day . the a c c e p t e d m a n u s c r i p t trial protocol was approved by a centralized institutional review board and was monitored by an independent data and safety monitoring board. each patient provided informed consent. if the patient was unable to provide consent, the patient's legally authorized representative provided surrogate consent. in the above-mentioned phase open-labeled trial, all trial participants received remdesivir, and there was no placebo-controlled study arm. for the purposes of the present study we created a control group consisting of hospitalized patients with pcr confirmed covid- who did not receive remdesivir. in order to identify controls, we screened all patients who were admitted to either rih or tmh from february th to may th and did not receive remdesivir. after identifying those patients and in an effort to minimize selection bias we used the following inclusion and exclusion criteria: ) hospitalized for at least h ) sars-cov- infection confirmed by pcr ) spo ≤ % on room air or requiring supplemental oxygen within the first h of admission ) presence of radiographic evidence of pulmonary infiltrates. in addition, patients who met any of the following clinical exclusion criteria were not considered eligible: ) alt or ast > times of the upper normal limit (unl); and ) creatinine clearance (crcl) < ml/min using the cockcroft-gault equation. patients from the remdesivir arm could have been enrolled in the remdesivir trial during any day of their hospital stay, as long as they met the predefined inclusion criteria. for the purposes of this study, this could have been a potential source of immortal time bias [ ] because those patients should have been alive at least until the day of remdesivir trial enrollment. as a result, after defining the date of hospital admission as day for both study arms, we included only patients who received remdesivir within the a c c e p t e d m a n u s c r i p t first h of their admission, while we excluded all patients who died within the first h from both study arms. we obtained data through our institution's electronic medical records (emrs). for each patient we extracted the following information: age, sex, race, ethnicity, days from onset of symptoms, imaging results, weight, vital signs and laboratory values (both on admission and during hospitalization), preexisting medical conditions, admission to the intensive care unit (icu), use of mechanical ventilation, use of systemic corticosteroids [ ] , hospitalization outcome (death or discharge) and incidence of acute kidney injury (aki) using the kdigo criteria [ ] . the first available vital signs and laboratory values within hours from admission were used to assess inclusion eligibility for patients in the supportive care arm. for patients in the supportive care arm we also calculated crcl on admission using the cockcroft-gault equation. finally, all hospitalized patients with pcr confirmed covid- were evaluated by id specialists for potential inclusion in the remdesivir trial and this evaluation was documented in the emr. for patients in the supportive care arm we additionally extracted the initial id evaluation and, if present, the reason/s for not enrolling in the remdesivir trial. the primary outcome of interest was the impact of remdesivir on all cause in-hospital death by day . as secondary outcomes we assessed the impact of remdesivir on time to clinical recovery, time to clinical improvement and time to discharge. all outcomes were censored at day for patients hospitalized more than days. recovery was achieved when a patient satisfied categories or on the following -point ordinal scale: =not hospitalized; =hospitalized without requiring further supplemental oxygen; =hospitalized requiring supplemental oxygen; =hospitalized requiring non-invasive positive pressure a c c e p t e d m a n u s c r i p t ventilation (nippv) or high-flow oxygen devices (hfod); =hospitalized requiring invasive mechanical ventilation or ecmo; =death. similarly, clinical improvement was achieved when a patient had a twopoint improvement on the aforementioned -point ordinal scale. finally, using the kdigo criteria, we assessed the incidence of aki in patients receiving remdesivir compared to patients receiving supportive care. kdigo defines aki as any of the following: increase in serum creatinine by . mg/dl or more within hours or increase in serum creatinine to . times baseline or more within the last days or urine output less than . ml/kg/h for hours [ ] . for patients' baseline characteristics, we represented continuous measurements as means (sds) or as medians (iqrs) and we compared them using student's t test and the mann-whitney-wilcoxon test, respectively. for categorical data, we used pearson's chi-square test. for the primary study outcome, i.e. the impact of remdesivir use on in-hospital death, we utilized both univariate and multivariate cox proportional-hazards models. in the multivariate model we accounted for potential confounders associated with covid- mortality such as age, sex, race, chronic comorbidities (heart disease, diabetes, hypertension, chronic pulmonary disease, obesity), use of systemic corticosteroids, as well as patients' oxygen requirements on admission. similar models were implemented to assess the risk of developing aki during the -day follow up period. for all models we assessed the proportional hazards assumption using weighted schoenfeld residuals. in order to evaluate the secondary outcomes of time to clinical recovery, time to clinical improvement and time to discharge (measured from the time of admission), we utilized a stratified logrank test and calculated the mantel-cox rate ratios. we stratified based on oxygen requirements on admission (i.e., room-air with spo < %, low-flow oxygen, nippv or hfod, mechanical ventilation), age group ( - , - , >/ years), race, sex and date of symptom onset (< days, >/ days). if a patient a c c e p t e d m a n u s c r i p t died before day , they were right censored at day . outcomes of patients who were discharged to a hospice before day where censored at day of discharge. for our analyses, % confidence intervals and p-values are shown. the statistical significance threshold was set at . . all analyses were performed using stata v . (stata corporation, college station, tx). a c c e p t e d m a n u s c r i p t from february th to may th we identified consecutive patients hospitalized with pcr confirmed covid- . among those patients, received supportive care and received remdesivir. among, patients who received supportive care, met the inclusion criteria of our study and comprised the control group. more specifically, patients were excluded due to crcl < l/min or because crcl could not be calculated due to missing weight measurement, patients did not meet severity inclusion criteria, were excluded due to alt or ast > times the unl, patients were excluded due to normal chest imaging findings, and patients were excluded due to death within the first hours after admission. among the patients who received rdv we excluded patients who received remdesivir for the purposes of other clinical trials (a moderate severity trial or compassionate use) and patients who received rdv after the first h (supplementary table ). in figure , we present the detailed patient selection flowchart. as of june th , all patients had completed the -day observational period, were discharged, or died. of note, none of the patients included in this analysis met the criteria for remdesivir discontinuation. in total patients were included in the study and their baseline characteristics are depicted in table among the control group, reasons for not enrolling in the remdesivir trial included: patients ( . %) were deemed eligible for enrollment by the trial investigators but they were not enrolled for undocumented reasons; patients ( . %) refused participation; patients ( . %) were not eligible given their sars-cov- pcr was older than hours (trial exclusion criterion) but met the rest inclusion/exclusion criteria; patients ( . %) were eligible but the trial was paused to enrollment at the time of assessment; and patients ( . %) were eligible but were unable to provide consent and a legally authorized representative was not available. in total, / patients ( . %) died within days of their hospital admission. more specifically, / patients ( . %) who received supportive care and / patients ( . %) who received remdesivir died. in our primary unadjusted analysis, the risk of -day all cause in-hospital death was lower for patients who received remdesivir compared to patients who received supportive care (hazard ratio (hr) . ; % ci: . - . ), albeit it did not reach statistical significance. these estimates remained after adjusting for age, sex, race, oxygen requirements on admission (ahr . ; % ci: . - . ), use of systemic corticosteroids and chronic comorbidities such as hypertension, heart disease, chronic pulmonary disease, obesity and diabetes (ahr . ; % ci: . - . ) ( table and supplementary figure ). the median time to clinical recovery was days for the remdesivir arm ( % ci: - ) and days for the supportive care arm ( % ci: - ). using mantel-cox rate ratios we found no significant difference in time to recovery, regardless of the stratification variable. similarly, we found no significant differences between the two study arms in terms of time to clinical improvement and time to discharge. although a c c e p t e d m a n u s c r i p t not reaching statistical significance, the rate ratios for time recovery, clinical improvement and discharge were higher in women and black or african american patients who received remdesivir. finally, the rate ratio for time to recovery and time to discharge, was higher among patients who received remdesivir during the first days of their symptoms onset, albeit without reaching statistical significance [rr . ( . - . ) and . ( . - . ), respectively]. results are presented on table . utilizing the kdigo criteria for aki and the common terminology criteria for adverse events (ctcae v . ), we studied the incidence of aki, transaminitis and hyperbilirubinemia and found no statistically significant difference among the two groups ( table ). the use of remdesivir was not associated with an increased risk of aki in both univariate (hr . ; % ci: . - . ) and multivariate cox proportional hazards models which were adjusted for age, sex, race and oxygen requirements on admission (ahr . ; % ci: . - . ) as well as use of systemic corticosteroids and chronic comorbidities (ahr . ; % ci: . - a c c e p t e d m a n u s c r i p t in order to provide a cohesive assessment of the efficacy of remdesivir, we compared the clinical outcomes of patients who were hospitalized with severe covid- (requiring supplemental oxygen and having abnormal imaging findings) and received either remdesivir or supportive care. after using similar inclusion and exclusion criteria for both study arms, we found that patients on remdesivir had lower allcause in hospital mortality, but this did not reach statistical significance. in addition, we observed a shortened time to recovery, time to clinical improvement and time to discharge among women and black or african american patients, again without reaching statistical significance. importantly, the use of remdesivir did not increase liver test abnormalities and the risk for aki. to date, there are limited studies describing the safety and efficacy of remdesivir in patients with covid- . in the study by grein et al. [ ] , authors described the compassionate use of remdesivir in patients with severe covid- . in this multicenter study, patients received remdesivir for days ( mg on day followed by mg for days) and had a median follow-up of days. authors reported oxygen need improvement in % of patients, while out of patients ( %) died. however, the interpretation of those findings was limited by the lack of a control arm and the small sample size. in april , wang et al. reported the first randomized, double-blind, placebo-controlled trial, comparing patients with severe covid- who received either remdesivir or placebo [ ] . the study included patients from china and was terminated early due to lack of eligible study participants (initial sample goal was patients). the authors found that remdesivir use did not significantly improve the time to clinical improvement (hr . ) or improve -day mortality. the first study to yield a clear clinical benefit from remdesivir use in patients with covid- was the preliminary report from the ongoing double-blind, randomized, placebo-controlled trial by the niaid [ ] . in this study, authors found that patients who received days remdesivir had a significantly faster a c c e p t e d m a n u s c r i p t time to recovery compared to the placebo group. our study did not yield the same clinical benefit in terms of time to recovery, possibly due to a smaller sample size, differences in patient characteristics and baseline oxygen needs, and lack of randomization. however, our mortality estimates were similar. specifically, beigel et al. reported a . % and . % -day mortality for the remdesivir and the placebo group, respectively, while they reported a hr for death of . ( % ci: . - . ). similarly, we found a . % and . % -day in-hospital mortality for the remdesivir and the supportive care group, respectively, while our adjusted hr estimate for death was . ( % ci: . - . ). although the current literature and our study suggest that there are potential benefits from remdesivir use, the magnitude of those benefits will also be determined by remdesivir safety, access, and cost [ ] . in terms of safety, remdesivir appears to be tolerated well by most patients [ ] , and our findings showed that the risk of -day aki development was not increased compared to supportive care arm. regarding the access and cost, since current supplies of the drug and its worldwide availability remain questionable [ ] , it is important for future studies to confirm the non-inferiority of a -day compared to a -day regimen [ ] , as well as identify those patients who may benefit the most. by imposing the same exclusion criteria for patients who participated in the remdesivir trial and for those who composed our study's control arm, we minimized selection bias. this was also reflected by similar baseline characteristics and oxygen needs among the two arms. then, by determining the reasons that patients in the control arm were not enrolled in the remdesivir trial, we confirmed that indication bias was minimized in this observational study. in addition, by including only those patients who received remdesivir within the first h of their admission and excluding patients from the control arm who died within the first h of their admission, we minimized immortal-time bias. finally, utilizing data from consecutive patients hospitalized in the same institution, we minimized any differences in terms of treatment protocols (e.g. ventilatory strategies, concomitant medications) as well as hospitalization and discharge thresholds across study population. a c c e p t e d m a n u s c r i p t our study has limitations that should be taken into consideration. first, the observational, nonrandomized nature of the present study introduces the possibility of bias inherent to this study design. for example, the rationale behind a patient's decision to refuse participation in remdesivir trial may reflect less severe disease which cannot be measured by baseline oxygen needs alone. although baseline oxygen needs and other related conditions were similar among the two study arms, there is a chance that at least some patients in the supportive arm were less sick. furthermore, in order to minimize selection bias, we excluded patients who received remdesivir after the first h of admission. in supplementary table , we include the characteristics and outcomes of all the patients enrolled who received remdesivir, irrespective of time of treatment initiation, including those who received remdesivir after the first h of admission and were excluded from the analysis. in addition, as in all similar trials, many patients reported an estimated and not an exact date of symptom onset. finally, the present study might be underpowered [ ] . in conclusion, our single-center analysis adds to the understanding that remdesivir may have potential clinical benefits in patients with severe covid- , and the use of remdesivir did not increase liver test abnormalities and the risk for aki. notably, there was a trend for shortened time to recovery, time to clinical improvement, and time to discharge among women and black or african american patients. these promising signals need to be confirmed by future trials. such trials should include evaluation for women and racial groups. m a n u s c r i p t remdesivir: a review of its discovery and development leading to emergency use authorization for treatment of covid- prophylactic and therapeutic remdesivir (gs- ) treatment in the rhesus macaque model of mers-cov infection broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro compassionate use of remdesivir for patients with severe covid- first case of novel coronavirus in the united states remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial remdesivir for the treatment of covid- -preliminary report fact sheet for health care providers: emergency use authorization (eua) of remdesivir (gs- ™) remdesivir for or days in patients with severe covid- problem of immortal time bias in cohort studies: example using statins for preventing progression of diabetes effect of dexamethasone in hospitalized patients with covid- : preliminary report diagnosis, evaluation, and management of acute kidney injury: a kdigo summary (part ) remdesivir for covid- : challenges of underpowered studies gilead sciences inc. gilead sciences statement on expanding global supply of investigational antiviral remdesivir a c c e p t e d m a n u s c r i p t key: cord- -q k s authors: kösters, katrin; schwarzer, sitha; labuhn, achim; rübben, albert; yang, sara; hessler, frank; assaf, chalid title: cutaneous vasculitis in a patient with covid- date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: q k s we describe a -year-old patient with coronavirus disease who developed a bullous hemorrhagic rash that progressed to necrotic lesions. histopathology confirmed a vasculitis of small- and medium-sized cutaneous vessels. a -year-old patient with hypertension presented to our emergency department with suspected varicella infection. he had felt generally unwell for the past weeks, starting with a sore throat but without cough or shortness of breath. three days before presentation, he developed a vesiculous rash that started on the face and quickly progressed to involve the whole body, resembling chickenpox. on admission, he tested positive for severe acute respiratory syndrome coronavirus (sars-cov- ) by polymerase chain reaction of an oropharyngeal swab. the patient had a temperature of . °c, a respiratory rate of breaths per minute, and an oxygen saturation of % on room air. examination of the chest was unremarkable. laboratory tests showed leukocytosis ( . per nanoliter) with normal lymphocytes and an elevated c-reactive protein of mg per liter. chest computed tomography showed no abnormalities. within days, the skin lesions first progressed to painful hemorrhagic bullae and then necrotic lesions surrounded by diffuse erythema on the trunk, arms, and legs. the nasal septum, oral mucosa, and ears were also involved ( figure a -c). inflammatory markers increased markedly, with a c-reactive protein of . mg per liter and procalcitonin of . ng per milliliter. bacterial superinfection was suspected, and the patient was started on intravenous cefazolin. bacterial cultures of blood and skin swab remained negative. skin lesions were negative for hsv-and vzv-dna, and serum from the patient was negative for sars-cov- rna. a skin biopsy demonstrated a small-and medium-sized vessel vasculitis with neutrophils, some eosinophils, and histiocytes ( figure d ). small blood vessel occlusion by microthrombi, which has been described in patients with coronavirus disease (covid- ) [ ] , could not be demonstrated. direct immunofluorescence of the skin biopsies was negative, as were antineutrophil cytoplasmic autoantibodies and antiphospholipid antibodies. no symptoms or signs of systemic organ involvement were present. under suspicion of a sars-cov- -induced cutaneous vasculitis, the patient was treated with prednisolone at . mg per kilogram. within days, the vasculitic skin manifestations and general condition improved. variable and heterogenous skin manifestations in patients with covid- have been described that appear before, during, and after the disease [ ] . a rash [ ] . however, other groups have described skin manifestations in up to % of covid patients [ , ] . cutaneous manifestations have been classified in inflammatory/exanthematous eruptions, for example, urticaria, erythematous/maculopapular/ morbilliform rash, and papulovesicular exanthem, and in vasculopathic/vasculitic patterns including chilblain-like acral lesions, livedo reticularis-like lesions, and purpuric "vasculitic" rash [ ] . chilblain-like and livedo reticularis-like lesions have been explained by the occlusion of small blood vessels (occlusive thrombotic microvasculopathy) and an associated procoagulant state. magro described a pauci-inflammatory thrombogenic vasculopathy with complement deposition in patients with a purpuric skin rash [ ] . according to marzano, the vasculitic pattern was extremely rare. however, our case demonstrates a small/medium-sized vessel vasculitis with involvement of mucous membranes as the cause of skin manifestations in a patient with covid- that appeared late in the disease. no other explanation for the vasculitis was apparent, suggesting that it might have been caused by sars-cov- . viral infections represent a significant proportion of infection-associated cutaneous vasculitic syndromes [ ] . sars-cov- could be another virus that triggers an immunologic process that leads to cutaneous vasculitis. this case underscores the need for biopsy to determine the nature of the underlying disease-here covid-associated coagulopathy and microvasculopathy vs vasculitis. based on the histopathologic findings, an adequate anti-inflammatory treatment with steroids was initiated. complement associated microvascular injury and thrombosis in the pathogenesis of severe covid- infection: a report of five cases classification of the cutaneous manifestations of covid- : a rapid prospective nationwide consensus study in spain with cases clinical characteristics of coronavirus disease in china cutaneous manifestations in covid- : a first perspective coagulopathy and antiphospholipid antibodies in patients with covid- cutaneous manifestations in patients with covid- : a preliminary review of an emerging issue virus-induced vasculitis financial support. this work was supported by a grant from förderkreis stiftung herzchirurgie und kardiologie krefeld e. v. to s.s. potential conflicts of interest. all authors: no conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed.patient consent. the patient's written consent was obtained. study design. the design of the work conforms to standards currently applied in germany. the authorizing body is Ärztekammer nordrhein. key: cord- - jk vh authors: lindholm, david a; kiley, john l; jansen, nathan k; hoard, robert t; bondaryk, matthew r; stanley, elizabeth m; alvarado, gadiel r; markelz, ana e; cybulski, robert j; okulicz, jason f title: outcomes of coronavirus disease drive-through screening at an academic military medical center date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: jk vh drive-through coronavirus disease screening can evaluate large numbers of patients while reducing healthcare exposures and personal protective equipment use. we describe the characteristics of screened individuals as well as drive-through process and outcome measures. optimal drive-through screening involves rapid turnaround of test results and linkage to follow-up care. mitigation of the coronavirus disease (covid- ) pandemic requires increased access to testing for its causative agent, severe acute respiratory syndrome coronavirus (sars-cov- ) [ ] . drive-through delivery of healthcare was modeled in a training exercise as a safe and efficient mechanism to provide large populations access to testing during the h n pandemic [ ] . during the current pandemic, drive-through screening has processed large volumes of patients more efficiently than conventional in-clinic assessment, while reducing potential healthcare exposures and personal protective equipment (ppe) use [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . however, there are limited data regarding patient characteristics or outcomes in the drive-through setting [ ] [ ] [ ] [ ] ] . brooke army medical center (bamc) (san antonio, tx) implemented drivethrough screening for sars-cov- in march . we describe the demographic and clinical characteristics of screened individuals and report test turnaround time and hospital admissions as safety-outcome measures. drive-through covid- screening at bamc commenced march , . medical technicians, wearing single-patient gloves and extended-use surgical masks, used a questionnaire to interview patients through an open vehicle window in a designated parking lot adjacent to the hospital. the screening questionnaire collected demographics, military duty/beneficiary status, recent travel, contact with confirmed covid- cases, and current symptoms. each questionnaire was reviewed by a licensed medical provider to disposition patients for sars-cov- testing, no testing, or immediate referral to the emergency department (ed) for additional evaluation. severe acute respiratory syndrome coronavirus testing was performed, at the provider' s discretion, for any symptomatic beneficiary regardless of age or an epidemiologic link to covid- given local transmission. symptoms were defined as an affirmative answer to or more of the following: fever > . °f, chills, cough, dyspnea, or sore throat. all samples were obtained via nasopharyngeal swab by a nurse or medical technician wearing single-patient gloves and an extended-use gown, n respirator, and face shield. severe acute respiratory syndrome coronavirus testing was performed at bamc using the centers for disease control and prevention (cdc) -ncov real-time polymerase chain reaction (rt-pcr) diagnostic panel (cdc, atlanta, ga). due to limitations in testing capacity, samples were also outsourced (covid- rt-pcr test; laboratory corporation of america, burlington, nc). all patients were provided educational materials about covid- . this analysis was performed to optimize bamc's drive-through screening process and received a not research determination from bamc's institutional review board. questionnaires for all patients presenting to the drive-through from march to , were reviewed, and the first drive-through encounter for each patient was included. data for sars-cov- results, testing platform used, and turnaround time were obtained from our microbiology laboratory. the electronic medical record was reviewed ( ) for comorbid conditions in positive cases and ( ) for additional sars-cov- testing and bamc hospital admission within days of screening for all patients. descriptive statistics were performed using χ , fisher's exact, or wilcoxon rank-sum test, where appropriate; significance was set at p < . . a total of patients presented for screening during the evaluation period; ( . %) patients presented multiple times. the median age was years (interquartile range [iqr], - ), with a similar proportion of men and women (table ) . severe acute respiratory syndrome coronavirus testing was performed for ( . %) patients, ( . %) of which were performed in-house and ( . %) were outsourced, with a median turnaround time of hours (iqr, - ) and hours (iqr, - ), respectively. a significantly higher proportion of healthcare workers and active-duty members were tested. nine ( . %) patients were dispositioned directly to the ed, all of whom tested negative and were discharged from the ed. of those screened but not tested, ( . %) later received testing within days after their drive-through visit, and all had negative results. twenty-nine ( . %) patients with negative index-test results had a subsequent test performed within days, only one of whom converted to positive on day . severe acute respiratory syndrome coronavirus testing was positive in ( . %) patients and inconclusive in ( . %) patients. three ( . %) patients had cancelled drive-through tests due to a subsequent ed visit or hospitalization, where testing was repeated using the in-house assay to expedite results, or due to a sample-collection error; all repeated tests were negative. additional analyses were conducted for those with positive or negative drive-through testing (n = ). positive tests were more commonly observed in women than men ( . % vs . %; p = . ). chills were reported more often in patients who tested positive ( . %) versus negative ( . %; p = . ); there were no other significant differences in reported symptoms. comorbidities for confirmed cases included allergic rhinitis/ seasonal allergies ( . %), obesity ( . %), and hypertension ( . %) ( table ) . no healthcare workers involved in screening or sample collection were diagnosed with covid- . eleven ( . %) patients were hospitalized, of whom had been tested for sars-cov- . two patients had positive tests and an admitting diagnosis of covid- , whereas the remaining patients were admitted for non-covid- illnesses. there was a trend towards hospitalization for patients testing positive ( . %) versus negative ( . %; p = . ). the median time from screening to hospitalization was day (iqr, - ), with the patients positive for sars-cov- admitted - days postscreening. a standardized approach to drive-through screening allows for consistent differentiation of possible covid- -related symptoms and provides a safe, efficient mechanism for screening large numbers of patients, while minimizing unnecessary exposure to the healthcare environment. drive-through screening was also an effective method to test healthcare workers [ , , ] , who represented approximately one quarter of those tested in our analysis. although our screening method involved face-toface interviews of patients in their vehicles, other drive-through programs have implemented a web-based questionnaire [ ] , telephone triage [ - , , ] , or onsite microphones [ ] for patient assessment or communication. although we had no cases of covid- in healthcare workers with direct patient interaction, these adaptations would allow for further decreased potential cross-exposure of healthcare workers and patients as well as decreased ppe use [ , [ ] [ ] [ ] [ ] ] . a potential risk of drive-through screening is that patients who would otherwise require further medical evaluation due to complex or concerning presentations could be missed due to anchoring on the presence or absence of indications for sars-cov- testing. in our analysis, < % of patients screened were dispositioned to the ed, and approximately % of patients screened required hospitalization within days, although we did not capture admissions to outside facilities. our proportion of cases hospitalized ( . %) was similar to that seen in a seattle drive-through for healthcare workers ( . %) [ ] . nonetheless, the median time from screening to admission suggests that some patients requiring additional medical evaluation may have reported to the drive-through. positioning the drive-through in close proximity to the ed [ , , ] and having provider oversight may have mitigated risk for our program. recognizing the need to mitigate risk, the mayo clinic has incorporated ( ) telehealth follow-up for confirmed cases and ( ) an in-person clinic for those with respiratory symptoms who tested negative but needed further evaluation [ , ] ; by contrast, a drivethrough program in malaysia transported all confirmed cases to their hospital via ambulance [ ] . the use of an algorithm to identify more seriously ill patients and linkage to primarycare and/or emergency follow-up are essential elements of a drive-through program. reflective of active-duty military, our analysis had a high proportion of young and healthy patients. drive-through platforms drawing older patients and/or those with more comorbidities may require an even greater emphasis on triage to follow-up or immediate care. a limitation to our process was the approximately -day turnaround time for outsourced tests due to high demand and limited testing options at that time. this significantly delayed contact tracing, which is critical in mitigating covid- [ ] . current guidance for outpatient testing states that sars-cov- results should return within hours of collection to inform decision making at the individual-patient and public health levels [ ] . other drive-through centers have reported a -to -hour turnaround time [ , [ ] [ ] [ ] . because access to testing with a relatively quick turnaround is important to optimize drive-through effectiveness, bamc eliminated outsourced testing after the analysis period and added a rapid sars-cov- assay. an additional limitation was that some patients who had symptoms recorded by questionnaire were not tested. although specific reasons were not captured, this may have been due to variability in self-reporting of symptom severity [ ] , additional clarification after provider review (eg, chronic or resolved symptoms), or ineligibility for testing due to lack of militarybeneficiary status. however, none of the screen-only patients later tested positive or were hospitalized for covid- within days. although our testing protocol focused on symptomatic patients, a universal-testing program in south korea found that . % of asymptomatic patients without a history of close contact tested positive [ ] . broader testing criteria to include asymptomatic individuals can be considered if resources allow to inform medical or public health decision making [ ] . given the ongoing need for mitigation of covid- as the economy reopens, optimized access to accurate, efficient, safe testing is important. the bamc experience shows this is possible through a drive-through platform employing medical technicians as physician extenders. drive-through screening should be optimized for quick turnaround time for test results and improved linkage to primary and/or emergency care. as sars-cov- testing availability increases and guidelines recommend testing selected asymptomatic patients [ ] , drivethrough screening could also be adapted to meet an increased future demand. disclaimer. the contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views or policies of the uniformed services university of the health sciences, brooke army infectious diseases society of america guidelines on the diagnosis of covid- drive-through medicine: a novel proposal for rapid evaluation of patients during an influenza pandemic drawing on israel's experience organizing volunteers to operationalize drive-through coronavirus testing centers drive-through screening center for covid- : a safe and efficient screening system against massive community outbreak innovative screening tests for covid- in south korea covid- drive through testing: an effective strategy for conserving personal protective equipment rapid deployment of a drive-through prenatal care model in response to the coronavirus disease (covid- ) pandemic establishing mayo clinic's coronavirus disease virtual clinic: a preliminary communication drive-through testing: a unique, efficient method of collecting large volume of specimens during the sars-cov- (covid- ) pandemic drive-through covid- testing during the pandemic: a safe, efficient, and scalable model for pediatric patients and healthcare workers analysis of sars-cov- screening clinic (including drive-through system) data at a single university hospital in south korea from comparing south korea and italy's healthcare systems and initiatives to combat covid- bonuses and pitfalls of a paperless drivethrough screening and covid- : a field report drive-through testing in covid- : experience from nhs lothian prevalence of covid- infection and outcomes among symptomatic healthcare workers in implementation of mitigation strategies for communities with local covid- transmission differences in self-reported severity of symptoms between women and men experiencing influenza-like illness medical center, the u.s. army medical department, the u.s. army office of the surgeon general, the department of the army, the department of the air force, the department of defense, or the u.s. government. mention of trade name, commercial products, or organizations does not imply endorsement by the u.s. government. the authors are employees of the u.s. government. this work was prepared as part of their official duties. title u.s.c. § provides that copyright protection under this title is not available for any work of the u.s. government. title u.s.c. § defines a u.s. government work as a work prepared by a military service member or employee of the u.s. government as part of that person's official duties.potential conflicts of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. key: cord- -phmd u d authors: siegler, aaron j; hall, eric; luisi, nicole; zlotorzynska, maria; wilde, gretchen; sanchez, travis; bradley, heather; sullivan, patrick s title: willingness to seek laboratory testing for sars-cov- with home, drive-through, and clinic-based specimen collection locations date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: phmd u d background: sars-cov- virus testing for persons with covid- symptoms, and contact tracing for those testing positive, will be critical to successful epidemic control. willingness of persons experiencing symptoms to seek testing may determine the success of this strategy. methods: a cross-sectional, online survey in the united states measured willingness to seek testing if feeling ill under different specimen collection scenarios: home-based saliva, home-based swab, drive-through facility swab, and clinic-based swab. instructions clarified that home-collected specimens would be mailed to a laboratory for testing. we presented similar willingness questions regarding testing during follow-up care. results: of participants, comprising a broad range of sociodemographic groups, % were willing to test with a home saliva specimen, % with home swab, % with drive-through swab, and % with clinic collected swab. moreover, % indicated they would be more likely to get tested if there was a home testing option. there were no significant differences in willingness items across sociodemographic variables or for those currently experiencing covid- symptoms. results were nearly identical for willingness to receive testing for follow-up covid- care. conclusions: we observed a hierarchy of willingness to test for sars-cov- , ordered by the degree of contact required. home specimen collection options could result in up to one-third more symptomatic persons seeking testing, facilitating contact tracing and optimal clinical care. remote specimen collection options may ease supply chain challenges and decrease the likelihood of nosocomial transmission. as home specimen collection options receive regulatory approval, they should be scaled rapidly by health systems. a central component of covid- disease containment strategies will be scaled-up testing and self-isolation/quarantine as applicable. , this strategy requires active identification of case patients, contact tracing, and testing of people within their networks. successful implementation of this strategy will require widespread access to testing; substantial efforts are underway to increase sars-cov- virus testing capacity in the united states and globally. in addition to access (e.g. supply), success of testing strategies will be contingent on the extent to which they are acceptable to patients (e.g. demand). case identification and contact tracing efforts depend greatly on willingness to test among patients experiencing covid- disease-like symptoms. to inform patient isolation strategy, those who have tested positive should be tested again during follow-up care (us centers for disease control and prevention recommends two consecutive tests collected ≥ hours apart) if supplies and laboratory capacity are sufficient,; alternatively, a symptom-based strategy is recommended. patient willingness to seek testing is especially critical because many persons infected with sars-cov- may experience only mild symptoms: in italy, % of diagnosed cases have been classified as mildly symptomatic, although such estimates may be an undercount due to the likely lower frequency of test seeking in this group. for other infectious diseases, self-collection procedures have long been practiced, , been identified as highly acceptable and preferred to in-clinic procedures, and having diagnostic metrics comparable to healthcare worker specimen collection. , calls for home-based specimen collection or drive-through specimen collection models to address sars-cov- virus test scale-up have cogently argued that these approaches have the benefit of ( ) avoiding burdening hospitals at a critical time, ( ) avoiding potential nosocomial infections (the risk of acquiring disease from clinical or laboratory settings), ( ) likely lowering costs, and ( ) potentially achieving rapid scale-up due to laboratory centralization. , one additional benefit of home specimen collection might be that supply chain issues, such as stockouts of swabs or personal protective equipment, could be alleviated if non-traditional specimens such as saliva or non-traditional locations such as home settings prove sufficient. drive-through sars-cov- virus testing sites already exist, and a number of laboratories are working to additionally validate home-based self-specimen collection for sars-cov- testing. protocols for the self-collection of specimens at home for sars-cov- testing are currently being explored. for instance, two saliva-based sars-cov- virus tests have recently received emergency use authorization from the us food and drug administration for home-based specimen collection. , these protocols involve persons being mailed specimen collection materials and instructions, self-collection of specimens at home, and return of specimens to a central laboratory using a supplied mailer. we conducted an online survey to assess patient willingness to use the following sars-cov- testing modalities for clinical care: home-based specimen collection, drive-through testing, and clinic-based testing. we hypothesized that persons would be more willing to use home-based and drive-through specimen collection modalities compared to clinic-based modalities. we recruited potential participants using online social media advertisements from march th to april st, . to be eligible, respondents had to be years of age or older. given the disproportionate impact of covid- on communities of color, on the final day of data m a n u s c r i p t collection eligibility criteria were adjusted to screen out non-hispanic white respondents in an effort to increase minority representation in the sample. participants completed a nonincentivized online survey after being recruited from social media sites with banner advertisements requesting participation in covid- survey research. survey measures included previously published demographic items, covid- disease knowledge, covid- disease stigma items, and a list of covid- disease symptoms based on several sources. [ ] [ ] [ ] regions were defined according to us census bureau classifications of states. to understand whether responses were differential by state covid- burden, we created a binomial variable with high burden states defined as having > cases per , population (ny, nj, ma, la, ct) at the time of the survey; these states accounted for over half of all covid- cases at that time. we developed a series of questions about willingness to use different testing modalities, each rated with a five-point likert scale ( -strongly disagree to -strongly agree). the questions were based on home test willingness questions we have previously used in hiv prevention research. definitions for each testing modality were: "a home saliva sample would involve you spitting in a tube and sending it to a certified laboratory," "a home throat swab would involve you using a throat swab and sending it into a certified laboratory," "a drive-through site for throat swab would involve your traveling to a drive-through facility in your car to have a healthcare worker collect the swab," and "a laboratory throat swab would involve your traveling to a laboratory facility in a clinic or private laboratory to have a healthcare worker collect the swab." other questions assessed whether persons rated themselves as more likely to seek testing if the option to collect specimens at home for mail-in testing were available. the full text of survey items can be seen in supplement . all participants completed a written electronic consent procedure, and study procedures were approved by the emory university irb. from , persons initiating the survey screener, , were ineligible, , did not consent or provided only partial survey responses, and , completed all willingness items for the analysis dataset (figure ). the sample was % (n= ) aged - , % ( ) aged - , % ( ) aged - , and % ( ) aged or older. females comprised % ( ), males % ( ), and other gender identity % ( ) . overall % ( ) were non-hispanic white, % ( ) were hispanic, % ( ) were non-hispanic black, % ( ) were asian/pacific islander, and % ( ) were native american/alaska native or identified as mixed race or other non-hispanic. covid- knowledge was high with % ( ) answering at least of knowledge questions correctly, and covid- stigma was moderate with % ( ) answering at least one of four stigma questions in a stigmatizing direction. a majority of % ( , ) thought they were unlikely to have covid- , although % ( ) reported or more of a broad range of potential covid- symptoms. m a n u s c r i p t home specimen collection solutions were most preferred with % ( / ) of participants agreeing or strongly agreeing that they would provide a saliva specimen, and % ( / ) agreeing that they would provide a throat swab (figure ). there was attenuated willingness for drive through swab testing ( %, / ), and substantially attenuated willingness for clinic or laboratory throat swab ( %, / ). differences in mean willingness scores across testing modalities were all significant (p<. ), with very small effect size for home saliva testing compared to home throat swab testing (d= . ), medium effect size for home saliva testing compared to drive-through testing (d= . ), and large effect size for home saliva testing compared to clinic-based testing (d= . ). we found highly similar willingness to seek testing for covid- follow-up care (figure ) , and identical significance and effect size findings (supplement ). willingness to seek testing for diagnosis and care within each testing modality was remarkably consistent across all covariates in the analysis, with no differences across age groups, race/ethnicities, covid- stigma scores, covid- knowledge scores, covid- symptomology, region, or state-level covid burden (table ) . to directly assess potential behavioral change associated with different home care testing modalities, we asked participants whether they would be more likely, no different, or less likely to seek testing for covid- disease if at-home specimen collection options were available. relative to availability of a drive-through modality, % ( ) noted they would be more likely to test if at-home specimen collection were available, % ( ) noted no difference, and % ( ) noted lower likelihood. relative to availability of a clinic-or lab-based modality, % ( ) noted they would be more likely to test if at-home specimen collection were available, % ( ) noted no difference, and % ( ) noted lower likelihood (results not reported in table). across a diverse sample of , participants, one-third more persons reported that they would be willing to collect specimens at home for sars-cov- testing if they experienced illness, compared to clinic-based testing. there was a hierarchy of willingness to test for sars-cov- that was decreased as the required degree of contact with healthcare systems increased: home testing was most preferred, followed by drive-through testing, and then by laboratory or clinicbased testing. if differences in reported willingness approximate those in actual willingness, the magnitude of the findings has considerable public health and clinical care implications. one indicator that the hypothetical may approach actual behavior is that participant preferences were consistent across covid- symptomology levels: persons currently experiencing covid- related symptoms reported similarly lower willingness to seek drive-through and clinic-based sars-cov- testing as persons not currently experiencing symptoms. preference differences were also constant across a wide variety of sociodemographic variables, which is important to note, considering the differential impact of sars-cov- on elderly persons and on african-americans, as reported in media and confirmed by coroner's offices in louisiana, chicago, and michigan. there are currently vast differences in how countries and jurisdictions are handling testing due to supply limitations. in iceland, testing has been widely provided as a strategy to combat epidemic spread, and not surprisingly this appears to be substantially contributing to their control of epidemic spread. with a combined approach for testing that included targeted recruitment of symptomatic persons or those in contact with symptomatic persons, an open invitation m a n u s c r i p t recruitment, and a random sample recruitment, iceland tested over , persons using an inperson testing strategy. at-home self-collection of specimens is one of several options worthy of exploration to achieve similar gains in other settings. home-based and drive-through testing strategies are promising in part because they may allow for rapid scale-up of newly validated approaches that may relieve supply chain problems. it is clear that, if sufficient laboratory capacity and supplies are available, increased testing using at-home specimen collection is critical for public health response for three reasons. first, it would facilitate increased initiation of contact tracing, a tool known to limit epidemic spread, by identifying people with mild symptoms and allowing public health authorities to test close contacts. second, it would reduce the risk of disease transmission from clinical settings. third, it would facilitate improved selfmanagement, because mild and moderate covid- symptoms are non-specific. persons receiving a formal sars-cov- diagnosis are likely to perform self-isolation activities with substantially more rigor than persons whose actions are informed only by their mild symptoms. conversely, those determined to be uninfected would be anticipated to have reduced anxiety, and be able to continue with their lives without an unnecessary isolation period. given our finding that people were more willing to test with home specimen strategies, making such an option available might allow for earlier informed discussions with a clinician via an office visit or telemedicine regarding the optimal next steps in their care. this is especially relevant given media reports, confirmed by local health authorities, of the substantial increases of persons found dead in their homes in some cities in the united states compared to historic averages. in detroit, there were more than persons founds dead in their homes first days of april compared to around during that same period in the three years prior. in new york city in early april , a spokesperson for the department of health confirmed that around deaths per day have been observed in homes, compared to - deaths per day in . it is likely that many of the deceased did not have an opportunity to receive clinical care, a problem that could potentially be mitigated through more wide-spread and easily accessible testing. other authors have previously called for sars-cov- home testing, but mainly for its social distancing and reduced healthcare system burdens. , such calls can and have equally supported drive-through facilities. but our findings indicate home collection was substantially preferred to drive-through methods, with over % more persons indicating willingness to complete a home test compared to a drive-through test. drive-through testing venues may achieve benefits of viral transmission control, but have lower benefits for increasing the demand for testing. these results are aligned with previous work that has found home specimen collection a highly preferred method of seeking clinical care, , , and can be understood as part of an already ongoing move towards remote care facilitated by at-home specimen collection. [ ] [ ] [ ] [ ] an additional benefit is that home testing has the potential to reach persons with limited access to transportation, or living far from available testing sites. this national online survey study has a number of limitations. participants volunteered to take an online survey regarding covid- , potentially skewing willingness values higher than among the general population. moreover, reported willingness has been observed to overestimate uptake for other interventions, and our findings are likely subject to similar bias. we do not think, however, that this would produce bias in the relative levels of support for the testing options presented. cost of different sars-cov- testing strategies will likely vary, and if the healthcare m a n u s c r i p t system does not cover the cost of some test options, this would likely influence willingness to use that modality. in unpublished work, the sensitivity performance of saliva-based tests has been found to be higher than nasopharyngeal swabs in clinical settings, yet a separate study identified poor sensitivity performance of saliva specimens in a community-based setting. further studies for saliva as a specimen type in community settings are needed. the high overall preference for home testing, including for pharyngeal specimen collection, indicates that other home-based specimens such as anterior nares swab may likewise be highly acceptable. the convenience sample used in the present study may not represent the broader population in other ways, although the consistent and strong differences in preference across categories and item types indicates this would likely have little influence on study results. we found strong preferences for home testing options. providing a home testing option is consistent with social distancing strategies and also patient-centered care strategies demonstrated to improve patient adherence to clinician-recommendations. home specimen collection and central laboratory testing can ease supply chain problems, and be quickly scaled up for contact tracing use by public health authorities. such home testing methods should be validated as soon as possible, and brought to scale by clinicians and health systems. all authors have no conflicts of interest to declare. m a n u s c r i p t willingness to seek laboratory testing for sars-cov- under different specimen collection scenarios *for home specimens, instructions clarified that specimens would be collected at-home and mailed to a central laboratory for testing covid- : towards controlling of a pandemic covid- epidemic in switzerland: on the importance of testing, contact tracing and isolation discontinuation of isolation for persons with covid- not in healthcare settings on the front lines of coronavirus: the italian response to covid- self-testing for hiv: a new option for hiv prevention? the lancet infectious diseases selfcollection of vaginal swabs for the detection of chlamydia, gonorrhea, and trichomoniasis: opportunity to encourage sexually transmitted disease testing among adolescents. sexually transmitted diseases developing and assessing the feasibility of a home-based preexposure prophylaxis monitoring and support program reliability of hiv rapid diagnostic tests for self-testing compared with testing by health-care workers: a systematic review and meta-analysis. the lancet hiv self-collected versus clinician-collected sampling for chlamydia and gonorrhea screening: a systemic review and meta-analysis self-service diagnosis of covid- -ready for prime time? proposed protocol to keep covid- out of hospitals self-service diagnosis of covid- -ready for prime time? paper presented at: jama health forum detection of sars-cov- rna and antibodies in diverse samples: protocol to validate the sufficiency of provider-observed, home-collected blood, saliva, and oropharyngeal samples food and drug administration. phosphorus covid- rt-qpcr test eua food and drug administration. rutgers clinical genomics laboratory taqpath sars-cov- assay eua the annual american men's internet survey of behaviors of men who have sex with men in the united states: protocol and key indicators report knowledge and perceptions of covid- among the general public in the united states and the united kingdom: a cross-sectional online survey. annals of internal medicine a novel coronavirus outbreak of global health concern coronavirus outbreaks: prevention and management recommendations loss of smell and taste in combination with other symptoms is a strong predictor of covid- infection. medrxiv. . . usa facts. coronavirus locations: covid- map by county and state clinical infectious diseases : an official publication of the infectious diseases society of america the strengthening the reporting of observational studies in epidemiology (strobe) statement: guidelines for reporting observational studies. the lancet clinical features of fatal cases of covid- from wuhan: a retrospective observational study spread of sars-cov- in the icelandic population. the new england journal of medicine there's been a spike in people dying at home in several cities. that suggests coronavirus deaths are higher than reported staggering surge of nyers dying in their homes suggests city is undercounting coronavirus fatalities. gothamist web site virtually perfect? telemedicine for covid- bringing hiv self-testing to scale in the united states: a review of challenges, potential solutions, and future opportunities attitudes and acceptability on hiv selftesting among key populations: a literature review an electronic pre-exposure prophylaxis initiation and maintenance home care system for nonurban young men who have sex with men: protocol for a randomized controlled trial usability and acceptability of a mobile comprehensive hiv prevention app for men who have sex with men: a pilot study acceptability of self-collecting oropharyngeal swabs for sexually transmissible infection testing among men and women the respiratory specimen collection trial (respect): a randomized controlled trial to compare quality and timeliness of respiratory sample collection in the home by parents and healthcare workers from children aged< years distinguishing hypothetical willingness from behavioral intentions to initiate hiv pre-exposure prophylaxis (prep): findings from a large cohort of gay and bisexual men in the u saliva is more sensitive for sars-cov- detection in covid- patients than nasopharyngeal swabs saliva is less sensitive than nasopharyngeal swabs for covid- detection in the community setting we appreciate and acknowledge the contributions of our study participants. all authors had full access to study data, and ajs had final responsibility for the decision to submit for publication. this work was supported by the national institute of allergy and infectious diseases ( r ai - s ). the study was facilitated by the center for aids research at emory university (p ai ). the content is solely the responsibility of the authors and does not necessarily represent the official views of the national institutes of health. 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 a c c e p t e d m a n u s c r i p t . there were no significant differences in testing scenario scores by any variable considered (e.g. home saliva specimen score differences across gender, age, etc), after bonferroni-holms correction for multiple hypothesis testing. . high burden states as of the time of the survey (april ), defined as > cases / , population.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 figure key: cord- -xzdh yum authors: huang, jing; liu, fangkun; teng, ziwei; chen, jindong; zhao, jingping; wang, xiaoping; wu, ying; xiao, jingmei; wang, ying; wu, renrong title: public behavior change, perceptions, depression, and anxiety in relation to the covid- outbreak date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: xzdh yum background: the covid- has spread rapidly and world-widely, which elicits public panic and psychological problems. public protective behaviors and perception play crucial roles in controlling the spread of illness and psychological status. methods: we conducted a cross-sectional online survey in the hardest-hit hubei province and other areas in china affected by covid- outbreak. questions about their basic information, the perception of the covid- outbreak, recent preventive or avoidance behaviors, and self-reported mental health scales including the patient health questionnaire (phq- ) and self-rating anxiety scale (sas) were included. binary logistic regressions were used to investigate the association between personal variables/perceptions and psychological distress. results: , people were included for analysis, with , ( . %) in hubei province ( , in wuhan). a majority of people have adopted preventive and avoidance behaviors. people from hubei, with contact history, and people who or whose family members were infected had much higher depression or anxiety prevalence. providing truthful and sufficient information, informing the public about the severity of the disease, and perceptions that the outbreak will be control by protective behaviors were associated with lower depression and anxiety prevalence. conclusions: assessing the public response, perception, and psychological burden during the outbreak may help improve public health recommendations and deliver timely psychological intervention. further researches can focus on the psychological status of a specialized group to identify ways for better support based on public response and psychological demand. in december , a new virus caused pneumonia emerged in wuhan, hubei province, has rapidly and widely spread in china and other countries, which caused an exponential increase in patients with infection , . within weeks, the numbers of confirmed cases, suspected cases, and deaths rose substantially. on jan , xizang raised its public health emergency response to level , which announced that all of the provincial-level regions in mainland china have set up the highest level of emergency public health alerts and responses. on jan , who declared the outbreak as a public health emergency of international concern (pheic). as of feb , , the number of during the outbreak, the government closed the schools, canceled the public activities, ordered everyone to stay at home and avoid outside activities as much as possible. the transmission of covid- from human-to-human, a large number of confirmed cases, suspected cases, and the increasing number of deaths elicited public fear of being infected . meanwhile, people were flooded with various and uncertain information from numerous sources, which may increase public panic and potential psychological problems . the uncertainty of the new virus outbreak, the a c c e p t e d m a n u s c r i p t extensive information or rumors, and the shortage of necessities may increase worries in the population. during the start of our survey on feb , the outbreak seems to reach a full point. to this, the national health commission of china has launched several policies and notices to cope with the psychological burden due to the covid- pandemic , . previous studies suggested the importance of early assessment of anxiety and behavioral response to the spread of an infectious disease [ ] [ ] [ ] [ ] . however, no study has performed to assess the public response, protective behavior changes, the relationship between perception and psychological burden in the covid- outbreak. therefore, a timely and accurate measurement of public responses and psychological distress is extremely important , . we conducted a large survey in the hardest-hit hubei province and other areas affected by the covid- outbreak, with , in hubei province and , outside hubei province. due to the extensive internet coverage and more than . billion mobile internet users in china, according to a recent report by the ministry of industry and information technology , the survey was conducted through the internet to avoid exposure and increase the response speed and participation . this survey provided a snapshot of public adoption of preventive behaviors or avoidance behaviors, perception and the psychological status during the peak period of the outbreak. the cross-sectional online survey was designed to perform in hubei province for about , participants, and outside hubei province for , participants. the sample size was chosen to allow for sufficient power to analyze likely differences between subgroups such as confirmed cases, a c c e p t e d m a n u s c r i p t people with a history of recent contact with covid- they needed to answer questions about their basic information, the perception of the covid- outbreak, recent preventive or avoidance behaviors, and self-reported mental health scales. after a complete description of the survey to the subjects, electronic informed consent was obtained. the basic information of the participants includes gender, age, job, marriage status, education level, and address. the survey also asked people seven questions about preventive behaviors (public mask-wearing, increases in handwashing and the frequency, surface sterilization) and avoidance behaviors (such as avoid crowded places or public transport or people with contact history, personal protective, and social distancing behavior, urge their family members or friends for these the perception of the covid- outbreak includes the severity of the disease, the attitude towards the disease, information, support, the worries of being infected and for their families. each question had five response options: strongly agreeing (scored as ), tend to agree, neither agree nor disagree, tend to disagree, or strongly disagree (scored as ). one question was related to the concern level about the outbreak to see whether participants have paid much attention to the covid- epidemic news. eight questions were about the understanding of the disease, timely and true information, basic supplies and support received from outside. one of the items assessed whether participants believed that recommended behaviors reduced their risk of being infected. six questions evaluated participant's worries and attitudes towards the outbreak, including worries about being infected, worries for their families or friends, worries for contacting an infected but symptomless individual, worries when get covid- related symptoms, and attitude of the disease. it should be noted that two questions related to worries about the infection of the participants or their loved one had six response options, five options were the worrying levels, the last option was confirmed infection, which means the participant/ his family has been confirmed infection. the nine-item depression module from the patient health questionnaire (phq- ) was employed in the survey to evaluate the depression level. each of the nine questions inside corresponds to one of the dsm-iv criteria scored as " " (not at all) to " " (nearly every day). people with phq- score ≥ had high sensitivity and specificity for major depression . people who scored or a c c e p t e d m a n u s c r i p t more were defined as having depression about covid- . anxiety was assessed using the self-rating anxiety scale (sas), which was well-validated and widely used for anxiety screening and severity measurement. participants were asked about their feelings over the past week concerning the covid- outbreak. previous studies showed the upper limit for the chinese general population was an index score of . in this study, people who scored or more were defined as having anxiety about covid- , and those with scores or more were defined as having moderate to severe anxiety , . spss . software was used for the analyses. we used binary logistic regression to investigate the univariate association between personal variables and psychological distress (prevalence of depression or anxiety), the association between public perceptions and psychological distress. another set of binary logistic regression was applied to assess the multivariate associations between personal variables and psychological distress after adjusting for significant personal variables. odds ratios were used to assess these associations. data were weighted to gender, age, marriage, and working status based on the data from the national statistics institute of china. the prevalence of public behaviors, perceptions, depression, and anxiety changed less than % or marginally % after weighting procedure, therefore the unweighted data were used for analysis in this study. overall, , completed the survey in five days at the peak of the table lists the public behavior changes in response to covid- outbreak. the most commonly ( . %) adopted preventive behavior was to wear a mask when going outside and the most commonly ( . %) adopted avoidance behavior was reducing the frequency of going out, dining together, and visiting others. a majority of people ( . %) had adopted at least one of these things. a c c e p t e d m a n u s c r i p t in total, (table ) , even after adjusting the other significant personal variables. next, we examine association between perceptions and psychological status. (table ). our results suggested that chinese general public had obvious responses and behavior changes after about two weeks that provincial-level regions in mainland china activated level public health emergency responses. people showed high adoption rates of various protective behaviors, such as mask-wearing, disinfection, and social distance maintenance. the most affected province, hubei, is still been engulfed by the outbreak. most restaurants, hotels, malls, cinemas and other public place of entertainment have been closed. several ways of restrictions on access have been adopted by the communities and villages including locking all unused doors or blocking roads to limit access, restricting all unauthorized individuals, distributing cards for temporary access. community members need to take temperature and will only be allowed in with normal temperature. newspapers, television, broadcast, internet, magazines and other media take efforts to strengthen people awareness of protective behaviors and personal health to control virus infection. the high percentage of protective behavior adoptions proved the notable effects of these measures. the prevalence of psychological distress is associated with several personal variables. people from hubei province, single, having contact history, being confirmed infection, whose family has been a c c e p t e d m a n u s c r i p t further studies can be performed to explore the psychological status of people in a specialized group to understand their different demands and provide better psychological support. with more than , confirmed cases reported in china on feb , the covid- outbreak has developed into a serious public health problem. a majority of people have adopted various preventive and avoidance behaviors. people from hubei, with contact history, and people who or whose family members were infected had much higher depression or anxiety prevalence which requires urgent psychological intervention. providing clear and sufficient information, informing the public about the severity of the disease, and perceptions that the outbreak will be control by protective behaviors were associated with lower depression and anxiety prevalence. further researches can focus on the psychological status of a specialized group to offer effective psychological counseling and support. the study is supported by the national nature science foundation of china (grant no. and no. ). none declared. m a n u s c r i p t manuscript. jc, jz, and xw revised the survey and the design. yw, zt, jx, yw were involved in data collection. rw is the principal investigator of this clinical trial. all authors read and approved the final version of the manuscript. we also want to thank several anonymous reviewers for their valuable comments and suggestions to improve the quality of the paper. data not publicly available. 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 table behavior response to covid- . percentage of positive responses (n= ) preventive behavior sterilize the surface of the floor, desktop, mobile phone and other objects more often than usual % cover your mouth and nose with bent elbows when coughing or sneezing % washed my hands with soap and water more often than usual % in the past days, you certainly wear masks when you went out % keep away from potential infected people % try to keep at least one meter away from others, especially when going out % reduce the frequency of going out, dining together, and visiting others % avoid crowded places % reduce the frequency of taking public transport % have you advised your family and friends in the following areas during the epidemic avoid crowded places % wash hands with soap and water more often than usual % wear masks when going out % reduce the frequency of taking public transport % reduce the frequency of going out, dining together, and visiting others in the past hours, how many times have you washed your hands with soap - % a c c e p t e d m a n u s c r i p t genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding. the lancet -ncov epidemic: address mental health care to empower society. the lancet the immediate psychological and occupational impact of the sars outbreak in a teaching hospital early assessment of anxiety and behavioral response to novel swineorigin influenza a (h n ) public perceptions, anxiety, and behaviour change in relation to the swine flu outbreak: cross sectional telephone survey public response to the influenza a h n pandemic: a polling study in five countries. the lancet infectious diseases the public's response to the h n influenza pandemic the ebola outbreak and mental health: current status and recommended response timely mental health care for the novel coronavirus outbreak is urgently needed the phq- : a new depression diagnostic and severity measure chinese version of zung's self-rating anxiety scale behavioral medicine scale manua severe acute respiratory syndrome (sars) in hong kong in : stress and psychological impact among frontline healthcare workers medical management of radiation accidents communicating with the public about emerging health threats: lessons from the pre-event message development project the dark side of information: overload, anxiety and other paradoxes and pathologies pandemics: good hygiene is not enough we would like to acknowledge the valued contribution of the participants. rw, jh, and fl had the original idea for the study and designed the survey. fl carried out the analyses, jh wrote the 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 a c c e p t e d m a n u s c r i p t adjusted odds ratio ( % ci) † i believe that taking protecting efforts will reduce risk of catching covid- i am worried that i will be infected . ( . ), . ( . to . ) . ( . to . ) . ( . to . ) . ( . to . ) i am worried that my family members or friends will be infected . *scores from to . each question had five response options: strongly agreeing (scored as ), tend to agree, neither agree nor disagree, tend to disagree, or strongly disagree (scored as ). high scores indicate greater agreement with the statements. †adjusting for gender, age, marriage, and working status. key: cord- -mw ec u authors: salton, francesco; confalonieri, paola; meduri, g umberto; santus, pierachille; harari, sergio; scala, raffaele; lanini, simone; vertui, valentina; oggionni, tiberio; caminati, antonella; patruno, vincenzo; tamburrini, mario; scartabellati, alessandro; parati, mara; villani, massimiliano; radovanovic, dejan; tomassetti, sara; ravaglia, claudia; poletti, venerino; vianello, andrea; gaccione, anna talia; guidelli, luca; raccanelli, rita; lucernoni, paolo; lacedonia, donato; foschino barbaro, maria pia; centanni, stefano; mondoni, michele; davì, matteo; fantin, alberto; cao, xueyuan; torelli, lucio; zucchetto, antonella; montico, marcella; casarin, annalisa; romagnoli, micaela; gasparini, stefano; bonifazi, martina; d’agaro, pierlanfranco; marcello, alessandro; licastro, danilo; ruaro, barbara; volpe, maria concetta; umberger, reba; confalonieri, marco title: prolonged low-dose methylprednisolone in patients with severe covid- pneumonia date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: mw ec u background: in hospitalized patients with covid- pneumonia, progression to acute respiratory failure requiring invasive mechanical ventilation (mv) is associated with significant morbidity and mortality. severe dysregulated systemic inflammation is the putative mechanism. we hypothesize that early prolonged methylprednisolone (mp) treatment could accelerate disease resolution, decreasing the need for icu and mortality. methods: we conducted a multicenter, observational study to explore the association between exposure to prolonged, low-dose, mp treatment and need for icu referral, intubation or death within days (composite primary endpoint) in patients with severe covid- pneumonia admitted to italian respiratory high-dependency units. secondary outcomes were invasive mv-free days and changes in c-reactive protein (crp) levels. results: findings are reported as mp (n= ) vs. control (n= ). the composite primary endpoint was met by vs. [adjusted hazard ratio (hr) . ; % confidence interval (ci): . - . ]. transfer to icu and need for invasive mv was necessary in vs. (p= . ) and vs. (p= . ), respectively. by day , the mp group had fewer deaths ( vs. , adjusted hr= . ; % ci: . - . ) and more days off invasive mv ( . ± . vs. . ± . ; p= . ). study treatment was associated with rapid improvement in pao( ):fio( ) and crp levels. the complication rate was similar for the two groups (p= . ). conclusion: in patients with severe covid- pneumonia, early administration of prolonged mp treatment was associated with a significantly lower hazard of death ( %) and decreased ventilator dependence. treatment was safe and did not impact viral clearance. a large rct (recovery trial) has been performed that validates these findings. clinical trial registration: clinicaltrials.gov nct italy was the first european country overwhelmed by the sars-cov- pandemic, experiencing an unsustainable burden on the healthcare system. the greatest impact was on intensive care units (icus) because % of hospitalized cases developed acute respiratory failure (arf) requiring icu admission. [ ] covid- patients with arf necessitate weeks of mechanical ventilation (mv) and have an unacceptably high mortality rate. [ ] this is an unprecedented global emergency where even countries with advanced health care systems rapidly reach icu saturation, and intensivists are forced to make difficult ethical decisions that are uncommon outside war zones. any intervention directed at decreasing dependence on ventilators and mortality in covid- patients is an ethical imperative and would have a significant global impact on public health. over the last few decades, italy has built-up a diffuse network of respiratory high dependency units (rhdus) which also treat patients with severe pneumonia-related arf requiring continuous monitoring and noninvasive positive pressure ventilation (nppv). [ ] patients with disease progression who require endotracheal intubation are transferred to the icu. during the pandemic, rhdus were pivotal in reducing icu referral. [ ] indeed, patients with severe covid- have exhausted antiviral defenses and massive tissue and systemic inflammatory response. corticosteroids are powerful anti-inflammatory drugs that could have a role in promoting the resolution of arf in patients with severe covid- infection. [ ] the rationale for prolonged, low-dose, corticosteroid treatment in severe covid- was recently reviewed. [ ] we hypothesized that early mp treatment in hypoxemic patients with severe sars-cov- pneumonia at higher risk for arf progression requiring invasive mv, may quicken disease resolution, reducing the need for icu support and mortality. we investigated the association between early intervention with prolonged mp treatment in this high-risk group and the risk for icu admission, the need for invasive mv or all-cause death by day . we conducted a multicenter, observational, longitudinal study to evaluate the association between mp treatment and outcome in consecutive patients with severe covid- pneumonia admitted to fourteen italian rhdus between february th and april th , . follow-up continued through may st , . the composite primary endpoint included admission to icu, need for invasive mv, or all-cause death by day , while secondary endpoints were mv c-reactive protein (crp) levels. the study was carried out in accordance with the declaration of helsinki. it was registered on a c c e p t e d m a n u s c r i p t clinicaltrials.gov (nct ) after approval by the referral ethics committee for the coordinating centre (university hospital of trieste, #ceur- -os- ). study baseline was defined as the time of inclusion criteria fulfillment after admission to rhdu. inclusion criteria were the followings: ) sars-cov- positive (on swab or bronchial wash); ) age > years and < years; ) pao :fio < mmhg; ) bilateral infiltrates; ) crp > mg/l; and/or ) diagnosis of acute respiratory distress syndrome (ards) according to the berlin definition [ ] as an alternative to criteria ) and ). exclusion criteria were: heart failure as main cause of arf, decompensated liver cirrhosis, immunosuppression (i.e. cancer on treatment, postorgan transplantation, hiv-positive, on immunosuppressant therapy), dialysis-dependence, on longterm oxygen or home mechanical ventilation, idiopathic pulmonary fibrosis, neuromuscular disorders, dementia or a decompensated psychiatric disorder, severe neurodegenerative conditions, on chronic steroid therapy, pregnancy, a do-not-resuscitate order, and use of tocilizumab or other experimental treatment. patients in both study groups received standard of care, comprising noninvasive respiratory support, antibiotics, antivirals, vasopressors, and renal replacement therapy as deemed suitable by the healthcare team. exposure to methylprednisolone (non-patented drug, atc code h ab ) complied with the following protocol: a loading dose of mg iv at study entry (baseline), followed by an infusion of mg/day in ml normal saline at ml/h for at least days, until achieving either a pao :fio > mmhg or a crp < mg/l. after which, oral administration at mg or mg iv twice daily until crp reached < % of normal range or a pao :fio > (alternative sathbo ≥ % on room air). the mp protocol was developed by the coordinating center in accordance with the "recommendation for covid- clinical management" by the national institute for the infectious diseases "l. spallanzani", rome. [ ] the decision to apply the protocol to covid- was left to the discretion of the treating team for each individual patient. unexposed patients (controls) were selected from concurrent consecutive covid- patients with the same inclusion and exclusion criteria. demographic details, laboratory, clinical and outcome variables were manually extracted from electronic medical records or charts and anonymously coded onto in a standardized data collection form. three independent physicians checked the data and two researchers adjudicated any difference in interpretation between the primary reviewers. serial measurements included: arterial blood gas, crp, d-dimer, white cell count with differential, hemoglobin, variables for the calculation of the sofa score, [ ] days free from invasive or noninvasive mv until study day . laboratory methodologies, including sars-cov- detection by reverse-transcriptase polymerase chain reaction (rt-pcr) and reference values were comparable a c c e p t e d m a n u s c r i p t between centers. other collected data included: date of death, admission to icu, dates of discharge from hospital and icu, intra-hospital medications, in-hospital adverse events and comorbidities. samples from seriated nasopharyngeal swabs were collected in each group to evaluate viral shedding. considering a study power ( -beta) of % and a probability of type error (alpha) of . , assuming that the proportion of treated patients having the primary endpoint was . under the null hypothesis (according to available information from fang et al. [ ] ) and . under the alternative hypothesis, and considering a % dropout rate, a minimum study sample of patients was established. data were described using absolute and relative frequencies (percentage) or position indices (mean or median) and relative dispersion indices (standard deviation or interquartile range), as appropriate according to the type and distribution of the variable analyzed. the differences between study groups (mp-treated and control) in the proportion of patients reaching the primary endpoint was evaluated by a two-sided chi-square test. the difference in numerical variables between groups was calculated using student's t-test or wilcoxon rank-sum test, depending on the distribution of the variables. differences between study groups concerning categorical or dichotomous variables were evaluated by means of the chi-square test or fisher's exact test, as appropriate. time-to-event analyses were performed for both the composite primary endpoint and death alone. time at risk for all-cause death was computed from the date of study enrollment up to the date of death, hospital discharge, or days, whichever came first. event-free probabilities were estimated by the kaplan-meier method and differences between groups were assessed by the log-rank test. multivariable cox proportional-hazard models estimated the hazard ratio (hr) of both the primary composite endpoint and all-cause death, with the corresponding % confidence intervals ( % ci), taking into account the confounding factors (i.e., sex, age, and baseline values of sofa score, pao :fio , crp levels) potentially associated with the outcome. these variables and others with baseline differences (e.g. smoke) were tested in univariate survival models and variables significant at p= . were tested in the multivariable models. proportional hazards assumption was assessed by visual inspection of the log(-log(survival)) plot. there were no missing data with regard neither to the composite primary endpoint and the adjustment factors included in the final cox models, nor to mv-free days. available case analysis was performed for time variation of c-reactive protein (crp) and pao :fio levels. all tests were two-sided and a p-value of < . was considered as statistically significant. sensitivity analyses were completed as recommended by strobe guidelines for reporting observational studies. [ ] although a protocol was used to standardize study measures, we conducted a sensitivity analysis to account for potential variance in medical decision making that a c c e p t e d m a n u s c r i p t could potentially impact the primary composite outcome. we examined hypothetical scenarios against the hypothesis by varying the number of subjects meeting the primary composite outcome by and subjects to account for potential bias in both groups. between february th and april th , , consecutive sars-cov- -positive patients who were admitted to one of rhdus with severe pneumonia, were assessed for study eligibility. a total of patients ( mp-treated exposed and untreated controls) were enrolled, while were excluded as detailed in figure . findings are reported as mp group vs. control group. rhdu admission days to study enrollment were comparable ( . ± . vs. . ± . , p= . ). table shows how the patients' baseline characteristics did not differ between groups. the mean duration of iv mp treatment was . ± . days, while the total duration of mp treatment was . ± . days. for the secondary endpoints ( table ) , we observed a significant increment in both mv-free days by day outcomes, combined invasive mv and nppv ( . ± . vs. . ± . , p= . ), and invasive-mv-free days alone ( ± vs. . ± . , p= . ). mp exposure was associated with a table and shown in figure . the hospital length of stay did not differ between the groups (p-value= . ). no tracheostomy was necessary in mp patients vs. controls (or . , % ci . to . , p-value < . ). concerning intra-hospital adverse events of any type (table s ) only the occurrence of hyperglycemia in non-diabetic patients, or severe glycemic decompensation in diabetic patients, and agitation was significantly higher in the mp group compared to control ( vs. , p= . and vs. , p= . respectively). no adverse event led to mp discontinuation. concomitant in-hospital treatments are summarized in table s . there were no relevant differences in viral genome sequencing in the two first recruited patients compared to the average sequences reported in open-source repositories (figure s ) . nor was any observed in viral shedding, determined as time lapse (days) between hospital admission and the first negative rt-pcr for sars-cov- nasopharyngeal swabs, in a sample of mp-treated patients compared to untreated ones ( . ± . vs. . ± . , p-value= . ). sensitivity analysis (table s ) show that the primary composite outcome still significantly differs between the mp and control group in scenarios biased against the original hypothesis. in our multicenter study, patients exposed to mp encountered the primary composite endpoint of icu referral, need for invasive mv or in-hospital all-cause death significantly less compared to the control group (adjusted hr . ). by day , mp treatment was associated with a significant reduction in mortality (adjusted hr . ) and an increase in mv-free days. among patients transferred to the icu, mp treated patients had a . days median reduction (p= . ) in the duration of invasive mv. in line with this data, fewer mp-treated patients required tracheotomy than controls ( vs. , p < . ). mp-treated patients had a higher reduction in crp levels than controls. this was statistically significant on days and from baseline and there was a quicker improvement in pao :fio ratio on day for mp-treated patients. there was no overall increase in adverse events between groups, except for an increase in hyperglycemia and mild agitation in the mp-treated patients; no adverse event necessitated mp discontinuation. no difference was observed in viral shedding, determined as the number of days between hospital referral and the first negative nasopharyngeal swab. early interventions aimed at down regulating the sars-cov- -associated hyper-immune response in severe covid- patients may well avoid disease progression and enhance pneumonia resolution. the cytokine profile reported for these patients [ ] is within the broad range of regulation provided by corticosteroids [ ] , particularly mp that is associated with an optimal lung penetration. [ ] our study protocol involved an initial iv bolus to achieve rapid, almost complete a c c e p t e d m a n u s c r i p t glucocorticoid receptor saturation, followed by an infusion to reach a total -milligram dose over the first hours and to maintain high levels of response throughout the treatment period. after day , treatment duration was guided by monitoring the anti-inflammatory response and oxygenation parameters. our study investigated a dose more than double the one investigated in the recovery rct and included tapering to minimize the risk of rebound inflammation. this might explain the rapid reduction observed in inflammatory markers. treatment duration was guided by monitoring the anti-inflammatory response and oxygenation after at least days. our mp treatment response is similar to that of randomized controlled studies (rcts) in covid- [ ] , non-viral ards [ ] and severe pneumonia [ ] , as well as of large-scale observational studies in severe pneumonia caused by sars-cov (n= ) [ ] [ ] [ ] and h n influenza (n= ). [ ] additional support for the use of methylprednisolone in covid- originates from transcriptomics data. after matching the expression changes induced by sars-cov in human lung tissue tissues and a lung cell line against the expression changes triggered by , fdaapproved drugs, methylprednisolone was found to be the drug with the greatest potential to revert the changes induced by covid- . [ ] this study has been carried out before the results of the recovery rct became available, as visible by clinicaltrials.gov posting records (results first posted june , ). in the recovery trial, patients were randomized to receive dexamethasone at a dose of mg/day or standard of care alone, providing evidence of a lower -day mortality in the dexamethasone group compared to the usual care group only among those who were receiving either invasive mechanical ventilation ( . % vs. . %) or oxygen alone ( . % vs. . %) at randomization, but not among those receiving no respiratory support. in our study, both mortality and mortality reduction in the mp group were better than reported in the recovery trial. apart from the different study design and setting, we speculate this difference is possibly due several reasons: first, the recovery trial uses a different drug (dexamethasone) at a lower dose, equivalent to approximately mg of methylprednisolone. [ ] second, it is likely that mp has pharmacokinetic and pharmacodynamic advantages over dexamethasone, despite lung penetration needs further comparison. [ ] third, in the recovery trial, the impact of the study treatment on survival seems to correlate with the need for respiratory support and therefore with illness severity. in this support, it was already noticed that glucocorticoids are not effective in patients without ards and/or sepsis. [ ] while permissive inclusion criteria are needed to recruit large populations in rcts, we have designed strict criteria that allowed us to include in the analyses only patients affected by severe pneumonia/ards with high levels of systemic inflammation and need for respiratory support. it is worth stressing that inflammatory organ injury with subsequent dysregulated host response is thought to be the main a c c e p t e d m a n u s c r i p t mechanism of damage in covid- ; as a consequence, the subgroup of patients having markedly elevated levels of inflammatory markers is the one supposed to benefit most from therapeutic interventions aimed at reducing inflammatory organ injury, including corticosteroids. the safety profile reported in our study is consistent with the findings of multiple rcts investigating prolonged corticosteroid treatment in thousands of patients with severe sepsis, septic shock and ards. [ ] in these rcts, hyperglycemia was transient in response to the initial loading bolus and did not impact negatively on outcome. [ ] viral shedding in both groups of our study was in agreement with international literature. [ , ] the who quotes a middle east respiratory syndrome coronavirus study to warn about the risk for reduction in viral clearance with corticosteroid treatment. in the arabi et al. study [ ] , however, those that received corticosteroid treatment for greater than seven days (similar to our study) had a fifty percent reduction in mortality [aor: . , % confidence interval (ci) . - . ; p= . ] and no impact on viral clearance (ahr: . , % ci . - . ; p= . ). moreover, there is no evidence linking delayed viral clearance to worsened outcome in critically ill covid- patients, and it is unlikely that it would have a greater negative impact than the host's own cytokine storm. [ ] the observational design of our study implies some obvious limitations, namely a possible restricted control over data collection and potential inclusion biases. however, internal validity was achieved by ( ) the comparability of concurrent groups at baseline, ( ) . accounting for potential confounders into the multivariable cox regression analyses, and ( ) conducting sensitivity analysis to assess for potential bias in outcome ascertainment potentially influenced by medical decision making. our study's strengths include a prospective evaluation of a pre-designed intervention protocol based on established pharmacological principles in patients at high risk of progression to arf and death. limitations of the study is that we did not control for center effects and site investigators were not blinded to treatment as with any observational study. despite these limitations, we believe that our findings represent valid and generalizable conclusions, that have been further strengthened by the recently published recovery rct. indeed, we observed benefits when mp treatment was started early and prolonged in the hospitalization of hypoxemic patients with covid- pneumonia at high risk of arf progression. mp treatment was demonstrated to be safe, and also allowed for a significant reduction in mortality and immediate improvements in systemic inflammation and oxygenation markers, as well as reducing invasive mv times. we believe our data support the evidence that early low-dose prolonged mp treatment can decrease icu burden and mortality, therefore contributing to reduce the concern surrounding this therapeutic approach in patients admitted with arf due to severe sars-cov- pneumonia in the current state of affairs. fs, pc, ps, sh, rs, sl, vv, to, ac, vp, mt, as, mp, mv, dr, st, cr, vp, av, atg, lg, rr, pl, dl, mpfb, sc, mm, md, af, ac, mr, sg, mb, failed to meet inclusion criteria (n= ): age > years old (n= ), criteria for pao :fio , c-reactive proteron level, or ards (n= ). met exclusion criteria (n= ): heart failure as main cause of arf (n= ), decompensated liver cirrhosis (n= ), on long-term oxygen therapy and/or home ventilation (n= ), dementia or severe neurodegenerative condition (n= ), active cancer (n= ), on chronic steroid therapy (n= ), use of tocilizumab or other experimental treatment (n= ). patients who reached the primary endpoint before admission to rhdu or within hours from admission to rhdu were excluded from the analysis; out of these patients did not start mp treatment. upper panel: time-course of c-reactive protein levels (mean ± standard error). the differences between groups were significant at days and . middle panel: time course of mean pao :fio . the differences between groups was significant at day . lower panel: time course of mean lymphocyte count showing no significant differences between groups. m a n u s c r i p t control m a n u s c r i p t critical care utilization for the covid- outbreak in lombardy, italy: early experience and forecast during an emergency response covid- in critically ill patients in the seattle region -case series respiratory intensive care units in italy: a national census and prospective cohort study early consensus management for non-icu arf sars-cov- emergency in italy: from ward to trenches complex immune dysregulation in covid- patients with severe respiratory failure rationale for prolonged corticosteroid treatment in the acute respiratory distress syndrome caused by coronavirus disease statistical evaluation of ventilator-free days as an efficacy measure in clinical trials of treatments for acute respiratory distress syndrome acute respiratory distress syndrome: the berlin definition national institute for the infectious diseases "l recommendations for covid- clinical management use of the sofa score to assess the incidence of organ dysfunction/failure in intensive care units: results of a multicenter, prospective study low-dose corticosteroid therapy does not delay viral clearance in patients with covid- the strengthening the reporting of observational studies in epidemiology (strobe) statement: guidelines for reporting observational studies hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease (covid- ): a meta-analysis general adaptation in critical illness: glucocorticoid receptoralpha master regulator of homeostatic corrections accessed penetration of corticosteroids into the lung: evidence for a difference between methylprednisolone and prednisolone dexamethasone in hospitalized patients with covid- -preliminary report prolonged glucocorticoid treatment is associated with improved ards outcomes: analysis of individual patients' data from four randomized trials and trial-level meta-analysis of the updated literature hydrocortisone infusion for severe communityacquired pneumonia: a preliminary randomized study clinical recommendations from an observational study on mers: glucocorticoids was benefit in treating sars patients treatment of severe acute respiratory syndrome with glucosteroids: the guangzhou experience corticosteroid treatment of severe acute respiratory syndrome in hong kong effect of low-to-moderate-dose corticosteroids on mortality of hospitalized adolescents and adults with influenza a(h n )pdm viral pneumonia covid- : disease pathways and gene expression changes predict methylprednisolone can improve out-come in severe cases pharmacokinetics and pharmacodynamics of systemically administered glucocorticoids virological assessment of hospitalized patients with covid- re: low-dose corticosteroid therapy does not delay viral clearance in patients with covid- corticosteroid therapy for critically ill patients with middle east respiratory syndrome covid- : consider cytokine storm syndromes and immunosuppression pao :fio , mmhg, mean (sd) lymphocyte count, mean (sd) legend: sd, standard deviation; iqr inter-quartile range sofa, sequential organ failure assessment; pao :fio , ratio of partial pressure of arterial oxygen (pao in mmhg) to fractional inspired oxygen copd, chronic obstructive pulmonary disease obstructive sleep apnea syndrome/obesity-hypoventilation syndrome °p -value of the fisher's exact test for dichotomous variables, unpaired student's t-test or wilcoxon. rank-sum test for numerical variables, as appropriate pao :fio at day vs baseline, median (iqr) pao :fio at day vs baseline, median (iqr) the authors would like to thank barbara wade, contract professor at the university of torino, for her linguistic advice; amanda busby, university of hertfordshire, for her statistical suggestions; dr.valentina luzzi and dr. marco de martino for their help in data collection. all patients signed written consent for this study.the design of the study has been approved by the local ethical committee (#ceur- -os- ) and it conforms to the standards currently applied in italy. the authors have no conflicts of interest to disclose. ( to ) . legend: hr, hazard ratio; ci, confidence interval; sd, standard deviation; iqr, inter-quartile range; crp, c-reactive protein; pao :fio , ratio of partial pressure of arterial oxygen (pao in mmhg) to fractional inspired oxygen (fio ). * p-value of chi-square or fisher's exact test for dichotomous variables, unpaired t-test or wilcoxon rank-sum test for numerical variables as appropriate.°hr of event among methyprednisolone vs. control group, estimated using cox-regression model. the crude odds ratio and % ci for the composite outcomes is . ( . - . ). § cox-regression model was adjusted for sex, age, baseline sofa score, baseline pao :fio , and baseline crp. ¶ only ventilated patients ** both invasive and noninvasive 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 key: cord- -w ig mrl authors: nori, priya; madaline, theresa; munjal, iona; bhar, shubha; guo, yi; seo, susan k.; porrovecchio, andrea; gancher, elizabeth; nosanchuk, joshua; pirofski, liise-anne; ostrowsky, belinda title: developing interactive antimicrobial stewardship and infection prevention curricula for diverse learners: a tailored approach date: - - journal: open forum infect dis doi: . /ofid/ofx sha: doc_id: cord_uid: w ig mrl background. to impart principles of antimicrobial stewardship (as) and infection prevention and control (ipc), we developed a curriculum tailored to the diverse aptitudes of learners at our medical center. methods. we integrated case-based modules, group learning activities, smartphone applications (apps), decision support tools, and prescription audit and feedback into curricula of the medical school, medicine residency program, infectious diseases (id) fellowship program, and hospital medicine program operations. interventions were implemented in – using a quasi-experimental before-and-after study design, and this was assessed using pre- and postintervention surveys or audit of antibiotic prescriptions. results. over medical students participated in the as and ipc seminars. after smartphone app introduction, % reported using the app as their preferred source of antibiotic information. approximately % of students felt comfortable prescribing antibiotics for a known infection compared with % at baseline (p = . ), and approximately % were able to identify the appropriate personal protective equipment for specific scenarios. approximately % agreed that they have a role in promoting patient safety and preventing healthcare-associated infections as medical students. at months, appropriateness of trainee antibiotic prescriptions increased by % (p < . ). almost all id fellows indicated that the as and ipc seminar was a vital training supplement. uptake of internist antibiotic recommendations using as decision support tools was approximately %. conclusions. all interventions addressed learning objectives and knowledge gaps and are applicable across a range of environments. evaluating long-term impact of our curriculum is the focus of future study. in , the infectious diseases society of america (idsa) noted that traditional infectious diseases (id) curricula were failing to stimulate active participation, recognize medical students as individual learners, or spark enthusiasm for id [ ] . in , abbo et al [ ] surveyed faculty and residents at teaching hospitals to assess knowledge, attitudes, and perceptions about antimicrobial use and resistance. the majority of respondents desired further education on antibiotics and agreed that better use of antibiotics would reduce resistance, but they did not feel responsible for antibiotic over prescribing. in a follow-up multicenter survey of fourth year medical students, % desired further education on antimicrobial prescribing, but only % were familiar with the role of antimicrobial stewardship (as) in promoting judicious antimicrobial use and preventing multidrug resistance [ , ] . authors also noted that only % of students surveyed completed a clinical id rotation, an underused opportunity to augment id knowledge and explore a potential career path [ ] . likewise, studies in medical student education reveal ( ) poor knowledge and practices of infection prevention and ( ) gaps in understanding of healthcare-associated infections (hais) due to lack of emphasis and suboptimal practices among supervising physicians [ ] [ ] [ ] [ ] . successful strategies in early medical education include active practice and feedback on proper hand hygiene, use of uv hand gel, with reinforcement of best practices in later years of training [ , ] . however, there is no consensus on optimal techniques or implementation of an infection prevention curriculum. stewardship literature has established that education alone cannot sustain improvements in antimicrobial prescribing behaviors [ ] . furthermore, new regulatory requirements will require concerted educational outreach to enable global improvements in antibiotic prescribing. president obama's national action plan for combating antibiotic resistant bacteria proposed a widespread implementation of antimicrobial stewardship programs (asp) to reduce antibiotic use by %- % across all healthcare settings [ ] . the centers for medicare and medicaid services and the joint commission proposed similar asp standards in [ , ] . per ohl and luther [ ] , the goal of stewardship education is not only to reduce total antibiotic use, but also to ensure that antibiotics are prescribed only when indicated, at the correct dose, route, and for the proper duration for each infection. in this study, we describe an integrated, multidisciplinary curriculum developed by the unified antimicrobial stewardship and infection prevention and control programs at the montefiore health system in bronx, new york. it consists of educational strategies designed to bridge perceived learning gaps and lay the foundation for best practices in stewardship and infection prevention in medical students, postgraduate trainees, and mature clinicians. we conducted a series of diverse educational processes across distinct learning environments within our medical center. these were layered over time as an outgrowth of observed patterns of antibiotic prescribing and infection prevention behaviors across the spectrum of our learners. the majority used a quasi-experimental, before-and-after study design with preand postintervention knowledge assessment questions, surveys of learners, or chart review with post-antibiotic prescription audit as methods of evaluation. the χ analysis was used to measure pre-and postintervention differences (microsoft excel). statistical significance was set at a p value of <. where applicable. montefiore medical center institutional review board approval was obtained where appropriate, and remaining studies were registered as quality improvement (qi) initiatives through the montefiore network performance group. the targeted learner, educational strategy, and method of assessment are detailed below. we developed seminars integrated into the microbiology and infectious diseases course for second-year medical students at the albert einstein college of medicine, conducted annually in the medical school's state-of-the-art active learning studio. antimicrobial stewardship and infection prevention seminars were added to the existing curriculum to introduce students to patient-centered topics such as safety, quality, and antimicrobial resistance. attendance at both seminars, conducted over hours each, was a course requirement. in the first seminar on appropriate antibiotic use, stewardship team members presented fundamental concepts of "bug-drug" matches, de-escalation, and use of the hospital antibiogram/ local susceptibility data using case-based multiple-choice questions as reinforcement. in small groups, they assembled a "toolkit" of core stewardship strategies to improve antibiotic use in mock clinical scenarios. in year ( ), a printed antibiogram was provided. in years and ( and ), students downloaded a smart phone application (app) named, "appropriate use, " containing antibiograms and clinical practice guidelines developed by montefiore asp (supplementary figure ). using an audience response system ([ars] turning technologies), students answered questions in primary domains: ( ) general antibiotic use, ( ) principles of microbiology and testing, and ( ) prescribing using the local antibiogram. students additionally participated in an anonymous, voluntary survey about their antibiotic overuse perceptions and preferred antibiotic resources. questions were adapted from a previously published study by abbo et al [ ] . students were introduced to infection prevention bundles, personal protective equipment (ppe), and the transmission-based isolation precautions during a multidisciplinary patient safety seminar. in small groups, students identified appropriate precautions for mock patient scenarios, including clostridium difficile infection and tuberculosis, then practiced hand hygiene and proper donning and doffing of ppe. infection preventionists moderating the small group sessions used uv-reactive wash (glo germ) to identify areas of ongoing contamination and improve technique. they also worked with prevention bundles for hais such as catheter-associated bloodstream and urinary tract infections. a video describing the comprehensive patient safety seminar can be viewed at https://www.youtube.com/ watch?v=p zybuoc vy. at the conclusion of the patient safety seminar, students participated in an anonymous, voluntary survey evaluating the program. students' clinical microbiology/id final examination integrated questions on infection prevention drawn from the session. in , we developed an id core curriculum for the medicine residency program consisting of recurring, -minute, case-based lectures on the recognition and management of typical inpatient infections (eg, community-acquired and healthcare-associated pneumonia, urinary tract infections, skin and soft tissue infections, etc). as an adjunct, we distributed a hospital antibiogram and a syndrome-based pocket antibiotic prescribing guide adapted from national guidelines and tailored to local microbiology (supplementary figure ) . before the first lecture, we distributed an antibiotic pretest with multiple-choice questions on common clinical scenarios designed to assess baseline prescribing knowledge. house staff inpatient antibiotic prescriptions were obtained from queries of the pharmacy's electronic database from november to september . antibiotic regimens recommended by consulting services (ie, id, critical care medicine) were excluded from review, as were antiretroviral and antifungal prescriptions, because these often involved id comanagement. appropriateness of prescriptions was scored using criteria. ( ) were antibiotics indicated for a "true infection" (no alternative noninfectious primary diagnosis)? ( ) did the "selected regimen" cover the infection and pathogens in question? ( ) were antibiotic "dose" and "duration" appropriate? a senior medical resident and id attending physician independently reviewed each chart. antibiotic appropriateness by indication was assessed at month preintervention and month and months postintervention. appropriateness of antibiotic dose and duration was assessed at months postintervention. in , the montefiore medical center and memorial sloan kettering cancer center jointly developed a free, half-day, intensive workshop on as and infection prevention and control (ipc) for id fellows. the first half-session consisted of interactive ipc cases, including emerging infections, hospital outbreaks, hazardous exposures in laboratory personnel, among others. cases varied each year to include practical, everyday scenarios as well as relevant and timely global threats, such as ebola virus, middle east respiratory syndrome coronavirus, and zika virus. the second half-session addressed challenging as scenarios, including drug shortages and conflict resolution with the "obstinate" prescriber. a premeeting survey evaluated fellows' existing participation in as and ipc. fellows answered multiple-choice questions using ars (turning technologies). solutions were discussed openly with a panel of experts from area hospitals (hospital epidemiologists, id pharmacists, and infection preventionists) and the new york city department of health. fianlly, fellows answered a postmeeting survey on perceptions, training needs, and the value of the workshop itself. in , we developed an audit tool containing sepsis criteria, risk stratification for multidrug resistance, and diagnostic criteria for pneumonia, skin and soft tissue infections, and urinary tract infections for a smaller community hospital without fulltime asp (see supplementary figure ). a -month qi initiative was designed to enable internal medicine faculty to serve as asp extensions (stewardship liaisons) to offer antibiotic recommendations to floor teams without providing direct patient care. initially, stewardship liaisons systematically screened all patients initiated on empiric antibiotics upon admission to geriatric units using postprescription audit. liaisons used the audit tool and a validated antibiotic prescribing guide to assist chart review. cases were then discussed with asp, and recommendations on regimens, dose adjustments, or additional management were conveyed to the floor teams by the stewardship liaison in real-time, using one-to-one academic detailing and feedback. electronic medical record was reviewed for patient age, sex, nursing home residence, comorbidities, renal function, allergies, microbiology, imaging results, and length of hospitalization. acceptance rate of recommendations was determined from review of clinical notes and orders. unadjusted hospital length of stay was compared before and the after pilot. one hundred eighty-three students participated per year ( - ), and an average of students answered the voluntary survey per year ( %). eighty percent of survey respondents believed that antibiotics are nationally overused. at least % believed that better use of antibiotics will reduce antibiotic resistance and that strong knowledge of antibiotics is important for success in medicine. forty percent admitted to taking antibiotics for a viral upper respiratory infection, and % reported that their friends have done the same. the appropriate use app was the preferred source of antibiotic information for % of students surveyed. two hundred twenty-two students downloaded the app over years ( downloads in and downloads in ). pre-and post-app, there were no significant differences in the percentage of correct responses to questions on general antibiotic use (p = . ) or principles of microbiology and testing (p = . ). an increase in correct responses from % to % was observed for questions involving antibiogram use (p = . ) ( table ). the app hits peaked at in the immediate time frame after the february session. after app introduction, approximately % of students felt comfortable prescribing antibiotics for a known infection compared with % at baseline (p = . ) [ ] . one hundred eighty-three students participated each year ( and ) and answered the preintervention survey, which revealed that only % of students felt either "very comfortable" or "somewhat comfortable" using ppe. only % of students recognized that central line insertion bundles reduce infection rates. only % were able to identify the appropriate ppe and isolation precautions for measles; however, % identified the appropriate hand hygiene associated with c difficile infection (soap and water instead of alcohol-based rubs). posttest results showed a significant improvement in ppe proficiency and knowledge of hai bundles (table ) . on average, students per year ( %) completed an anonymous survey evaluating the program. the majority of students rated the session as "effective" or "very effective" in achieving the learning objectives ( % and %, respectively, in and ) and answered exam questions about isolation, ppe, and hais correctly (range, %- %). approximately % agreed that they have a role in promoting patient safety and preventing hais as medical students [ ] . one hundred four internal medicine residents completed the antibiotic pretest, and the majority had - of correct responses. one hundred fifty residents received the id core lectures with antibiogram and pocket prescribing card from november to september , with an average of lectures per resident per year. antibiotic orders of unique prescribers were audited for appropriateness, with an average of orders per resident. fifty-four percent of prescribers were interns, % were second-year residents, and % were thirdyear residents. a total of patient charts were analyzed. antibiotics were indicated for a true infection in at least % of all cases reviewed (no alternative noninfectious diagnosis such as congestive heart failure, cardiac ischemia, or pulmonary embolism was encountered). preintervention appropriateness by indication was %, which improved to % at month and % at months postintervention (p = . and p < . , respectively). at months, appropriateness of antibiotic doses and durations was % and %, respectively (table ) . a preand postintervention analysis by syndrome showed a statistically significant prescribing improvement only for urinary tract infections ( % preintervention, % at months postintervention; p = . ) and respiratory infections ( % preintervention, % at months postintervention; p < . ) [ ] . syndrome-specific prescribing improvements for gastrointestinal, skin and soft tissue infections/osteomyelitis, and "other" infections (bloodstream, meningitis, c difficile, etc) were not statistically significant. on average, id fellows attended the course annually, or > % of second-or third-year id fellows, and % of all id fellows in the greater new york area. sixty-four percent of participants reported some formal as and ipc didactics and participation in regular as and ipc activities at their home institutions (ie, committee meetings or approval of restricted antibiotics). although % of participants expressed a professional interest in an ipc or as career after fellowship, more than half felt uncertain about possessing the skills to implement a stewardship program in future employment, and only half felt comfortable managing everyday ipc scenarios. more than % of participants agreed that the program was a valuable supplement to their id training and that case studies are an effective strategy for reinforcing as and ipc concepts. almost all participants desired additional training during fellowship. the primary critique each year was the limited time allotted for the workshop. in , fellows from smaller programs with less as and ipc exposure also attended ( table ). fellows from of local training programs have attended since the inaugural session in [ ] . from august to november , the asp/physician liaison collaborative team reviewed a total of cases from inpatient geriatric units. the mean age of patients was : % were male and % female. the most common syndromes reviewed were skin and soft tissue infections, osteomyelitis, pneumonia, urinary tract infections, and bloodstream infections. thirty-eight percent met sepsis criteria on admission, and % were residents of long-term care facilities. a variety of adjustments were recommended in . % of reviewed cases, including dose reduction for diminished creatinine clearance, penicillin allergy clarification, optimization of gram-negative coverage based on local susceptibility patterns, and facilitation of id consultation. uptake of asp/physician liaison recommendations determined from postprescription audit was . %. as a secondary outcome, we observed a -day reduction in average length of hospitalization compared with a similar time frame in ( . days [august -november ] vs . days [august -november ]) [ ] . the idsa suggests real-time electronic question-answer sessions, peer instruction, and small group discussions as tools to enhance preclinical curricula in id [ ] . these tools can effectively introduce as concepts to medical students, because studies indicate that only % of medicals schools address stewardship in their curricula [ , ] . a recent collaborative study by macdougall et al [ ] at the university of california san francisco suggests that early introduction of core as concepts to both pharmacy and medical students may foster appropriate antibiotic use as a shared responsibility of both professions. since its introduction in , our as student seminar has evolved to better suit students' needs, and it has become a cornerstone of einstein's preclinical clinical microbiology and id curriculum. introduction of the appropriate use app resulted in a % increase in the percentage of students who felt more confident prescribing antibiotics for a given syndrome. likewise, introduction of an id core curriculum and tailored antibiotic guide for medical residents enabled a % increase in appropriate antibiotic prescriptions over time. to further leverage this success, we adapted our antibiotic guide to a smart phone app for all montefiore prescribers, which we launched during the centers for disease control's "get smart about antibiotics" campaign in november . this "version . " of the appropriate use app was downloaded onto over devices and accessed over times within the first months of introduction [ ] . thus, similar tools, adapted across a range of learners, have proven successful and are popular throughout our institution. our experience also suggests that stewardship tools can aid experienced, non-id clinicians select appropriate antibiotic regimens for complex, elderly patients. attending physicians often serve in leadership roles in the medical unit, and they are charged with a myriad of responsibilities, including improving hospital throughput and use as well as teaching and evaluating trainees. challenges of outreach to the mature prescriber include ( ) time constraints, ( ) long-standing prescribing behaviors, ( ) staff turnover, and ( ) emphasis on individual patients over aggregate outcomes. education to improve prescribing at the senior level needs to respect existing attitudes, expectations, and knowledge, and maintain a collegial and collaborative atmosphere. our strategy has focused on recurring feedback sessions to prescriber groups and discrete detailing to individual prescribers. subtle reminders evoking the "public commitment" to responsible prescribing has been referred to as "antibiotic judo" [ ] . our senior prescribers have also benefited from the prescribing tools initially developed for our students and trainees. our ipc session for second-year medical students enforced proper hand hygiene technique and introduced transmission-based isolation precautions and appropriate ppe at an early stage. many students requested additional training before the start of their clinical rotations, and they judged ours to be the most interactive session held in the education center in . after the seminar, students felt much more comfortable identifying the appropriate ppe and isolation precautions for each scenario. our findings suggest that emphasis on ipc best practices in medical school promotes a culture of patient safety and lays the groundwork for sustained infection prevention behaviors as students mature into clinicians. the as and ipc interventions were implemented in different time frames and settings, which served to reduce potential confounding between learner groups. smartphone app was disseminated at the medical center only after it was introduced and studied in medical students. strategies presented herein share common themes and lessons learned (table ) , but collective and individual limitations should be mentioned. we did not conduct an educational needs assessment before study implementation. interventions were designed based on our perceived educational needs extracted from daily interactions with learners. for example, we observed from > stewardship pager interactions per year that %- % of requests are for empiric antimicrobial regimens, often broad spectrum, or intended for patients with remote penicillin allergies, for whom more streamlined β-lactam regimens are more appropriate. quasi-experimental, before and after study design, particularly when applied to small sample sizes, has several limitations, including lack of random assignment and internal validity, generalizability of results, and robustness of conclusions on the effectiveness of educational techniques [ ] . however, this methodology is common to published studies in stewardship and infection prevention. techniques described herein are best suited for adaptation at an academic medical center, because they have not been studied outside this setting. only of the interventions was designed for and implemented in a community hospital. student learners were assessed using pre-and postintervention surveys and knowledge assessment questions, and thus the true impact on prescribing and infection prevention practices is not currently known. in the postgraduate residency curriculum, appropriateness of antibiotic dose and duration was not assessed at month due to time constraints, and an antibiotic posttest was not administered due to a wide distribution of resident rotations across multiple sites throughout the bronx. in addition, a statistically significant improvement in syndrome-based antibiotic prescribing was not demonstrated in all categories due to insufficient sample sizes. in the id fellows' seminar, content of the program, mix of learners, and preand postassessment questions varied slightly each year, which may have affected survey results. although a majority of local id fellows attended our as and ipc workshop, the study was not powered to demonstrate statistically significant differences in pre-and postsurvey responses. past course attendees have not been surveyed to determine the role of as and ipc in their current careers and their perceived preparedness after completion of the workshop. a baseline audit of patient characteristics and antibiotic prescribing on the geriatric units was not conducted before stewardship implementation, and unadjusted length of stay was obtained from hospital discharge data only. reduced length of stay observed during the pilot was likely due to other factors in addition to asp intervention. fianlly, we have not yet studied the long-term impact of the curriculum as a whole or tracked individual learner progress on the path from medical student to mature clinician. the as and ipc curriculum development is a multidisciplinary endeavor of id specialists and clinical pharmacists, infection preventionists, medical school course directors, and residency and fellowship training program directors. we also suggest collaborating with other institutions to benefit from their particular expertise. to our knowledge, this is the first report describing a comprehensive as and ipc curriculum across a range of learners and environments. all strategies achieved intended short-term goals of addressing knowledge and training gaps, increasing confidence, and actively engaging participants. evaluating the long-term impact of individual strategies as part of an integrated curriculum such as ours should be the focus of future study. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. commentary: idsa guidelines for improving the teaching of preclinical medical microbiology and infectious diseases faculty and resident physicians' attitudes, perceptions, and knowledge about antimicrobial use and resistance medical students' perceptions and knowledge about antimicrobial stewardship: how are we educating our future prescribers? implementing an antibiotic stewardship program: guidelines by the infectious diseases society of america and the society for healthcare epidemiology of america hand-hygiene behaviour, attitudes and beliefs in first year clinical medical students now please wash your hands': the handwashing behaviour of final mbbs candidates usage of ultraviolet test method for monitoring the efficacy of surgical hand rub technique among medical students critical gaps in knowledge of the epidemiology and pathophysiology of healthcare-associated infections hand hygiene in medical students: performance, education and knowledge infectious diseases society of america and the society for healthcare epidemiology of america guidelines for developing an institutional program to enhance antimicrobial stewardship new societal approaches to empowering antibiotic stewardship cms issues proposed rule that prohibits discrimination, reduces hospital-acquired conditions, and promotes antibiotic stewardship in hospitals health care provider education as a tool to enhance antibiotic stewardship practices is there an app for that? expanding the stewardship education armamentarium laying the foundation for better infection prevention and control practices through active learning in early medical education improving antimicrobial use starts with our trainees pooling nyc resources to educate fellows about antimicrobial stewardship and infection prevention and control engaging internists to champion antimicrobial stewardship on the wards a comprehensive survey of preclinical microbiology curricula among us medical schools an interprofessional curriculum on antimicrobial stewardship improves knowledge and attitudes toward appropriate antimicrobial use and collaboration is there an app for that . : using an app to help house staff make more informed antimicrobial prescribing choices antibiotic judo working gently with prescriber psychology to overcome inappropriate use the use and interpretation of quasi-experimental studies in medical informatics we acknowledge dr. rosemarie conigliaro (montefiore internal medicine residency program director) for guidance and support for pursuits in medical education.financial support. our preclinical curriculum was supported by funding from the albert einstein college of medicine, grants for excellence in medical education program. dr. susan k. seo is supported in part through the nih/nci cancer center support grant p ca .potential conflict of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -c mv eve authors: christensen, paul a; olsen, randall j; perez, katherine k; cernoch, patricia l; long, s wesley title: real-time communication with health care providers through an online respiratory pathogen laboratory report date: - - journal: open forum infect dis doi: . /ofid/ofy sha: doc_id: cord_uid: c mv eve we implemented a real-time report to distribute respiratory pathogen data for our -hospital system to anyone with an internet connection and a web browser. real-time access to accurate regional laboratory observation data during an epidemic influenza season can guide diagnostic and therapeutic strategies. we implemented a real-time report to distribute respiratory pathogen data for our -hospital system to anyone with an internet connection and a web browser. real-time access to accurate regional laboratory observation data during an epidemic influenza season can guide diagnostic and therapeutic strategies. keywords. analytics; epidemic; epidemiology; influenza; laboratory. the us centers for disease control and prevention (cdc) provides data regarding influenza activity, aggregated from state data sources that generally lag or more weeks behind the date of release [ ] . however, real-time data summarizing regional hospital system observations are more relevant for local clinical decision-making. clinicians frequently request updates from the microbiology laboratory on influenza test positivity, in addition to other common respiratory pathogens, during the respiratory virus season to help inform their daily practice. in addition, clinical laboratories should routinely monitor local influenza data to determine if epidemics are occurring, if continued testing is necessary, or if patients can be treated based on positive symptoms alone [ , ] . to address these local needs in a major us metropolitan area, our clinical microbiology laboratory implemented an online dashboard to distribute respiratory pathogen data for our -hospital system to clinicians, epidemiologists, infection control practitioners, system leadership, and the public. the report provides easy access from any workstation or mobile device with an internet connection. development of this report began in the fall , before the respiratory virus season, during which influenza reached an epidemic status across the united states that resulted in supply shortages, testing difficulties, and a widespread public health crisis [ , ] . respiratory pathogen panel test result data were extracted from our laboratory information system (scc soft computer). the extracts included de-identified laboratory result data, including specimen collection date, facility, and result for all influenza and respiratory pathogen tests. the data were further analyzed and aggregated to produce interactive charts published to a public-facing web server. the accuracy of the report was validated by comparison with data generated natively by our laboratory information system, as well as a manual review of all test results from day. we gathered visitor statistics from the server log files. internet protocol addresses were mapped to internet service provider, country, city, and organization using ipinfo.io [ ] . four distinct data summary analyses were performed. first, for our most commonly detected pathogens (influenza a, influenza b, respiratory syncytial virus, and rhinovirus/enterovirus), we calculated the number of positive tests for each day and week. second, we calculated the number of positive tests at each facility. third, we calculated the daily and weekly positivity rates of our respiratory pathogen molecular test. fourth, we calculated the frequency with which each pathogen was identified by our molecular test. these counts reflected anonymized and aggregated data devoid of protected health information. to present users with interactive and dynamic data, we elected to use hypertext markup language (html) [ ] and javascript [ ] as our visualization modality. we used chart.js [ ] as the framework for producing our interactive charts. the data analyses generated javascript arrays that were stored in chart.js data structures to produce charts ( figure for both chart and chart , we created radio buttons that allowed the user to toggle between a weekly or daily summary. for chart , we built a radio button to switch between basic view and detailed view. in basic view, the influenza a molecular and antigen results are grouped together; in detailed view, the subtypes of influenza a detected by our molecular platform are graphed separately. three distinct time intervals were supported, including the most recent weeks, the past year, and -present. the charts were packaged into an html report and uploaded to a public-facing web server. we unveiled the report and requested informal feedback at the system infection control meeting, the system antimicrobial stewardship meeting, and the hospital infection prevention and control committee meeting. we included a link to the report in an e-mail distributed to all employees from the executive vice president of the hospital system. we updated the graphs daily. over the subsequent weeks, the report was accessed times, and over the next weeks, the report was accessed times. approximately % of the originating ip addresses were from within our hospital system, and % were from locations outside the united states. views on mobile devices accounted for % of the traffic, and % of views were referred from the department of pathology and genomic medicine website. views peaked at per hour right after the link was distributed by our executive vice president. during the first week, % of all hour intervals saw at least page view, with an average of views per hour. daily view counts decreased as the influenza season ended and stabilized at views per week on average. at the height of the influenza epidemic at our hospital system, % ( / on december , ) of all influenza antigen tests and % ( / on december , ) of respiratory pathogen molecular tests were positive for influenza a or influenza b. forty-six percent ( / on december , ) of these molecular tests were positive for any respiratory pathogen. vendor supply stocks were limited nationwide [ ] , and in january , our supply of universal transport media diminished, requiring the creation of : aliquots to preserve material for sample collection. based on these data and following cdc/world health organization (who) guidelines for epidemics [ , ] , our primary care group stopped testing for influenza and treated symptomatic patients as if they were influenza positive. our interactive website provided near real-time data, which allowed this decision to be made a week earlier than otherwise would have been possible using federal and state data. furthermore, our inpatient pharmacy was able to anticipate oseltamivir utilization and stock accordingly while remaining prepared for potential drug shortages. brief report • ofid • we developed a near real-time report that presents statistics regarding respiratory pathogen testing from our microbiology laboratory. the population tested includes all inpatient and outpatient individuals across our -hospital system ( operating beds) and all patients in the associated free-standing emergency and primary care clinics. the report is available to any device with an internet connection and is updated daily to provide critical data to clinicians, epidemiologists, infection prevention and control committees, hospital leadership, and the public. we developed the site with mobile devices in mind, which allows the graphs and fonts to be readable on any platform. the user can switch between daily and weekly data aggregations using radio buttons. the time interval of interest can be modified using preconfigured buttons. data can be filtered by clicking the data labels in the chart legends. these features are possible because of our decision to develop a web-based report, as opposed to a pdf, spreadsheet, or word processing document. anecdotal feedback collected at the time of rollout was universally positive. interest in the report quickly peaked after the initial announcement but continued to be viewed daily. as the influenza season ended, infectious diseases clinicians asked that we add a rhinovirus/enterovirus trend to the website so they could track the summer respiratory virus season as well. at least clinician changed ordering practice in early september after identifying a spike in rhinovirus/enterovirus positivity frequency. in november , the chief physician executive and specialty physician group ceo sent an e-mail to physician leaders across the system regarding a significant uptick in respiratory syncytial virus isolates and rising influenza a pathogens detected by laboratory testing, which was identified through our website report. based on the data provided by our laboratory in this report and cdc/who guidelines for epidemics, our primary care group stopped laboratory testing for influenza and treated symptomatic patients as if they were influenza positive. access to accurate real-time data during an epidemic influenza season can guide diagnostic and therapeutic strategies. during the epidemic, there was a nationwide shortage of testing reagents [ ] . earlier identification of high positivity rates by monitoring real-time data allows for an institution to implement "treat don't test" guidelines earlier, preserving test reagents for critical situations where they are most needed. in summary, our microbiology laboratory implemented a near real-time internet report to distribute respiratory pathogen data for our -hospital system to clinicians, hospital epidemiologists, infection control committees, system leadership, and the public. facile access to accurate real-time data during an epidemic influenza season can guide diagnostic and therapeutic strategies. the report is available at https://flu.houstonmethodist.org/. fluview: a weekly influenza surveillance report prepared by the influenza division guide for considering influenza testing when influenza viruses are circulating in the community world health organization. who recommendations on the use of rapid testing for influenza diagnosis centers for disease control and prevention. summary of the - influenza season labs take stock of surprising flu season ip address api and data solutions -geolocation, company, carrier info, type and more world wide web consortium. w c html ecmascript language specification financial support. this work was supported by the department of pathology and genomic medicine at houston methodist hospital. this research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.potential conflicts of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -j i ozsz authors: mccreary, erin k; pogue, jason m title: coronavirus disease treatment: a review of early and emerging options date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: j i ozsz severe acute respiratory syndrome coronavirus (sars-cov- ), the cause of coronavirus disease (covid- ), has spread across the globe resulting in a pandemic. at the time of this review, covid- has been diagnosed in more than patients and associated with over deaths (centers for disease control and prevention, world health organization). on behalf of the society of infectious diseases pharmacists, we herein summarize the current evidence as of march , to provide guidance on potential covid- treatment options. it is important to caution readers that new data emerges daily regarding clinical characteristics, treatment options, and outcomes for covid- . optimized supportive care remains the mainstay of therapy, and the clinical efficacy for the subsequent agents is still under investigation. antimicrobial stewardship programs, including infectious diseases pharmacists and physicians, are at the forefront of covid- emergency preparedness. we encourage all readers to continue to assess clinical data as it emerges and share their experience within our community in a well-controlled, adequately powered fashion. in december , several patients in wuhan, hubei, china were diagnosed with pneumonia secondary to an unknown virus. in response, an epidemiological alert was placed with the world health organization (who) dated december , . by january , chinese scientists had isolated severe acute respiratory syndrome coronavirus (sars-cov- ) [ ] . in the months that followed, sars-cov- , the cause of coronavirus disease (covid- ) , spread across the globe resulting in the current pandemic. at the time of this review, covid- has been diagnosed in more than patients and associated with over deaths (centers for disease control and prevention [cdc] , who). on behalf of the society of infectious diseases pharmacists, we herein summarize the current evidence as of march , to provide guidance on potential covid- treatment options. it is important to caution readers that new data emerges approximately every hour regarding clinical characteristics, treatment options, and outcomes for covid- . optimized supportive care remains the mainstay of therapy, and the clinical efficacy for the subsequent agents is still under investigation. most existing preclinical and clinical data on antiviral therapy are derived from other viruses, including sars-cov- (first reported in ), middle east respiratory syndrome coronavirus ([mers-cov] first reported in ), and non-coronaviruses (eg, ebola virus disease). it is unclear how well these data can be extrapolated to sars-cov- . furthermore, the clinical relevance of antiviral in vitro activity (defined as half-maximal effective concentration [ec ] values) remains unclear given an absence of pharmacokinetic/pharmacodynamic or clinical data that equates achievable exposures relative to these values to a treatment effect. finally, in vitro data should be compared cautiously across studies given the potential variability in testing methodologies that could impact perceived activity. antimicrobial stewardship programs, including infectious diseases pharmacists and physicians, are at the forefront of covid- emergency preparedness [ ] . we encourage all readers to continue to assess clinical data as it emerges and share their experience within our community, preferentially evaluating these agents in the context of randomized, controlled trials. gilead sciences, inc. in response to the ebola outbreak in west africa from to . in its active triphosphate nucleoside form, remdesivir binds to ribonucleic acid (rna)-dependent rna polymerase and acts as an rna-chain terminator. it displays potent in vitro activity against sars-cov- with an ec at hours of . µm in vero e cells [ ] . similar activity has been demonstrated against other zoonotic coronaviruses with ec values of . µm demonstrated for both sars-cov- and mers-cov [ ] [ ] [ ] [ ] . remdesivir is highly selective for viral polymerases and is therefore expected to have a low propensity to cause human toxicity. accordingly, sheahan et al [ ] demonstrated a wide therapeutic index for remdesivir in a human airway epithelial cell model. the drug also displays a high genetic barrier to resistance in coronaviruses and has a long intracellular half-life that allows for once-daily dosing [ , ] . the dose under investigation for treatment of covid- is mg intravenously (iv) on day followed by mg iv daily for up to days, infused over - minutes ( table ) . the therapeutic efficacy of remdesivir was first described in an animal model against ebola among infected rhesus monkeys in which once-daily dosing resulted in suppression of viral replication and protection from lethal disease [ ] . however, in a human study, remdesivir-treated patients with ebola experienced a -day mortality rate of % in a randomized controlled trial of experimental therapies conducted in response to the democratic republic of congo outbreak of , resulting in early termination of this study arm [ ] . it is worth noting that this trial did not have an active control arm, and mortality rates for the other experimental treatments were . % (zmapp), . % (mab ), and . % (regn-eb ). against mers-cov, sheahan et al [ ] evaluated the therapeutic efficacy of remdesivir among infected mice and found treatment significantly reduced virus lung titers, weight loss, lung hemorrhage, and lung injury scores. the authors proposed the importance of early therapy initiation to diminish virus replication and promote pulmonary repair because remdesivir demonstrated less clinical benefit with high-titer virus inoculum. most notably, the authors also noted that prophylactic remdesivir diminished mers-cov replication and disease, which was similar to their findings in a murine model with sars-cov- [ , ] . the first report of a remdesivir-treated patient with covid- in the united states was a -year-old male in snohomish county, washington who received treatment on hospital day (illness day ) due to developing pneumonia and persistent fevers [ ] . the patient experienced clinical improvement and negativity of oropharyngeal swab on hospital day , although nasopharyngeal swab remained positive. no adverse events to remdesivir were reported for the patient, which is consistent with previous case reports of use in other viruses [ , ] . among the first patients confirmed by the cdc to have covid- in the united states, were treated with remdesivir via compassionate use protocol [ ] . all patients reported transient gastrointestinal symptoms and aminotransferase elevation. all patients are reportedly recovering, but the authors were unable to assess the efficacy or safety of remdesivir based on the lack of comparator and confounding treatments, including concomitant use of corticosteroids in one patient. there are clinical trials currently enrolling patients in the united states (table ) . two additional trials recruiting only in china have been registered on clinicaltrials.gov nct (severe disease) and nct (mild/moderate disease). remdesivir may also be obtained through compassionate use and the emergency investigational new drug (eind) application process. at the time of this review, requests for compassionate use must be submitted online via https://rdvcu.gilead. com/. compassionate use is only considered for hospitalized patients with polymerase chain reaction (pcr)-confirmed sars-cov- requiring mechanical ventilation in whom enrollment in a clinical trial is not feasible. patients are excluded from the compassionate use program if they do not meet the above criteria, have evidence of multiorgan failure, are receiving vasopressors for hypotension, have liver disease defined as alanine aminotransferase (alt) > × upper limit of normal (uln) or renal impairment defined as creatinine clearance (crcl) < ml/min, or receiving dialysis or continuous venovenous hemofiltration. inclusion and exclusion criteria for compassionate use may change, so applicants are encouraged to review the most up to date criteria for all potential patients. clinicians should be cognizant that it typically takes a minimum of hours for institutions to receive emergency institutional review board authorization (if required), protocol, and consent forms from gilead, us food and drug administration (fda)-approval for the eind, and eventual drug shipment. clinicians should coordinate with their local information technology teams to build a medication order sentence into the electronic health record during this time. patients may receive other antiviral therapies during the waiting period but must immediately discontinue them if they receive remdesivir for compassionate use. it is interesting to note that the adaptive clinical trial protocol originally stated "remdesivir is a prodrug that is metabolized to its active form as a substrate of cyp- a ". this implies the existence of a drug-drug interaction with cyp a substrate inhibitors such as ritonavir or voriconazole. however, the protocol also stated "although remdesivir is a substrate for cyp c , cyp d , and cyp a in vitro, coadministration with inhibitors of these cyp isoforms is unlikely to markedly increase remdesivir levels, as its metabolism is likely to be predominantly mediated by hydrolase activity." unlike the former, the latter statement is substantiated by well described chemistry of the molecule. the national institute of allergy and infectious diseases was contacted about this discrepancy and in collaboration with gilead, this has been corrected. there is no reason to believe that any significant drug interactions between remdesivir and cyp a inhibitors or inducers are likely [ ] . emerging clinical evidence and available in vitro data suggest remdesivir is a promising agent for the treatment of covid- . institutions should explore clinical trial enrollment or compassionate use remdesivir for moderate-to-severe patients. additional clinical data are eagerly anticipated and should help further define the role of this agent in covid- . chloroquine, an antimalarial agent with anti-inflammatory and immunomodulatory activities, has gained significant interest as a potential therapeutic option for the management of covid- . in early february, wang et al [ ] demonstrated potent in vitro activity of chloroquine against sars-cov- with an ec at hours of . µm in vero e cells. these data were consistent with previous data for chloroquine's inhibitory activity against sars-cov- and mers-cov in various cell lines, where ec values of - . and . µm were demonstrated, respectively [ ] . these findings have supported the clinical use of chloroquine, at a dose of mg by mouth twice daily, in numerous clinical trials in china during this outbreak. although the rationale for this dosing regimen remains unclear, and peer reviewed data from the trials are currently unavailable, it was announced in mid-february that promising early results have been demonstrated. per gao et al [ ] , "thus far, results from more than patients have demonstrated that chloroquine phosphate is superior to the control treatment in inhibiting the exacerbation of pneumonia, improving lung imaging findings, promoting a virus-negative conversion, and shortening the disease course according to the news briefing. severe adverse reactions to chloroquine phosphate were not noted in the aforementioned patients. " although this development has been encouraging, supply issues in the united states and cardiovascular toxicity concerns limit the use of chloroquine. as an alternative, hydroxychloroquine, a compound that differs from chloroquine only by a single hydroxyl group, has garnered interest. hydroxychloroquine is perceived as having better tolerability than chloroquine, which has led to long-term usage in rheumatological disorders. historically, very limited data were published assessing the activity of hydroxychloroquine against coronaviruses. in , biot et al [ ] assessed the comparative inhibitory activity of chloroquine and hydroxychloroquine against sars-cov- in vero cells. the authors demonstrated that chloroquine had an approximately -fold increased potency (ec of . ± . µm) compared with that of hydroxychloroquine (ec of ± µm). against sars-cov- , yao et al [ ] performed a -part study assessing the comparative in vitro activity of chloroquine and hydroxychloroquine and performed pharmacology-based pharmacokinetic (pbpk) modeling to assess comparative exposure and predicted activity of these compounds in the lung. in vitro analyses in vero cells demonstrated that the potency of hydroxychloroquine (ec of . µm) was greater than that of chloroquine (ec of . µm) against sars-cov- [ ] . to inform optimal dosing of hydroxychloroquine, the investigators then performed pbpk modeling. in this analysis, the investigators utilized human population pharmacokinetic and rat lung penetration data for each compound to estimate free trough concentrations in the lung to ec ratios (r ltec ) [ ] . because mg of chloroquine by mouth twice daily has been reported to demonstrate efficacy against sars-cov- , the target r ltec for hydroxychloroquine regimens was set to ≥ . (day ), . (day ), and . (day ), which were the r ltec values predicted with the "efficacious" mg by mouth twicedaily dosing of chloroquine [ ] . various dosing regimens were simulated, but are particularly notable. the first was an oral loading dose of mg (divided mg then mg) on day , followed by mg daily. this regimen led to significantly higher r ltec on day ( . ), day ( . ), and day ( ) than those values demonstrated with chloroquine. the second regimen was a loading dose of mg ( mg × ) on day followed by mg twice daily. this was also associated with higher r ltec values than chloroquine on day , , and (corresponding to . , . , and . , respectively) [ ] . the authors concluded that these data support the lower dose regimen because r ltec values were significantly higher than those with the "proven efficacious" regimen of mg of chloroquine by mouth twice daily. clinicians should note that both chloroquine and hydroxychloroquine have half-lives of ~ days [ ] , and therefore short durations would likely provide prolonged courses of therapy. this was exemplified in the pbpk modeling in which r ltec values with hydroxychloroquine were predicted to still be above the targeted efficacy threshold on day , even with a -day course of therapy. although these data are encouraging for the potential role of hydroxychloroquine against sars-cov- , we caution against solely relying on these data to support dosing regimens for patients. the use of mg of chloroquine by mouth twice daily as the reference for efficacy is rational given initial reports from china [ ] , but it is important to note that this dosing still requires validation, and the improved r ltec values reported are largely driven by the finding that hydroxychloroquine was . times more potent than chloroquine in vitro. although this enhanced potency may very well prove true as more data become available, this report is counter to the relative potency demonstrated with the structurally similar sars-cov- strain in in which chloroquine was approximately times more potent than hydroxychloroquine. in addition, a recently published study has demonstrated that the ec value for chloroquine is . µm [ ] , similar to the value reported for hydroxychloroquine in the analysis by yao et al [ ] . because there are currently no efficacy data available for hydroxychloroquine in covid- , additional consideration should be given to the optimal dosing strategy. we use the following example to illustrate this point. if one were to consider these compounds to be equally potent (identical ec values) and utilize the pbpk data from yao et al [ ] , the mg load, mg daily regimen for hydroxychloroquine would yield r ltec values of . , . , and . on day , , and , respectively. these r ltec values would be slightly lower than those achieved with mg by mouth twice daily of chloroquine on day and significantly lower than those on day , suggesting the potential need for a higher dose to have similar activity. although the mg daily regimen is the most common regimen currently being assessed in clinical trials, the rationale for that dose is currently unclear, and at least clinical trial in china is using a higher dose of mg by mouth daily. to this point, gautret et al [ ] recently published their initial experience on the impact of mg of hydroxychloroquine by mouth every hours on viral eradication in patients with covid- . the authors reported on patients ( hydroxychloroquine and control) who were covid- positive and able to have nasopharyngeal sampling for the first days of therapy (in the treated arm). the investigators demonstrated that hydroxychloroquine ( of , %) was superior to standard of care ( of , . %; p = . ) in eradicating sars-cov- from the nasopharynx. it is interesting to note that patients were prescribed azithromycin "to prevent bacterial super-infection" and the investigators found that viral eradication was numerically superior in this subgroup ( of , %) compared with those who received hydroxychloroquine alone ( of , %). the authors concluded that azithromycin "reinforced" the sars-cov- viral load achieved by hydroxychloroquine. although these data are intriguing, certain limitations to this data set must be acknowledged. first, although viral eradication is an important endpoint, the authors did not report clinical outcomes in these patients. second, the cohort initially contained hydroxychloroquine patients, but of them were removed from the analysis due to early cessation of hydroxychloroquine therapy including pcr-positive patients who were transferred to the intensive care unit (icu), pcr-negative patient who passed away, and pcr-positive patient who discontinued hydroxychloroquine due to nausea. finally, the hydroxychloroquine monotherapy arm included patients with significantly higher viral loads, represented by lower cycle threshold (c t ) values than those who received combination therapy. if the hydroxychloroquine monotherapy patients with c t values < are separated from those with c t values ≥ , there is a notable discordance in viral eradication rates ( of , % vs of , %), with this latter number approaching the of demonstrated with hydroxychloroquine and azithromycin combination therapy in which all patients had c t values ≥ . given this finding, the small numbers in this study, the lack of clinical outcomes presented, the potential for additive toxicity with hydroxychloroquine and azithromycin, and the desperate need to practice good antimicrobial stewardship during the covid- pandemic, we would caution clinicians against using these data to support combination therapy. despite all of the unknowns, the initial experience in china is encouraging for the potential role of chloroquine, or alternatively hydroxychloroquine, for the management of covid- . clinicians are encouraged to closely follow subsequent peer-reviewed publications from the ongoing chloroquine and hydroxychloroquine trials, because others have raised concerns regarding the apparent in vitro and/or in vivo discordance witnessed with chloroquine in other viral infections [ ] . furthermore, if hydroxychloroquine is utilized, careful consideration for dose selection should be given in accordance with the aforementioned data, as well as considerations for when to initiate during the course of illness. lopinavir is a human immunodeficiency virus (hiv)- protease inhibitor administered in fixed-dose combination with ritonavir (lpv/r), a potent cyp a inhibitor that "boosts" lopinavir concentrations. lopinavir seems to block the main protease of sars-cov- , inhibiting viral replication [ ] . in , chu et al [ ] evaluated a series of antivirals for in vitro activity against sars-cov- . they reported lopinavir at µg/ml and ribavirin at µg/ml inhibited sars-cov- after hours of incubation and that the agents were synergistic when used together [ ] . de wilde et al [ ] later described the antiviral activity of lopinavir against sars-cov- and demonstrated an ec . ± in vero e cells, which is near the upper range of lpv plasma concentrations previously measured in patients with hiv [ ] . sheahan et al [ ] evaluated the in vitro efficacy of lpv/r in combination with interferon beta (infb) against mers-cov and found the addition of lpv/r did not significantly enhance antiviral activity of infb alone (ec = vs iu/ml, respectively). they also described the ec of lpv/r ( . µm) and lpv alone ( . µm), suggesting similar activity to that described for sars cov- . despite in vitro activity against mers-cov, therapeutic doses of lpv/r + infb in mice models failed to reduce virus titer and exacerbated lung disease [ ] . this is notable because this was the same study in which remdesivir demonstrated both more potent in vitro activity as well as in vivo efficacy. however, the in vivo animal data for mers-cov appears equivocal given that a nonhuman primate model demonstrated improved clinical and pathological features after lpv/r treatment [ ] . a randomized controlled trial of lpv/r and recombinant interferon-β b versus placebo is currently enrolling for patients with mers-cov, which might help clarify the apparent discrepancy between in vitro and animal models [ ] . based on in vitro findings, chu et al [ ] utilized combination therapy with lpv/r, ribavirin, and corticosteroids for any newly diagnosed patient with sars-cov- without acute respiratory distress syndrome (ards) starting in april . patients receiving lpv/r combination therapy (n = ) were matched to historical patients receiving ribavirin plus corticosteroids (n = ), and a significant reduction in the development of ards or death at days was observed ( . % vs . %, p < . ). this was corroborated by an expanded case-control matched study of lpv/r-treated patients from the same center that demonstrated a significant reduction in pulse steroid use ( . % vs . %), intubation ( % vs %), and mortality ( . % vs . %) among patients who received lpv/r combination versus no lpv/r, respectively, as initial therapy [ ] . more important, the benefits of lpv/r were only demonstrated in patients who received initial treatment with lpv/r (defined as initiation of drug at time of sars-cov- diagnosis). there was no observed benefit when lpv/r was added as rescue or salvage therapy (death rate . % vs %). this compelling mortality difference in sars-cov- and continued investigation in mers-cov led to inclusion of lpv/r in the chinese sars-cov- guidelines at a dose of mg/ mg ( capsules/tablets) by mouth twice a day for no more than days even though to our knowledge, no in vitro data for lpv/r in sars-cov- exist [ ] . in pediatric patients weighing - kg, the recommended dose in the united states is mg/kg suspension by mouth twice daily. there are ongoing registered clinical trials in china, korea, thailand, and hong kong evaluating lpv/r as monotherapy or in combination with other antivirals (eg, ribavirin, interferon beta- b) or traditional chinese medicine for treatment of covid- . real-world data for treatment of covid- with lpv/r are emerging. young et al [ ] reported outcomes of the first patients infected with sars-cov- in singapore, of whom received lpv/r monotherapy. three patients had reduction in oxygen requirements after treatment initiation; deteriorated to respiratory failure. two of patients ( %) experienced clearance of viral shedding on treatment, and of ( %) experienced adverse events that precluded completion of the planned -day treatment course. other published case reports or case series from korea and china comprising total patients describe decreased viral load and clinical improvement after lpv/r initiation. these data are difficult to interpret in light of concomitant drug therapies, varied time points of therapy initiation, heterogeneous severity of illness amongst patients, and the lack of comparator treatments [ ] [ ] [ ] . finally, early reports from wuhan have described some patients receiving lpv/r in addition to other therapies (including corticosteroids), but clinical outcomes and adverse events are either not described or not delineated by treatment group [ ] [ ] [ ] . most recently, cao [ ] et al reported the results of an openlabel randomized trial comparing lpv/r / mg twice daily (n = ) to standard care (n = ) for the treatment of covid- pneumonia. the primary endpoint was defined as the time from randomization to an improvement of points on a -category ordinal scale or discharge from the hospital. secondary outcomes included -day mortality, time until discharge, and virologic response on repeat oropharyngeal swabs over the course of the study. the median time from symptom onset to randomization was (interquartile range [iqr], - ) days, and this did not differ between the groups. there was no significant difference in time to clinical improvement ( [iqr, [ ] [ ] [ ] [ ] [ ] , − . % to . %) between patients receiving lpv/r and standard care. when the patients who died after randomization but before receiving lpv/r were removed, there remained no difference in mortality ( . % vs . %; absolute difference, − . percentage points; % ci, − . to . ). more important, there was no difference between treatment arms in reduction of viral loads over time between the groups. with the available data, it is difficult to assess whether lpv/r has a role for the treatment of covid- either as monotherapy or in combination. the data from sars-cov- are encouraging, but this must be weighed against the inferior performance in mouse models against mers-cov, the less potent in vitro activity compared with remdesivir and chloroquine for sars-cov- , and limited data suggesting no advantage over standard care for sars-cov- . more important, it warrants comment that in the recent randomized controlled trial in covid- pneumonia, the median time from symptom onset to initiation of therapy was days, and in the sars-cov- experience, therapy appeared effective if started early, but not as rescue and/or salvage. if used, drug interactions must be screened, and gastrointestinal toxicities, including diarrhea, nausea, and vomiting, and hepatotoxicity, require close monitoring, particularly because elevated aspartate transaminase or alt may exclude patients with covid- from clinical trials. the lpv/r tablets can be taken without regard to food but should not be crushed because this decreases systemic exposure; solution should be used in patients who cannot receive intact tablets [ ] . nitazoxanide has demonstrated potent in vitro activity against sars cov- , with an ec at hours of . µm in vero e cells [ ] . this potent activity is consistent with ec values for nitazoxanide and its active metabolite, tizoxanide, against mers-cov in llc-mk cells in which ec values of . and . µm, respectively, have been demonstrated [ ] . nitazoxanide displays broad-spectrum in vitro antiviral activity against influenza, respiratory syncytial virus, parainfluenza, rotavirus, and norovirus among others in addition to coronaviruses [ ] . this broad-spectrum antiviral activity is believed to be due to the fact that the mechanism of action is based on interference with host-regulated pathways involved in viral replication rather than virus-specific pathways [ ] . due to its broad-spectrum antiviral activity, nitazoxanide is being investigated for the management of influenza and other acute respiratory infections. positive results were demonstrated in a phase b/ study for the outpatient management of influenza, in which a dose of mg by mouth bid of nitazoxanide was associated with a ~ -day improvement in time to resolution of symptoms when compared with placebo (p = . ) [ ] . three phase randomized controlled trials in uncomplicated influenza have since been completed (clinicaltrials. gov identifier nct [march ], nct [april ], and nct [september ]), although results are unavailable. nitazoxanide failed to reduce the duration of hospitalization or the time to symptom alleviation in a phase randomized controlled trial in patients with severe acute respiratory illnesses requiring hospitalization, predominantly caused by respiratory viruses [ ] . although the in vitro activity of nitazoxanide against sars-cov- is encouraging, more data are clearly needed to determine its role in the management of covid- . tocilizumab is a humanized monoclonal antibody that inhibits both membrane-bound and soluble interleukin- (il- ) receptors. interleukin- , which is secreted by monocytes and macrophages, is one of the main drivers of immunologic response and symptoms in patients with cytokine-release syndrome (crs). although tocilizumab was first approved by the fda in for the treatment of rheumatoid arthritis, it has gained traction in recent years for treatment of patients with crs following chimeric antigen receptor t-cell (car t) therapy as a corticosteroid-sparing agent [ ] . indeed, it received fda approval for severe or life-threatening car t-associated crs in due to its efficacy and safety profile. although criteria for grading crs severity varies by cancer center, it has been proposed to administer tocilizumab to crs patients with any of the following: oxygen requirement < %, hypotension responsive to fluids or a low dose of a single vasoactive agent, or grade organ toxicity as defined by the common terminology criteria for adverse events [ ] . interleukin- antagonism may make a patient more susceptible to bacterial infection and has been associated with neutropenia and thrombocytopenia in patients receiving chronic therapy with tocilizumab for giant cell arteritis or rheumatoid arthritis. in a case series of adult patients with relapsed or refractory b-cell acute lymphoblastic leukemia, grade crs or higher was associated with increased risk of subsequent infection, but it was unclear whether tocilizumab or corticosteroid use promoted this risk [ ] . there were no reported adverse events in the tocilizumab-treated patients submitted to the fda for the crs indication, which recommends a maximum of doses for treatment [ ] . hyperinflammatory states and cytokine storming, including elevated il- , has been reported in severe covid- and were associated with increased mortality in patients in china [ ] . a preprint (nonpeer reviewed) case series of patients treated with tocilizumab between february and , in china reported marked success, including rapid resolution of fever and c-reactive protein, decreased oxygen requirements, and resolution of lung opacities on computerized tomography imaging [ ] . the authors state the patients all had "routine treatment for a week" before tocilizumab, which was described as "standard care according to national treatment guidelines" including lopinavir, methylprednisolone, and other supportive care. all patients had il- analyzed before tocilizumab administration with a mean value of . ± . pg/ml (normal < pg/ml). it should be noted that in the united states, il- monitoring is a send-out laboratory for most institutions with a turnaround time of - days. no adverse events were described in the chinese cohort; however, long-term assessment was not done. immunotherapy with tocilizumab is listed as a treatment option for severe or critical cases of covid- with elevated il- in the th edition of the national health commission of the people's republic of china covid- diagnosis and treatment guide [ ] . the recommended dose is - mg/kg or mg standard dose iv once, with the option to repeat a dose in hours (not to exceed a total dose of mg). there are ongoing trials in china evaluating safety and efficacy of tocilizumab for patients with covid- pneumonia, but none registered in the united states. we anticipate that more data regarding tocilizumab use in patients with covid- will emerge, and it will be imperative for clinicians to evaluate it closely. the optimal timing of tocilizumab administration during the disease course is not yet defined, nor is there a known il- threshold for progression to severe disease. it is imperative to continue to follow the longterm outcomes in these patients to assess the risk versus benefit of tocilizumab. similar to other severe respiratory tract infections, there is significant interest and controversy surrounding the role of corticosteroids for the management of severe pneumonia due to coronaviruses. the potential benefit of these agents to blunt the inflammatory cascade seen in severe disease needs to be carefully weighed against the concerns for secondary infections, adverse events, and other complications of corticosteroid therapy. the data assessing the role of corticosteroids as adjunctive care for severe coronavirus (sars-cov- , mers-cov, and sars-cov- ) pneumonia are difficult to interpret. given the retrospective observational nature of these analyses, there is significant confounding by indication that is difficult to control or correct for in addition to limited sample sizes. patients who receive corticosteroids have a higher severity of illness, are more likely to require invasive interventions, and are more likely to be receiving intensive care. in addition, there is significant heterogeneity with regard to timing of corticosteroid initiation, which can significantly impact disease progression and likelihood of response. all of these features lead to patients who receive steroids being at increased risk for poor outcomes. in addition, there is great variation in agent and dosage used, which can impact both safety and efficacy. therefore, clinicians making any therapeutic decisions based on the literature for corticosteroids need to keep these considerations in mind. the clinical data for use of corticosteroids in sars-cov- infections are mixed. multiple analyses show no impact on outcomes [ ] , one report demonstrates decreased mortality in critically ill patients [ ] , and others have documented worse outcomes for patients receiving steroids, including increased time to viral clearance [ ] or an increase in the composite endpoint of icu admission or death [ ] . in mers-cov, receipt of corticosteroids has been associated with a delayed time until viral clearance in a large cohort (n = ) of infected patients [ ] . however, this same data set showed a nonsignificant reduction in -day mortality in patients receiving corticosteroids (adjusted odds ratio = . ; % ci, . - . ) after accounting for differences between the groups in a regression model accounting for time-varying exposures. finally, recent evidence in sars-cov- suggested a decrease in mortality in patients with ards with the receipt of corticosteroids ( of [ %] vs of [ %] without; hazard ratio, . ; % ci, . - . ) [ ] . as demonstrated, the data for corticosteroids are inconsistent, confusing, and inconclusive. although target patients in whom corticosteroids will improve outcomes may exist (eg, those with cytokine-related lung injury who may develop rapidly progressive pneumonia), that population remains ill-defined [ ] . clinicians need to carefully weigh the risks and benefits of corticosteroids on the individual patient level. this need for a risk-benefit assessment in individual patients and careful consideration of dose is exemplified in the covid- diagnosis and treatment guide from the national health commission of the people's republic of china where the authors state, "based on respiratory distress and chest imaging, may consider glucocorticoid that is equivalent to methylprednisolone - mg/kg/day for - days or less. note that large-dose glucocorticoid suppresses immune system and could delay clearance of sars-cov- ." [ ] a recent consensus statement from the chinese thoracic society recommends a lower dose, ≤ . - mg/kg per day methylprednisolone for ≤ days in select patients, after careful consideration of risks and benefits [ ] . randomized controlled trial data are urgently needed to clearly define the role of corticosteroids in covid- . ribavirin, a guanosine analog that terminates rna synthesis, was first approved in the s and has been used clinically for respiratory syncytial virus, viral hemorrhagic fever, and in combination with interferon for hepatitis c. as mentioned previously (see lpv/r section), it was evaluated against sars-cov- in and used clinically in combination with corticosteroids and/or interferon in the absence of other treatment options; however, outcomes were either poor or ill-defined [ , ] . the doses required for antiviral activity against sars range from . to . grams by mouth every hours, which are associated with excessive toxicity to patients [ ] . wang et al [ ] evaluated the in vitro activity of ribavirin against sars-cov- and found an ec of . µm, which was over times less potent than remdesivir. the risk of hematologic toxicity at high doses likely outweighs potential clinical benefit, and therefore ribavirin was not considered a viable candidate for further investigation by the who research and development plan for sars-cov- given its lack of in vitro efficacy, toxicity profile, and poor outcomes. interferons (α, β) may stimulate innate antiviral responses and are expected to have in vitro activity against sars-cov- , given the previously described activity demonstrated against mers-cov (ec iu/ml). however, toxicities are substantial including severe cytopenias, hepatotoxicity (including fatality), neuropsychiatric events, and risk of developing fatal or life-threatening ischemia or infection, particularly when combined with ribavirin. this combination was not associated with improved mortality or enhanced viral clearance in a retrospective analysis of patients infected with mers-cov who were initiated on combination therapy within - days of icu admission [ ] . despite the limited to poor data, chinese guidelines recommend ribavirin mg iv - times daily in combination with lpv/r or inhaled interferon-α ( million units nebulized twice daily) as one of the "standard treatment" options for covid- . various combinations of ribavirin, interferon, and other antiviral agents are currently being studied in several clinical trials. based on the poor in vitro activity, an absence of animal or human data supporting its use, and a significant toxicity profile, we recommend avoiding use of ribavirin in patients with covid- at this time. although interferons may be useful as adjunctive care, they pose a significant risk to critically ill patients, and in the absence of supportive data they also cannot be currently recommended. given their antiviral activity against influenza, considerable attention has been paid to oseltamivir, and to a lesser degree baloxavir, as potential treatment options for covid- . this was exacerbated by the initial report from huang et al [ ] in wuhan where patients managed with covid- received oseltamivir in addition to broad-spectrum antimicrobials. it is important to note that use of oseltamivir was not as targeted therapy of sars-cov- but rather driven by the lack of a knowledge of the causative pathogen at the time of treatment and the desire to empirically treat influenza. the authors do not suggest the use of oseltamivir for covid- in that publication, and there are no data that suggest in vitro activity of oseltamivir against sars-cov- . in fact, the only data assessing oseltamivir activity against coronaviruses demonstrated it to be ineffective at inhibiting sars-cov- , even at a concentration of µm/l [ ] . coronaviruses do not utilize neuraminidase, and thus there is no enzyme to be inhibited by oseltamivir. this would hold true for zanamivir, peramivir, or any other neuraminidase inhibitor agents. similarly, neither a defined mechanism nor in vitro data have suggested that baloxavir would demonstrate activity against sars-cov- or other coronaviruses. therefore, given the critical need for these agents in the management of influenza and concern for drug shortages with oseltamivir, these agents should be avoided in patients with covid- once influenza has been ruled out. table lists agents that are being investigated and/or theoretically considered for the management of sars-cov- -infected patients. at this time, no recommendation can be made for any of these agents. in general, they should be avoided without additional supporting evidence. appropriate management strategies for patients with covid- are a rapidly evolving therapeutic challenge, and the optimal agents (if any) to treat infection or prevent progression to critical illness remain ill-defined. although certain agents listed in this review are encouraging, and the potential benefit of therapy likely outweighs the relatively minor risk of adverse events from short-course therapy, the evidence remains inconclusive and changes almost daily. patient populations who warrant therapy and the timing of initiation of therapy need to be defined. given that disease progression can occur rapidly in stable patients and that viral loads are highest early in the infection course, the authors of this review opine that rapid initiation of therapy in high-risk populations (patients who are hospitalized or outpatients who are at high risk of complications) is rational and should be considered, ideally in the context of a well-controlled, adequately powered trial. more important, however, this strategy is not without risk and needs to be weighed against potential adverse events (that remain poorly defined) and impending drug shortages with increases in use of these agents. to help address these concerns, careful consideration should be given to duration of therapy with many clinical trials and institutional protocols recommending - days for uncomplicated disease. duration of therapy should be individualized to the patient and the progression of disease. clinicians must continually monitor and adapt as new literature becomes available. caution should be applied because the bulk of the available clinical data are uncontrolled, not peer reviewed, or even unpublished. given these [ ] . the safety and efficacy of convalescent plasma transfusion in sars-cov- -infected patients has not been established, and no protocols exist currently in the united states. protocols are reportedly being developed at the johns hopkins university hospital. darunavir/cobicistat hiv- protease inhibitor currently being evaluated in a clinical trial (nct ), but no in vitro or human data exist to support use at this time. thiuram derivative that blocks alcohol oxidation. demonstrated ability to competitively inhibit the papain-like proteases of sars; however, no clinical data exist [ ] . no in vitro or clinical data exist for covid- . humanized, monoclonal igg antibody that binds to complement protein c and prevents formation of membrane attack complex (mac). being evaluated in a clinical trial (nct ) for covid- to quell immune response, no data exist at this time to support use. favipiravir rna-dependent rna polymerase inhibitor with broad-spectrum antiviral activity; however, demonstrated high ec (decreased potency) against sars-cov- but was effective in protecting mice against ebola virus despite similarly high ec values [ ] . currently being evaluated in clinical trial nct for patients with covid- . this agent is not fda approved or available in the united states. galidesivir (bcx ) nucleoside rna polymerase inhibitor with reported wide spectrum of antiviral activity, currently in pipeline of biocryst pharma and previously evaluated for ebola and other hemorrhagic fever virus infections. algae-derived lectin and potent hiv entry inhibitor agent that demonstrated in vitro activity against sars-cov- [ ] . ivig ivig remains on critical national shortage in the united states. the benefit in patients with covid- is unclear. nelfinavir, an hiv- protease inhibitor, might be active against sars-cov- based on a preprint publication that utilized homology modeling [ ] . no clinical data exist. anthelminthic drug with in vitro efficacy against sars-cov- ; however, low absorption and oral bioavailability resulting in a wide range of serum concentrations in healthy volunteers after a single dose may limit utility as antiviral treatment [ ] . human monoclonal antibody discovered by regeneron that reportedly binds to the s protein of mers-cov. currently in phase trial in healthy volunteers (nct ). the company reportedly announced recruitment for phase and trials for sars-cov- ; however, these are not registered on clinicaltrials.gov. sarilumab il- receptor antagonist fda-approved for rheumatoid arthritis. recently announced a us-based trial will begin enrolling at medical centers in new york for patients with severe covid- disease. sofosbuvir antiviral used to treat hepatitis c, in vitro activity against sars-cov- , no clinical data exist [ ] . a novel, fully human anti-il r by tiziana life sciences. the company recently announced they are moving forward with clinical development for patient use in patients with covid- and excessive il- production. vitamin c there is an ongoing clinical trial of grams iv bid vitamin c in china for treatment of covid- (nct ). use of this agent is not recommended at this time. chinese herbal medicine extract infusion formulation given at ml iv twice daily, suggested as a "may consider" treatment for severe and critical cases in the national health commission of the people's republic of china: the covid- diagnosis and treatment guide, th edition. this previously demonstrated improved mortality in patients with severe community acquired pneumonia in china [ ] . limitations, it is critical that institutions and clinicians report their experiences with the management and treatment of covid- to the medical community so that we may further modify and optimize treatment recommendations and pathways. clinical features of patients infected with novel coronavirus in wuhan, china involving antimicrobial stewardship programs in covid- response efforts: all hands on deck remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro the antiviral compound remdesivir potently inhibits rna-dependent rna polymerase from middle east respiratory syndrome coronavirus comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease discovery and synthesis of a phosphoramidate prodrug of a pyrrolo[ , -f][triazin- -amino] adenine c-nucleoside (gs- ) for the treatment of ebola and emerging viruses therapeutic efficacy of the small molecule gs- against ebola virus in rhesus monkeys a randomized, controlled trial of ebola virus disease therapeutics washington state -ncov case investigation team. first case of novel coronavirus in the united states late ebola virus relapse causing meningoencephalitis: a case report first newborn baby to receive experimental therapies survives ebola virus disease first patients with coronavirus disease (covid- ) in the united states chloroquine and hydroxychloroquine as available weapons to fight covid- breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies design and synthesis of hydroxyferroquine derivatives with antimalarial and antiviral activities in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) clinical pharmacokinetics of slow-acting antirheumatic drugs hydroxychloroquine and azithromycin as a treatment of covid- : results of an open label non-randomized clinical trial of chloroquine and covid- a noncovalent class of papain-like protease/ deubiquitinase inhibitors blocks sars virus replication role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture population pharmacokinetics of lopinavir/ritonavir (kaletra) in hiv-infected patients treatment with lopinavir/ritonavir or interferon-β b improves outcome of mers-cov infection in a nonhuman primate model of common marmoset treatment of middle east respiratory syndrome with a combination of lopinavir/ritonavir and interferon-β b (miracle trial): statistical analysis plan for a recursive two-stage group sequential randomized controlled trial treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicentre retrospective matched cohort study national health commission (nhc) of the people's republic of china. the diagnosis and treatment guide of covid- pneumonia caused by new coronavirus infection th edition epidemiologic features and clinical course of patients infected with sars-cov- in singapore case of the index patient who caused tertiary transmission of covid- infection in korea: the application of lopinavir/ritonavir for the treatment of covid- infected pneumonia monitored by quantitative rt-pcr the course of clinical diagnosis and treatment of a case infected with coronavirus disease clinical characteristics and therapeutic procedure for four cases with novel coronavirus pneumonia receiving combined chinese and western medicine treatment clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study a trial of lopinavir-ritonavir in adults hospitalized with severe covid- pharmacokinetics of lopinavir/ritonavir crushed versus whole tablets in children nitazoxanide, a new drug candidate for the treatment of middle east respiratory syndrome coronavirus effect of nitazoxanide in adults and adolescents with acute uncomplicated influenza: a double-blind, randomised, placebo-controlled, phase b/ trial efficacy and safety of nitazoxanide in addition to standard of care for the treatment of severe acute respiratory illness tocilizumab for the treatment of chimeric antigen receptor t cell-induced cytokine release syndrome astct consensus grading for cytokine release syndrome and neurologic toxicity associated with immune effector cells cytokine release syndrome grade as a predictive marker for infections in patients with relapsed or refractory b-cell acute lymphoblastic leukemia treated with chimeric antigen receptor t cells fda approval summary: tocilizumab for treatment of chimeric antigen receptor t cell-induced severe or life-threatening cytokine release syndrome effective treatment of severe covid- patients with tocilizumab sars: systematic review of treatment effects treatment of severe acute respiratory syndrome with glucosteroids: the guangzhou experience effects of early corticosteroid treatment on plasma sars-associated coronavirus rna concentrations in adult patients the use of corticosteroid as treatment in sars was associated with adverse outcomes: a retrospective cohort study corticosteroid therapy for critically ill patients with middle east respiratory syndrome risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease pneumonia in wuhan, china on the use of corticosteroids for -ncov pneumonia clinical features and short-term outcomes of patients with sars in the greater toronto area a major outbreak of severe acute respiratory syndrome in hong kong inhibition of sars coronavirus infection in vitro with clinically approved antiviral drugs ribavirin and interferon therapy for critically ill patients with middle east respiratory syndrome: a multicenter observational study baricitinib as potential treatment for -ncov acute respiratory disease convalescent plasma as a potential therapy for covid- disulfiram can inhibit mers and sars coronavirus papain-like proteases via different modes broad-spectrum in vitro activity and in vivo efficacy of the antiviral protein griffithsin against emerging viruses of the family coronaviridae nelfinavir was predicted to be a potential inhibitor of -ncov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation broad spectrum antiviral agent niclosamide and its therapeutic potential anti-hcv, nucleotide inhibitors, repurposing against covid- xuebijing injection versus placebo for critically ill patients with severe community-acquired pneumonia: a randomized controlled trial we acknowledge and thank jovan borjan, julie ann justo, liza vaezi, ryan shields, and jason gallagher for thorough review of this manuscript.potential conflicts of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. key: cord- -fn m cn authors: philpott, erin k; englund, janet a; katz, joanne; tielsch, james; khatry, subarna; leclerq, stephen c; shrestha, laxman; kuypers, jane; magaret, amalia s; steinhoff, mark c; chu, helen y title: febrile rhinovirus illness during pregnancy is associated with low birth weight in nepal date: - - journal: open forum infect dis doi: . /ofid/ofx sha: doc_id: cord_uid: fn m cn background: adverse birth outcomes, including low birth weight (lbw), defined as < grams, small-for-gestational-age (sga), and prematurity, contribute to %– % of infant mortality worldwide and may be related to infections during pregnancy. the aim of this study was to assess whether febrile human rhinovirus (hrv) illness is associated with adverse birth outcomes. methods: active household-based weekly surveillance was performed for respiratory illness episodes in pregnant women as part of a community-based, prospective, randomized trial of maternal influenza immunization in rural nepal. rhinovirus (hrv) febrile illness episodes were defined as fever plus cough, sore throat, runny nose, and/or myalgia with hrv detected on mid-nasal swab. multivariate regression analysis evaluated the association between febrile hrv respiratory illness and adverse birth outcomes. results: overall, ( %) of pregnant women had hrv-positive febrile respiratory illnesses. infants born to pregnant women with hrv febrile illness had a . -fold increased risk of being lbw compared with those with non-hrv febrile illness ( of [ %] vs of [ %]; relative risk [rr], . ; % confidence interval [ci], . – . ). no difference in risk of lbw was observed between infants born to mothers with non-hrv febrile respiratory illness and those without respiratory illness during pregnancy ( of [ %] vs of [ %], respectively; rr, . ; % ci, . – . ). conclusions: febrile illness due to rhinovirus during pregnancy was associated with increased risk of lbw in a rural south asian population. interventions to reduce the burden of febrile respiratory illness due to rhinovirus during pregnancy may have a significant impact on lbw and subsequent infant mortality. adverse birth outcomes, including low birth weight (lbw), small-for-gestational age (sga), and preterm birth (ptb), contribute to %- % of infant mortality worldwide [ ] . infections during pregnancy impact risk of adverse birth outcomes and congenital anomalies [ , ] . respiratory viruses have been recognized as significant contributors to morbidity and mortality worldwide. influenza during pregnancy, in particular avian influenza and pandemic h n , has been associated with spontaneous abortion, stillbirth, and prematurity [ , ] . a prospective randomized trial in bangladesh and an observational us-based study each found an association between influenza immunization during pregnancy and a reduction in sga and an increase in mean birth weight [ , ] . an impact on lbw and ptb was additionally noted in a meta-analysis of randomized trials of maternal influenza immunization [ ] . human rhinovirus (hrv) is a respiratory virus first isolated in the s and historically implicated as the etiology of the common cold [ , ] . with improvements in molecular diagnostics, hrv has been increasingly recognized to cause serious illness requiring hospitalization and death among infants and young children, immunocompromised individuals, adults with chronic obstructive pulmonary disease, or asthma. human rhinovirus has also been identified as the most common etiology of pneumonia in hospitalized adults [ ] [ ] [ ] . however, the clinical presentation of hrv infection during pregnancy and effect on birth outcomes is not well established. the risk of increased susceptibility and severity associated with certain infections during pregnancy is likely related to a complex interplay of the maternal-placental-fetal unit that is not well understood. it has been postulated that infection causes activation of the innate immune system stimulating the release of proinflammatory cytokines, which may underlie the pathogenesis of both ptb and lbw [ ] . identification of a relationship between hrv infection during pregnancy and adverse birth outcomes has the potential to drive improvement of diagnostics, infection control measures, and treatment options for hrv infection. methods we conducted an analysis using samples and clinical data collected in a community-based, prospective placebo-controlled, randomized trial of maternal influenza immunization of pregnant women and their infants conducted in rural southern nepal from to . methods of the parent study have been previously published [ ] . in brief, illness episodes were identified through longitudinal household-based active weekly surveillance of women from the second trimester of pregnancy until months postpartum. mid-nasal swabs were collected from women meeting criteria for respiratory illness episode, which was defined as subjective fever plus or more symptom (cough, sore throat, runny nose, or myalgia). fever was included in the illness episode definition as part of the primary trial of maternal influenza immunization to capture influenza-like-illness during pregnancy [ ] . febrile hrv respiratory illness was defined as a respiratory illness episode with a nasal swab with hrv detected by real-time polymerase chain reaction (rt-pcr) assay. a unique illness episode was defined as an illness episode followed by symptom-free days. only the primary hrv illness episode was included in the analysis. adverse birth outcomes were defined as lbw (birth weight less than grams), ptb (birth at less than weeks gestation), and sga (birth weight < percentile of weight for gestational age). gestational age was calculated based on last menstrual period according to a house-to-house census conducted every weeks of all women of childbearing age [ ] . if a woman had a missed period, then a urine pregnancy test was performed and she was enrolled in the study if her urine pregnancy test was positive. therefore, the last menstrual period was used to date the infant's gestational age in the study with a -week recall period. the frequencies of each adverse outcome were compared between infants born to mothers with febrile hrv respiratory illness during pregnancy and those without febrile hrv respiratory illness during pregnancy. infant weights were included if they were obtained at less than hours after birth. small-for-gestational age was calculated based on the intergrowth- st criteria [ ] . a composite adverse birth outcome was defined as an infant being preterm, lbw, and/ or sga. real-time pcr for detection of hrv was performed as described, with the modification of a degenerate c/t base at the ' end of the forward primer [ ] . real-time pcr for additional respiratory viruses, including respiratory syncytial virus, human metapneumovirus, parainfluenza viruses - , influenza, coronavirus, bocavirus, and adenovirus, was performed using previously published methods [ ] [ ] [ ] [ ] [ ] . although the hrv rt-pcr assay has been shown to detect some enterovirus from culture lysates in which enterovirus was present in high copy numbers, this assay has not been positive when enterovirus-positive clinical respiratory specimens were tested as part of other studies and therefore less likely in this case to misdiagnose enterovirus as rhinovirus [ , ] . rhinoviruspositive samples collected from pregnant and postpartum women with cycle threshold values less than were selected for sequencing using a previously published protocol [ ] . for sequencing, previously extracted samples were used to generate complementary deoxyribonucleic acid using random hexamers, and sequencing was performed using primers targeting the ' noncoding region. gel-extracted amplicons were sequenced (genewiz) and analyzed using sequencher . software and compared with hrv reference sequences from genbank using the nucleotide-nucleotide basic local alignment search tool ([blast] www.blast.ncbi.nlm.nih.gov) algorithm. trimmed sequences were aligned using geneious r . (biomatters) and seaview . [ ] . phylogenetic reconstruction was performed using the maximum likelihood method with bootstrap replicates using phyml . within divein [ ] . neighbor joining trees were drawn and edited using figtree v . . . sequences were considered to be divergent genotypes if they differed from other study sequences by > % when compared using blast [ ] . sequence data were not of sufficient length to be submitted to genbank but are available upon request. log-linear regression was used to assess the association of baseline characteristics of pregnant women with the incidence of hrv respiratory illness during pregnancy; person-years (p-y) at risk of infection was included as an exposure. adverse birth outcomes such as lbw, sga, and ptb were also assessed using log-linear regression. potential risk factors analyzed include ( ) maternal febrile respiratory illness during pregnancy and, simultaneously, ( ) a specific history of hrv-associated respiratory illness. for the outcomes of lbw, we also included a term indicating hrvassociated respiratory illness in the second trimester, to assess whether timing during pregnancy was influential. to avoid confounding, additional covariates included season of birth and infant sex in the analysis. the wilcoxon-rank sum statistic was used to compare symptom duration between pregnant and postpartum women with febrile hrv as well as pregnant women who gave birth to lbw infants compared with those who did not. institutional review board (irb) approval for the parent study was obtained from the johns hopkins university bloomberg school of public health, seattle children's hospital, cincinnati children's hospital, the institute of medicine at tribhuvan university, and the nepal health research council. oral consent was obtained from study participants due to low literacy rates in the population. this procedure was approved by the irb. the trial in which this substudy was conducted is registered at clinicaltrials.gov (nct ). a total of ( %) of women had a febrile hrv respiratory illness episode, ( %) of which occurred during pregnancy and ( %) occurred after delivery. the median person-weeks (p-w) of follow up was weeks (interquartile range [iqr], - ) for febrile hrv respiratory illness during pregnancy and weeks (iqr, - ) for those without hrv-associated illness while pregnant. febrile hrv respiratory illness incidence was . / p-y. the incidence of febrile hrv illness while pregnant was of p-y, or . / p-y, and incidence after delivery was of p-y, or . / p-y (p = . ). characteristics of women with and without febrile hrv respiratory illness during pregnancy and their infants are outlined in table . the median gestational age at infection among the febrile hrv respiratory illness group was weeks (iqr, - ). incidence of hrv was similar by baseline characteristics, including maternal age, maternal literacy, nulliparity, indoor biomass cookstove use, and number of children in the household. in particular, no difference in maternal body mass index was observed. in addition, no difference was observed in influenza vaccination status between the groups. other viruses detected in association with febrile respiratory illness episodes included respiratory syncytial virus, human metapneumovirus, parainfluenza viruses - , influenza, coronavirus, bocavirus, and adenovirus each occurring at notably lower frequency compared with hrv. seventy-four of ( . %) infants born to pregnant women with febrile hrv respiratory illness and of ( . %) infants born to mothers without hrv-associated illness were weighed within hours of birth and therefore included in the assessment of lbw and sga. of infants with birth weight measured in the first hours, % ( ) were taken on the day of birth. median weight in those measured on days and of life was approximately . kg lower than those measured on day ( . at day and . at day vs . on day ), and the proportion determined to be of lbw increased from % on day to % on day to % on day . had all days observed exactly the same rate of lbw designations of %, it is expected then that approximately infants ( weighed on day and weighed on day of life) would not have been determined to have lbw. with infants classified as lbw, however, is only % of that group, so this comprises a very low potential misclassification rate. prevalence of lbw was significantly higher among infants born to pregnant women with febrile hrv respiratory illness compared with those born to mothers with a febrile respiratory illness of another viral etiology during pregnancy, after adjusting for season of birth and gender of the infant, with a . -fold increased risk of lbw ( (figure ; table ). when comparing pregnant women with non-hrv febrile viral respiratory illness to those . ) in the group of infants exposed to maternal febrile hrv illness compared with . kg ( . - . ) among infants not exposed to respiratory illness during pregnancy. three hrv infections occurred in the first trimester of pregnancy, in the second and in the third. the lack of hrv infection in the first trimester is due to enrollment of women into the study beginning at weeks gestation or later rather than lack of rhinovirus infection during the first trimester of pregnancy. low birth weight prevalence was not affected by the trimester of pregnancy in which the hrv infection occurred (p = . ). febrile hrv respiratory infection occurred yearround with a peak in october ( figure ) and accounted for a consistent % of respiratory virus infections each month. low birth weight occurred at a monthly rate of %- % (supplementary figure ) . due to the nature of enrollment, the number of patients under surveillance and therefore the numbers of samples collected were not constant over time, and this is reflected in the numbers of proportions of births and specimens tested (figure and supplementary figure ) . small-for-gestational age appeared higher among infants born to mothers with febrile hrv respiratory illness versus those with non-hrv febrile respiratory illness, although this did not reach statistical significance ( of [ . %] vs ( ) illness and symptom duration subdivided by lbw and pregnancy status are outlined in table . the median duration of illness was days (range, - ) among pregnant and postpartum women. no difference between overall illness duration was observed when comparing women with febrile hrv respiratory infection with and without lbw infants or when comparing women with febrile hrv respiratory illness during pregnancy versus after delivery. six women died during the period of surveillance, none of whom had febrile hrv respiratory infection. thirty-seven of ( %) women with febrile hrv respiratory illness during pregnancy sought medical care. overall, women sought care from a physician or a hospital. among women with febrile hrv respiratory infection during pregnancy, care-seeking behavior was similar between women who had lbw infants and those who did not ( of [ . %] vs of [ . %]; p = . ). in this same group with febrile hrv respiratory illness during pregnancy, the proportion seeking the care of a physician or hospital was also similar by lbw status of the infant. three of ( . %) who had lbw infants saw a physician, compared with of ( . %) who did not (p = . ). of the women with lbw infants who sought care from a physician, woman sought care for severe headache and fever, whereas the reason for seeking care from a physician for the other women was not documented. of successfully sequenced (supplementary figure ). of these, ( . %) were from pregnant women, whereas the remainder were from women who had rhinovirus after giving birth. species a ( of [ %]) accounted for a majority of the samples sequenced, whereas species b and c accounted for of ( . %) and of ( . %), respectively. among women who gave birth to lbw infants, of ( %) were species a and of ( %) were species b. however, the proportion of samples sequenced compared with the total was small. eleven ( %) pregnant women with hrv had an additional respiratory virus detected including coronavirus (n = ), human metapneumovirus (n = ), adenovirus (n = ), and bocavirus (n = ), and respiratory syncytial virus and bocavirus (each, n = ). coinfections occurred at equal frequencies among mothers with and without lbw infants ( of [ %] vs of [ %], respectively; p = . ). the association between lbw and febrile hrv-illness episode remained when infants born to mothers with febrile hrv with viral coinfection illness episodes were excluded from the analysis (rr, . ; % ci, . - . ; p = . ). no hrv-associated respiratory illness was found in association with influenza coinfection. over a -year period of prospective active home-based weekly surveillance in a rural subtropical setting, we characterize the incidence of febrile respiratory illness due to rhinovirus in pregnant women. limited data exist examining the relationship between hrv infection during pregnancy and adverse birth outcomes. in this study, we found that pregnant women with a febrile hrv respiratory illness were at . -fold increased risk to have a lbw infant, compared with pregnant women without hrv illness. several aspects of the study design allowed for an accurate assessment of the impact of febrile rhinovirus illness during pregnancy on adverse birth outcomes. the study was conducted in a region of the world where ptb and lbw are common. in addition, in a setting with limited antenatal care and frequent home births, birth weight was measured within hours of birth in the majority of infants. dating of gestational age was performed using last menstrual period obtained through -weekly surveillance for pregnancy in women of childbearing age, leading to more accurate dating of gestational age compared with recall of last menstrual period at time of birth. finally, intensive active weekly home-based respiratory illness surveillance allowed for collection of daily symptom data, and specimen collection in temperature-stable buffer permitted detection of rhinovirus and other respiratory viruses by sensitive molecular assays. similar to other subtropical regions, we found that febrile hrv respiratory infection occurred year-round with a peak in october and a nadir in june. low birth weight has been shown to vary by season due to factors such as food insecurity [ ] ; however, we observed a relatively steady rate of lbw among infants born to women without febrile hrv respiratory illness ranging from % to % without significant fluctuations. pregnant women are at high risk for severe complications due to influenza, with increased rates of morbidity, mortality, and adverse fetal outcomes most clearly demonstrated with pandemic h n [ ] . previous studies, including a study in our region, showed that febrile respiratory infection due to rsv was rare during pregnancy [ ] . limited data exist regarding the clinical presentation and severity of rhinovirus illness among pregnant women. human rhinovirus accounts for %- % of cases of viral pneumonia in hospitalized children and was detected in approximately half of children admitted to the intensive care unit for lower respiratory tract infection [ , ] . in adults, hrv is the most frequent cause of community-acquired pneumonia requiring hospitalization in the united states [ , , ] . we find that % of women with rhinovirus infection sought care for their illness, and that % of these were seen by a physician or at a hospital. this compares to an international study of community-based elderly adults, where % of those with rhinovirus illness were hospitalized [ ] . the relationship between febrile rhinovirus infection during pregnancy and lbw has not been well studied. low birth weight is the result of either preterm delivery or poor growth of the fetus resulting in intrauterine growth restriction (iugr). rates of ptb did not differ in women with and without febrile hrv respiratory illness during pregnancy, suggesting that iugr was the primary mechanism leading to lbw associated with hrv during pregnancy. we did not find a significant effect of febrile rhinovirus illness during pregnancy on ptbs or sgas. we note that approximately half ( %, or of ) of infants with any poor outcomes are affected by only of adverse birth outcomes (lbw, ptb, or sga); and only ( %) of infants are affected by all adverse birth outcomes. of infants with lbw, % are also sga (compared with % of who are not lbw but are sga). likewise, of with lbw, % are also preterm (compared with only % of who are not lbw but are preterm). therefore, although there is evident correlation between these outcomes, they are not completely overlapping. therefore, these outcomes are defining distinct populations and, in our study, may demonstrate different associations with risk factors. factors associated with iugr, including low socioeconomic status, literacy, parity, poor nutritional status, smoking, and alcohol use, were similar between the groups with and without rhinovirus in our study [ ] . nepal has one of the highest rates of malnutrition in south asia, with up to % of the general population having evidence of undernourishment [ ] . more importantly, in our study, pregnant women with and without hrv-associated respiratory illness had similar mean body mass indices of at the time of enrollment, suggesting that poor nutritional status associated with chronic illness is unlikely to be the etiology of the association with lbw. we also note that febrile illness during pregnancy alone was not associated with an increased risk of lbw in our study. of mothers with febrile non-hrv respiratory illness, only % of the infants were lbw, which is similar to the % without febrile respiratory illness during pregnancy. fever is associated with increased circulation of cytokines, in particular interleukin- , and has been postulated to be part of the reason why women with influenza may be at increased risk of severe disease and adverse birth outcomes [ ] . we did not find an effect of febrile respiratory illness without the detection of rhinovirus in this study, however, making this less likely to be responsible for the birth weight effect seen in this study. the birth weight effect in our study additionally does not appear to be due to increased duration or severity of illness in pregnant women with lbw infants. prolonged illness during pregnancy may be associated with decreased intake and poor weight gain. poor weight gain in pregnancy has been associated with iugr [ ] . we find that pregnant women with rhinovirus had a median days of symptoms, and that this did not differ in those with lbw or in those who had rhinovirus during pregnancy or after birth. no significant difference in hospitalizations, physician visits, or other care seeking was observed among pregnant women with febrile hrv illness who did and did not give birth to lbw infants. because of the potential for flu vaccination to reduce risk of lbw or ptbs, we evaluated for a difference in the incidence of rhinovirus febrile illness in women who did and did not receive the flu vaccine during pregnancy. we found no difference with flu vaccination. in addition, no mothers with rhinovirus febrile illness had evidence of influenza coinfection as a potential etiology of lbw. limitations of our study include our lack of active surveillance for respiratory viruses among asymptomatic or afebrile women, thereby limiting our ability to discern whether lbw was more strongly associated with hrv specifically or with any respiratory illness episode and its associated inflammation. use of subjective fever as criteria for respiratory illness rather than use of a measured temperature may have also decreased our ability to detect respiratory illnesses. we also did not conduct surveillance before weeks gestation, and, therefore, it is possible that some women had infections earlier in pregnancy that we were not able to identify in our study. gestational age dating was limited by lack of first-trimester ultrasound; however, -weekly prospective home surveillance minimized maternal recall error of last menstrual periods. illness episode severity measures, such as radiographic evidence of pneumonia or use of supplemental oxygen, were not evaluated because medical records of healthcare visits were not reviewed in this study. we were also unable to assess medical comorbidities in the participants, given the lack of access to primary or antenatal care in the study region. other limitations include lack of detection of bacterial pathogens in this study. human rhinovirus infections have been shown to augment respiratory bacterial colonization and infection; therefore, it is possible that bacterial infections may be contributing to the described febrile illnesses and play a role in the relationship with lbw. mid-nasal samples were only obtained once weekly, and brief episodes of viral shedding, as commonly observed in adults with pre-existing immunity, could have been missed. the association of virologic factors, such as viral load or subtype, with disease severity, were also unable to be assessed due to a lack of a method to quantify rhinovirus by our rt-pcr assay and our limited ability to sequence the majority of the isolates. the study was performed within a single geographic locale with specific demographics and risk factors, compromising generalizability. finally, because this is an observational study, we were unable to assess for a causal association between rhinovirus febrile respiratory illness and lbw. the groups with and without rhinovirus infection were similar in baseline sociodemographics, including factors that may affect lbw or risk of respiratory viral infections, such as maternal parity, maternal body-mass index, maternal literacy, household smoking, household density, and running water. in conclusion, we demonstrate that hrv is the most common cause of febrile respiratory illness in pregnant women in rural southern nepal during our study period, and that hrv during pregnancy was associated with an increased risk of lbw. because lbw infants have an increased risk of mortality compared with their heavier counterparts and hrv is a highly prevalent respiratory virus, this may represent a potential modifiable risk factor to reduce risk of lbw infants, particularly in developing countries. interventions to reduce the burden of febrile respiratory illness due to rhinovirus during pregnancy, such as measures to improve infection control, development of targeted therapies, or improvement of diagnostics, may have a significant impact on lbw and subsequent infant mortality worldwide. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. medimmune, and payments from glaxosmithkline for participation in a dsmb. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. global, regional, national, and selected subnational levels of stillbirths, neonatal, infant, and under- mortality, - : a systematic analysis for the global burden of disease study intrauterine infection and preterm delivery pregnancy and infection maternal and neonatal outcomes among pregnant women with pandemic influenza a(h n ) illness in florida, - : a population-based cohort study the effect of asian influenza on the outcome of pregnancy maternal influenza immunization and reduced likelihood of prematurity and small for gestational age births: a retrospective cohort study neonatal outcomes after influenza immunization during pregnancy: a randomized controlled trial the effects of influenza vaccination during pregnancy on birth outcomes: a systematic review and meta-analysis rhinovirus infections in tecumseh, michigan: frequency of illness and number of serotypes viruses and bacteria in the etiology of the common cold human rhinoviruses community-acquired pneumonia requiring hospitalization among u.s. adults community-acquired pneumonia requiring hospitalization among u.s. children the preterm parturition syndrome designs of two randomized, community-based trials to assess the impact of influenza immunization during pregnancy on respiratory illness among pregnant women and their infants and reproductive outcomes in rural nepal impact of newborn skin-cleansing with chlorhexidine on neonatal mortality in southern nepal: a community-based, cluster-randomized trial international standards for fetal growth based on serial ultrasound measurements: the fetal growth longitudinal study of the intergrowth- st project real-time reverse transcription-pcr assay for comprehensive detection of human rhinoviruses detection and quantification of human metapneumovirus in pediatric specimens by real-time rt-pcr comparison of real-time pcr assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children clinical disease in children associated with newly described coronavirus subtypes detection of bocavirus in saliva of children with and without respiratory illness molecular epidemiology of human rhinovirus infections in the pediatric emergency department rhinovirus disease in children seeking care in a tertiary pediatric emergency department seaview version : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building divein: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites a population-based prospective cohort emerging infections and pregnancy maternal effects of respiratory syncytial virus infection during pregnancy spectrum of respiratory viruses in children with community-acquired pneumonia lower respiratory infections among hospitalized children in new caledonia: a pilot study for the pneumonia etiology research for child health project respiratory viruses in exacerbations of chronic obstructive pulmonary disease requiring hospitalisation: a case-control study respiratory viruses, symptoms, and inflammatory markers in acute exacerbations and stable chronic obstructive pulmonary disease respiratory syncytial virus and other respiratory viral infections in older adults with moderate to severe influenza-like illness diagnosis and management of fetal growth restriction seasonal dietary intakes and socioeconomic status among women in the terai of nepal low maternal weight gain in the second or third trimester increases the risk for intrauterine growth retardation we thank the mothers and infants who participated in the trial and all the nepal nutrition intervention project-sarlahi staff involved in the study. key: cord- -kve fa authors: pastick, katelyn a; nicol, melanie r; smyth, elizabeth; zash, rebecca; boulware, david r; rajasingham, radha; mcdonald, emily g title: a systematic review of treatment and outcomes of pregnant women with covid- – a call for clinical trials date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: kve fa background: data pertaining to covid- in pregnancy are limited; to better inform clinicians, we collated data from covid- cases in pregnancy and summarized clinical trials enrolling this population. methods: we performed a systematic literature review of pubmed/medline to identify cases of covid- in pregnancy or the postpartum period and associated outcomes. we then evaluated the proportion of covid- clinical trials (from clinicaltrials.gov) excluding pregnant or breastfeeding persons (both through june (th), ). results: we identified , published cases of covid- in pregnancy. of those reporting disease severity, % ( / ) were severe/critical. maternal and neonatal survival were reassuring ( % [ / ] and % [ / ], respectively). neonatal disease was rare with only possible cases of infection reported in the literature. of ongoing covid- therapeutic clinical trials, were enrolling persons of reproductive age and % ( / ) excluded pregnant persons. pregnancy was an exclusion criterion for % ( / ) of chloroquine/hydroxychloroquine, % ( / ) of lopinavir/ritonavir, and % ( / ) of convalescent plasma studies. we identified actively recruiting or completed drug trials reporting inclusion of this population. conclusions: there are limited published reports of covid- in pregnancy despite more than million cases worldwide. to date, clinical outcomes appear reassuring, but data related to important long-term outcomes are missing or not yet reported. the large number of clinical trials excluding pregnant persons, despite interventions with safety data in pregnancy, is concerning. in addition to observational cohort studies, pregnancy specific adaptive clinical trials could be designed to identify safe and effective treatments. a c c e p t e d m a n u s c r i p t worldwide, it is estimated that there are nearly two billion women of reproductive age and women comprise upwards of % of the total healthcare workforce [ , ] . pregnant women and women of reproductive potential are therefore at a high risk of contracting covid- . in a recent centers for disease control and prevention (cdc) report of , patients with covid- in the united states, as many as % of cases occurred in pregnant women [ ] . in prior work examining influenza, severe acute respiratory syndrome (sars), and middle east respiratory syndrome (mers), pregnant women had increased morbidity and mortality when compared with non-pregnant women [ ] [ ] [ ] . currently, there is insufficient evidence to determine whether the same is true for pregnant women with covid- . it is hypothesized that the natural physiologic state of immune tolerance associated with pregnancy may increase the risk of infection and severe complications [ ] . there is a need to identify safe and effective treatment options for pregnant persons with covid- , as there is for all populations, but there are multiple barriers preventing their inclusion in clinical trials. due to safety concerns for the mother and the potential for teratogenicity, both pregnant and breastfeeding people are frequently excluded from clinical research studies, often in spite of established pharmacological safety data in pregnancy. however, drug metabolism (and therefore efficacy) in pregnancy differs from the general population, arguing for their inclusion in trials; optimal dosing requires special attention to physiologic changes (e.g. increased glomerular filtration rate or decreased plasma albumin concentrations), which can alter pharmacokinetics and pharmacodynamics of drug concentrations. fetal organogenesis also needs to be factored in when possible. finally, as pregnancy is a state of immunologic change to accommodate the fetus, it is unclear how therapeutic immune modulators used in covid- (e.g. tocilizumab and sarilumab) may impact maternal and fetal outcomes. in this systematic review, we sought to highlight the heterogeneity of treatment and outcome data for pregnant persons with covid- and summarize the literature related to covid- in pregnancy. we provide an overview of the proportion of completed and actively recruiting interventional clinical trials permitting the inclusion of pregnant or breastfeeding individuals to a c c e p t e d m a n u s c r i p t underscore how frequently this population is ineligible for trial participation and to discuss the potential implications. a systematic literature review was conducted to identify cases of covid- in pregnancy that were reported as of june th , following the prisma checklist. the first author searched pubmed/medline for all language publications and pre-prints using a combination of the following mesh keywords: "pregnancy," "postpartum," "covid- ," and "sars-cov- ." the first and third authors screened abstracts and reviewed the potential publications and references for relevance to identify any missing articles that were not identified using the above listed keywords. details as they pertained to presenting symptoms, any treatments received, and maternal, fetal/neonatal outcomes were recorded. studies unrelated to cases of covid- in pregnancy or the peripartum period were excluded. a second search was conducted to identify covid- clinical trials as of june th, that reported pregnancy/breastfeeding as an exclusion criterion. clinicaltrials.gov was searched for relevant studies, using the preprogrammed search terms "covid- ," "sars-cov- ," " -ncov," " novel coronavirus," and "severe acute respiratory syndrome coronavirus ." inclusion and exclusion criteria were examined to determine whether pregnant and/or breastfeeding patients were excluded from the study. studies listed as interventional clinical trials were then analyzed. information related to specific therapeutic intervention and the status of recruitment were summarized. of the actively ongoing interventional clinical trials investigating the use of a drug (including dietary supplements and biologic agents) that did not report the exclusion of pregnant or breastfeeding women, the first author contacted study personnel for each of these studies by email to discern whether or not pregnant or breastfeeding women were eligible to be enrolled. a c c e p t e d m a n u s c r i p t patient consent is not applicable as this article is a systematic review. in our systematic literature review, we identified , reported cases of covid- in pregnancy and the postpartum period from a total of case reports, case series, prospective/retrospective cohort studies, three governmental or national reports, and two case control studies (table , figure ). of those that reported estimated gestational age at the time of diagnosis (n= ), % ( / ) were in the third trimester of pregnancy (> weeks), with the majority in the peripartum/postpartum period; % ( / ) were in the second and % ( / ) were in the first trimester. the most common symptoms reported were cough ( %, / ) and fever ( %, / ), followed by fatigue, malaise, or myalgias ( %, / ), headache ( %, / ), and shortness of breath or dyspnea ( %, / ); overall, fewer than % were reported as entirely asymptomatic ( / or %). not all studies reported maternal symptoms. the majority of these covid- cases were mild to moderate in severity ( % m a n u s c r i p t there were reported neonatal deaths. neonatal testing for sars-cov- varied widely, making it challenging to draw any definitive conclusions about maternal fetal transmission. in many case series and case reports, sars-cov- was tested but not detected in: amniotic fluid, breast milk, umbilical cord blood, placental tissue, maternal vaginal secretions, nor in neonatal: serum, plasma, whole blood, feces, gastric secretions, or throat swabs. overall, we only identified neonates with possible sars-cov- infection based on positive pcr or antibody tests performed on neonatal specimens (e.g. nasopharyngeal/oropharyngeal swabs, blood, stool and/or unspecified sites) (supplemental table ) [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . the following specimens were also found to be sars-cov- pcr or igg/igm positive: placental specimen [ , , , [ ] [ ] [ ] , umbilical cord blood [ , , ] , breast milk [ , , ] , maternal stool or rectal/anal swabs [ , ] , and sample of maternal vaginal secretions [ ] . several reports discussed placental pathology associated with maternal sars-cov- infection, but did not specifically assess the placenta for the microbiologic presence of sars-cov- [ , , , , [ ] [ ] [ ] . reports in the literature on treatment received by peripartum women with covid- varied greatly or were not reported on. overall, we found reports of women who received hydroxychloroquine, lopinavir/ritonavir, remdesivir, interleukin- (il- ) or il- inhibitors, and intravenous immunoglobulin (ivig) or gamma globulin either during pregnancy or the postpartum period. as of june th , , there were ongoing covid- related clinical trials registered on clinicaltrials.gov [ ] . approximately % ( / ) were interventional clinical trials investigating the therapeutic use of a drug, device, procedure, screening/diagnostic tool, or behavioral intervention in reproductive age adults ( - table ). of the interventional studies registered on clinicaltrials.gov that did not specifically mention the exclusion of pregnant or breastfeeding women, only % ( / ) were studies investigating the therapeutic use of a drug. of these, were not yet recruiting, were withdrawn, and was suspendedthese studies were removed from further analyses. of the remaining trials, only % ( / ) reported specific inclusion of pregnant or breastfeeding patients. the remainder were contacted by email to verify whether or not pregnant and breastfeeding persons could be enrolled. a further studies whose investigators were contacted by email verified the inclusion of pregnant and breastfeeding patients; were investigating use of convalescent plasma, chloroquine/hydroxychloroquine, various other drugs, il- inhibitors, and remdesivir. the two remdesivir studies clarified that pregnant patients could be enrolled on a request for compassionate use basis only. one study assessing thromboprophylaxis clarified that only breastfeeding patients could be enrolled, and one hydroxychloroquine post-exposure prophylaxis study reported inclusion of pregnant persons into the control arm only. overall, trials did not respond to email inquiries, reported the exclusion of pregnant or breastfeeding women, had no email address provided and could not be contacted, and trials were either unsure or reported that they would discuss with an ethics committee (figure ) . a total of completed or actively recruiting clinical trials reported the inclusion of pregnant or breastfeeding persons ( table ) . data regarding the clinical presentation, disease evolution, treatment, and outcomes for covid- in pregnancy and lactation are scarce. despite nearly million cases of covid- worldwide [ ] , we identified only a few thousand reported cases of pregnant or breastfeeding persons with covid- . in general, published data mainly consisted of case series and reports, and the information was heterogeneous, with outcome reporting subject to major bias and was sometimes missing entirely. from the limited available literature, we found that when outcomes were reported, maternal and fetal/neonatal survival was overall excellent ( % and %) and that fetal/neonatal infection was rare but described. a c c e p t e d m a n u s c r i p t we found nearly two thirds of completed or ongoing interventional covid- related clinical trials have excluded pregnant or breastfeeding persons. this finding reaffirms prior reports [ ] . despite available safety data in pregnancy for hydroxychloroquine and lopinavir/ritonavir, we were surprised to find % and % of the respective clinical trials had excluded pregnant or breastfeeding persons. while some clinical trials may have had multiple study arms that might have prohibited the enrollment of this population due to known teratogenicity of other medications, many trials were singularly investigating hydroxychloroquine or lopinavir/ritonavir. both the american college of obstetrics and gynecology and the american college of rheumatology endorse the use of hydroxychloroquine in pregnancy for treatment and management of systemic lupus erythematosus [ , ] and lopinavir/ritonavir is one of the few drugs with an actual indication for pregnancy per the u.s. food and drug administration (fda) [ ] . while recent evidence suggests these drugs may not be effective in treating or preventing covid- [ ] [ ] [ ] [ ] , the large percentage of clinical trials that excluded pregnant persons should serve as a wake-up call to us all, including institutional review boards, regulatory authorities, and clinical trial investigators. is not without risk of harm to the fetus/neonate, the blanket exclusion of pregnant or breastfeeding persons from covid- clinical trials has serious implications [ ] . although we found that severe complications and death were rare ( - %), uncommon complications are important on a population level during a pandemic because of the sheer volume of cases (a % mortality rate still equates to deaths if one was to examine million cases). furthermore, while published outcomes were reassuring, outcomes may be worse in developing countries with less access to critical care resources, making a safe and effective drug therapy all the more important. only when drugs are intended to be used in pregnancy, does the fda require pharmaceutical companies to demonstrate safety and efficacy in pregnancy [ ] . between - , only % of pharmacokinetic clinical trials were conducted with the inclusion of pregnant women [ ] . through observation alone, it can take an average of years to develop enough data to estimate the teratogenicity risk of a drug [ ] , which is a prohibitively long timeline during a pandemic. enrolling pregnant persons into clinical trials with their informed consent can help circumvent this delay. in our search, we came across three observational cohort studies specifically capturing a c c e p t e d m a n u s c r i p t information regarding the treatment of pregnant women (nct , nct , nct ). while these studies will greatly increase our knowledge of the treatment and outcomes of this population, mores studies are needed, including examining the safety and efficacy of any potential vaccine. to improve care for pregnant persons with covid- , pregnancy-specific adaptive clinical trials, similar to those for human immunodeficiency virus (hiv) [ ], should be considered. these can allow for pregnancy-specific expertise in recruitment, consent, and assessment of pregnancy related outcomes. such studies could assess pharmacokinetics at varying stages in pregnancy to ensure dose optimization and can accommodate the rapid inclusion of promising new drugs that may emerge. these studies would complement ongoing clinical trials enrolling pregnant persons. a similar approach is currently underway for children (nct ). for future and ongoing trials that include or enroll pregnant persons, there should be a mechanism in place to systematically capture longitudinal pregnancy outcomes. this may include consenting women for long term follow-up should they become pregnant during the course of the trial. the availability of safety and efficacy data for investigational drugs for use in covid- is paramount in order to properly counsel people who become pregnant during infection and/or following an unintentional exposure. our review of the literature was timely and is the first study (to our knowledge) to systematically examine and compile the available data related to treatment and outcomes of covid- in pregnancy and related clinical trials. while we conducted a comprehensive search, our study has limitations. the major limitation relates to the data included in the published studies. there are several inherent biases (e.g. recollection and publication bias) present in case series and observational studies. these may be especially prevalent in our review, given the extent of missing data and the lack of uniform reporting on important pregnancy and neonatal outcomes. asymptomatic or mild cases of covid- may have been underreported and for cases that did not report outcomes, we cannot assume that none of these were without severe while we found reassuring maternal and fetal/neonatal outcomes with covid- , more rigorous, harmonized data collection and publication regarding all aspects of the disease, its treatment and outcomes in pregnant and breastfeeding individuals are needed. consideration should be given to establishing an international registry and pregnancy specific adaptive clinical trials with coordinated data collection for important outcomes. we urge investigators and regulatory health agencies to work together to find a sound ethical approach to include this population of consenting adults in interventional trials. this will ensure that trial results are generalizable, and that we have the necessary knowledge to guide safe, effective treatment in order to counsel the many pregnant and breastfeeding individuals who may go on to develop covid- during this evolving pandemic. this work was supported in part by the doris duke charitable foundation through a grant m a n u s c r i p t m a n u s c r i p t women of reproductive age ( - years) population (thousands) world health organization. women in the health workforce preliminary estimates of the prevalence of selected underlying health conditions among patients with coronavirus disease -united states pandemic influenza and pregnant women severe acute respiratory syndrome and pregnancy potential maternal and infant outcomes from (wuhan) coronavirus -ncov infecting pregnant women: lessons from sars, mers, and other human coronavirus infections why are pregnant women susceptible to covid- ? an immunological viewpoint clinical characteristics of neonates born to mothers with covid- clinical findings and disease severity in hospitalized pregnant women with coronavirus disease (covid- ) vertical transmission of covid- : sars-cov- rna on the fetal side of the placenta in pregnancies with covid- positive mothers and neonates at birth novel coronavirus-related acute respiratory distress syndrome in a patient with twin pregnancy: a case report characteristics and outcomes of pregnant women admitted to hospital with confirmed sars-cov- infection in uk: national population based cohort study probable congenital sars-cov- infection in a neonate born to a woman with active sars-cov- infection a snapshot of the covid- pandemic among pregnant women in france re: novel coronavirus covid- in late pregnancy: outcomes of first nine cases in an inner city london hospital covid- and hellp: overlapping clinical pictures in two gravid patients vaginal delivery in sars-cov- -infected pregnant women in northern italy: a retrospective analysis pre-labor anorectal swab for sars-cov- in covid- pregnant patients: is it time to think about it? neonatal late onset infection with severe acute respiratory syndrome coronavirus severe covid- during pregnancy and possible vertical transmission antibodies in infants born to mothers with covid- pneumonia clinical features and obstetric and neonatal outcomes of pregnant patients with covid- in wuhan, china: a retrospective, single-centre, descriptive study a case report of neonatal covid- infection in china association of covid- with pregnancy outcomes in health-care workers and general women possible vertical transmission of sars-cov- from an infected mother to her newborn detection of sars-cov- in placental and fetal membrane samples sars-cov- infection of the placenta report of positive placental swabs for sars-cov- in an asymptomatic pregnant woman with covid- coronavirus disease among pregnant chinese women: case series data on the safety of vaginal birth and breastfeeding placental pathology in covid- placental abruption in a twin pregnancy at weeks' gestation complicated by covid- , without vertical transmission to the babies the use of convalescent plasma therapy and remdesivir in the successful management of a critically ill obstetric patient with novel coronavirus infection: a case report immune modulating therapies in pregnancy and lactation american college of rheumatology guideline for the management of reproductive health in rheumatic and musculoskeletal diseases safety and efficacy of lopinavir/ritonavir during pregnancy: a systematic review world health organization. coronavirus disease (covid- ) situation report - importance of inclusion of pregnant and breastfeeding women in covid- therapeutic trials food and drug administration. kaletra (lopinavir and ritonavir) a randomized trial of hydroxychloroquine as postexposure prophylaxis for covid- hydroxychloroquine in nonhospitalized adults with early covid- : a randomized trial effect of hydroxychloroquine in hospitalized patients with covid- : preliminary results from a multi-centre, randomized a trial of lopinavir-ritonavir in adults hospitalized with severe covid- should pregnant women be included in phase iv clinical drug trials? obstetric pharmacokinetic dosing studies are urgently needed key: cord- -ver nrsz authors: sierra, beatriz; pérez, ana b; aguirre, eglis; bracho, claudia; valdés, odalys; jimenez, narciso; baldoquin, waldemar; gonzalez, guelsys; ortega, lilia m; montalvo, maria c; resik, sonia; alvarez, delmis; guzmán, maria g title: association of early nasopharyngeal immune markers with covid- clinical outcome: predictive value of ccl /mcp- date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: ver nrsz early recognition of severe forms of covid- is essential for an opportune and effective intervention, reducing life risk complications. an altered inflammatory immune response seems to be associated to covid- ´s pathogenesis and progression to severity. here we demonstrated the utility of the early nasopharyngeal swab sample for detection of the early expression of immune markers and the potential value of ccl /mcp- in predicting disease outcome a c c e p t e d m a n u s c r i p t in view of this we considered the possible utility of early nasopharyngeal swabs samples to detect the presence of messenger rna of proinflammatory and regulatory mediators already associated to covid- disease, like tnf, ccl /mcp- , ccl /mip- , and tgf and il- , respectively. we hypothesized that the activity of this set of cytokines/chemokines could trigger/suppress the severe outcome of infection, resulting in confirmed covid- patients with asymptomatic infections or different clinical evolutions. we found significant differences between the groups with favorable and unfavorable clinical evolution, suggesting the value of the early detection of tnfα, ccl /mcp- , ccl /mip- a c c e p t e d m a n u s c r i p t alpha mrna in nasopharyngeal swab samples, and the predictive value of ccl /mcp- for the covid- clinical outcome. nasopharyngeal samples were collected separately with sterile polyester tipped swabs (puritan medical products co., llc, guilford, me, usa) following the paho/who a c c e p t e d m a n u s c r i p t symptomatic cases were classified according to the number of symptoms, and the presence of symptoms previously associated to severity in cuban patients (distress respiratory, dyspnea and asthenia). patients with or symptoms, excluding those associated to severity, were classified as mild disease (eleven patients). patients with or more symptoms, including asthenia and dyspnea, were classified as very symptomatic (nine patients); those patients with respiratory distress (respiratory frequency> /min, o saturation index < %, pao /fio ratio < ) and intensive care requirement, but progressing to recovering phase, were classified as severe (three patients), and those with respiratory distress and intensive care requirement, that unfortunately died, as fatal (three patients). none of the asymptomatic or mild disease cases showed levels of c-reactive protein over mg/l, levels of ferritin over μg/l, or lymphopenia (lymphocyte count below . × /l). in order to identify biomarkers which discriminate between a favorable and unfavorable clinical evolution, we joined asymptomatic subjects and patients with mild disease in the category of "favorable evolution", and all those patients who developed a more severe picture (very symptomatic, complicated and fatal cases) in the category "unfavorable evolution" ( table ). all swab samples from symptomatic patients were collected between the first and fifth day after onset of symptoms for covid- . samples from healthy individuals confirmed as negative for sars-cov- were used as controls. the information about age, sex, days from symptoms onset to sample collection and co-morbidities of the studied subjects are shown in table . the cdna was synthesized from mrna with poly(dt) primers and superscript ii reverse experiments were conducted in triplicate. sequence of primers used in this work is described in supplementary data. distribution of data was tested using kolmogorov-smirnov test (data not normally distributed the objective of this study was to explore the early expression of tnf-alpha, ccl /mcp- , ccl /mip- alpha, il- , and tgfβ, previously associated with the uncontrolled cytokines response in the ards pathogenesis produced by human pathogenic coronaviruses, thereby taking advantage of the nasopharyngeal swab sample, mandatory for diagnosis of covid- diagnosis in cuban suspected cases. to determine the possible association of early gene expression of immune mediators in nasopharyngeal swab sample with the clinical evolution, we studied patients with a mild or severe covid- clinical picture, and asymptomatic subjects. sars-cov- negative individuals were included as controls. figure a shows the comparison of tnf alpha expression among negative controls, patients with favorable and unfavorable evolution. we did not find significant differences between the controls and patients with favorable evolution the group of unfavorable evolution showed a significantly higher tnf alpha expression in comparison to the patients with favorable evolution (p , ), and with negative controls (p , ). a significantly higher expression however of ccl was observed in cases with unfavorable outcome compared to cases with favorable evolution (p , ) or to negative controls (p , ) (figure b). similar results were obtained for ccl : also here a significantly a c c e p t e d m a n u s c r i p t higher expression in cases with unfavorable outcome was observed, compared to cases with favorable evolution (p , ) or to controls (p , ) (figure c). the analysis of tgfβ expression among the three groups is shown in figure d . individuals grouped as favorable outcome showed a significantly higher expression compared to controls (p , ) . patients with unfavorable outcome showed higher expression than controls (p , ), and cases with favorable outcome (p , ).in contrast, we did not find statistical relevant differences in il- expression between individuals with favorable and unfavorable evolution or with negative controls (supplementary data) we also analyzed if there were significant differences in the gene expression of each cytokine according to the time from symptom onset to sample collection. we found a significantly higher expression only for tgf beta in the period from to days, compared to the period from to days (p= . ). we checked then which group of cases, according to clinical evolution, was supporting this difference in the in the period from to days, and we found significantly higher expression in cases with unfavorable evolution compare those with favorable evolution (p= , ). an association of tnfα with marked asthenia (p= , ), and with the dyspnea presence (p= , ) in the unfavorable evolution group was found. dyspnea has been reported to be more frequent in covid- severe cases, and indeed, in some studies, it was included as a marker of severe disease ( , ) . a similar association with these clinical symptoms was observed for ccl /mcp- and tgfβ (asthenia: p= , and p= , resp.; dyspnea: p= , and p= , resp.) while ccl /mip- alpha was shown to be associated only with asthenia (p= , ). the univariate logistic regression models showed that the coefficients of three of the five cytokines evaluated were statistically associated with the unfavorable outcome (ccl /mcp-a c c e p t e d m a n u s c r i p t , tgfβ and tnfα). nevertheless, only ccl /mcp- was significant in the multivariate analysis-beta_(estimate = . , p= . ). early recognition of severe forms of covid- is crucial for an opportune and effective early intervention that reduces life risk complications. a deregulated antiviral immune response, resulting in the release of large amounts of proinflammatory cytokines and subsequent uncontrolled local or systemic inflammation, has been recognized as causal for severity and lethality in pathogenic human coronavirus infections, including covid- ( ) ( ). as a consequence, several inflammatory markers, in particular cytokines, have been associated to severity and prognosis of covid- ( ) . however, most of these were detected in peripheral blood, and after the fifth day of onset of symptoms, which is relatively late ( ). to our knowledge, this is the first study evaluating mrna expression of cytokines/chemokines, already linked to covid- pathogenesis, in swab samples from the upper airway at the early start of the symptoms (first days). although the sample size was rather limited ( healthy controls, patients with favorable evolution and patients with unfavorable evolution), clearly statistical differences were observed. a c c e p t e d m a n u s c r i p t concurring with recent reports in chinese covid- patients, we found significantly higher expression of tnf, ccl /mcp- and ccl /mip-  in covid- cases with an unfavorable evolution compared to those with a favorable evolution ( ) ( ). these markers have a high amplifying potential, quickly enhancing the inflammatory cytokine/chemokine responses in the upper airway, probably predicting later pathologic events in the lower airway associated to ards ( ) ( ) ( ) . the higher levels of tgfβ in cases with severest outcome could be in apparent contradiction with the regulatory and anti-inflammatory role attributed to this cytokine ( ) . however, the tgfβ function seems to be highly dependent on location and context and could play a major role under inflammatory conditions ( ) , in fact, it has been also associated to hypoxia and lung damage ( ) . the analysis of il- gene expression did not showed statistical relevant differences among the groups. cytokines are pleiotropic and interact as a network, in which the analysis of a single cytokine may not provide trustable information about serial immune events. considering this, univariate logistic statistical analysis was conducted to detect differences in concentrations of each measured cytokines, and to detect the confounders in patients with favorable versus patients with unfavorable evolution. also, in order to control the effect confounders like age, sex and the presence of comorbidities, a multivariate logistic regression analysis was used. the univariate logistic regression model confirmed the association of tnf, ccl /mcp- and tgfβ with the covid- outcome. however, after discard the "noise" introduced by confounder variables, with a multivariate logistic regression model, only ccl /mcp- was significant which suggested a predictive value for this marker. ccl /mcp- regulates the migration and infiltration of monocytes, memory t lymphocytes, and natural killer (nk) cells, favoring inflammatory process in tissues, including lung ( ) . 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 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 tables. table : characterization of the studied subjects. a c c e p t e d m a n u s c r i p t figure clinical features of patients infected with novel coronavirus in wuhan, china initial viral load and the outcomes of sars pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology covid- : consider cytokine storm syndromes and immunosuppression world health organization. laboratory testing strategy recommendations for covid- : interim guidance association of inflammatory markers with the severity of covid- : a meta-analysis mild versus severe covid- : laboratory markers transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in covid- patients monocyte chemoattractant protein- (mcp- ): an overview tnf-alpha signalling and inflammation: interactions between old acquaintances airway epithelial derived cytokines and chemokines and their role in the immune response to respiratory syncytial virus infection anti-and pro-inflammatory roles of tgf-β, il- , and il- in immunity and autoimmunity hypoxia down-regulates expression of secretory leukocyte protease inhibitor in bronchial epithelial cells via tgf-beta human fibrotic diseases: current challenges in fibrosis research plasma ip- and mcp- levels are highly associated with disease severity and predict the progression of covid- ip- and mcp- as biomarkers predicting disease severity of covid- ( / / ) a c c e p t e d m a n u s c r i p t key: cord- - kqtw s authors: toh, teck-hock; hii, king-ching; fieldhouse, jane k; ting, jakie; berita, antoinette; nguyen, tham thi; wong, see-chang; wong, toh-mee; lim, wei-honn; ha, siaw-jing; lau, chuet-zou; kong, sing-ling; bailey, emily s; warkentien, tyler e; husain, tupur s; gray, gregory c title: high prevalence of viral infections among hospitalized pneumonia patients in equatorial sarawak, malaysia date: - - journal: open forum infect dis doi: . /ofid/ofz sha: doc_id: cord_uid: kqtw s background: although pneumonia is a known cause of morbidity and mortality in sarawak, malaysia, the etiology and epidemiology of pneumonia are not well described in this equatorial region. routine clinical diagnostics for pneumonia etiology at government hospitals in sarawak had historically involved only bacterial diagnostics. viral diagnostics were only obtained through outside consultations. methods: from june , to may , , we collected nasopharyngeal swabs from patients of all ages older than month hospitalized with pneumonia at sibu and kapit hospitals. specimens were examined at our collaborating institutions with a panel of molecular assays for viral pathogens including influenza a (iav), ibv, icv, and idv, human adenovirus (adv), human enterovirus (ev), human coronavirus (cov), respiratory syncytial virus subtype a (rsv-a) or rsv-b, and parainfluenza virus (piv) types – . results: of samples examined, ( %) had molecular evidence of or more respiratory viruses. overall, the most prevalent virus detected was rsv-a ( . %) followed by adv ( . %) and iav ( . %), then rsv-b ( . %), ev ( . %), ibv ( . %), piv- ( . %), cov ( . %), piv- ( . %), piv- ( . %), and piv- ( . %). no specimens were confirmed positive for icv or idv. conclusions: the high prevalence of viruses detected in this study suggest that respiratory viruses may be responsible for considerable morbidity in equatorial regions such as sarawak. access to viral diagnostics are very necessary for medical staff to determine appropriate pneumonia treatments. as viral respiratory tract infectious diseases such as avian influenzas and severe acute respiratory syndrome coronavirus have emerged as increasing threats to global health security, international stakeholders such as the world health organization and the united nations international children's emergency fund (unicef) are calling for increased global surveillance for emerging and re-emerging respiratory viruses [ ] [ ] [ ] . locallevel surveillance systems are critical to understanding and monitoring the epidemiology of severe respiratory disease. understanding the etiology and epidemiology of pneumonia will guide antiviral interventions as well as enhance global emerging infectious disease preparedness. pneumonia is the second leading cause of death among children under the age of , resulting in more childhood deaths than diarrhea and malaria combined, with more than % of those cases occurring in low-and middle-income countries [ , ] . a meta-analysis of the global burden of childhood pneumonia found the greatest proportion ( %) of severe pneumonia cases occurred in southeast asia [ ] . however, because streptoccocus pneumoniae is the most common cause of vaccine-preventable severe pneumonia, much of the literature has focused on bacterial causes of pneumonia or antibiotic resistance, whereas fewer studies have prospectively investigated the viral etiology of pneumonia in southeast asia [ ] [ ] [ ] . one study of respiratory samples collected from children living in kuala lumpur under years of age between and found that . % of the samples were positive by immunofluorescence assays and viral cultures for viral pathogens, with a prevalence of . % for respiratory syncytial virus (rsv), . % for parainfluenza viruses (pivs), . % for influenza viruses, and . % for adenovirus [ ] . during the past years, the directors of government hospitals (sibu hospital and kapit hospital) in their namesake cities in sarawak, malaysia, have seen increasing pneumonia admissions (see supplementary figure kapit hospital serves a smaller population of approximately residents living along the rejang river [ ] , kilometers east and inland from sibu. the hospital has similarly experienced a recent increase in pneumonia admissions, estimated at more than per year. before this study, routine clinical diagnostics for pneumonia etiology at both sibu and kapit hospitals involved chiefly blood culture and gram stains of endotracheal secretion, if intubated, to detect bacteria. molecular and immunofluorescence laboratory diagnostics were only ordered for severe cases, for which clinicians had to send specimens to a specialized virology laboratory in kuala lumpur, malaysia or the university centre in kuching, sarawak. the overall objective of this study was to examine the viral etiology of and risk factors for pneumonia among patients admitted to sibu and kapit hospitals between june and may and, in doing so, to assist malaysian collaborators with setting up sustainable real-time molecular assays for viral respiratory pathogens. study enrollment took place between june and may at sibu and kapit hospitals. the major ethnic groups in sarawak are iban, chinese, malay, melanau, bidayuh, and orang ulu. as of , approximately . % of the population in sibu was iban and . % of the population in kapit was iban [ ] . as previously described [ ] , we adapted inclusion and exclusion criteria from united states, large and comprehensive, community-based pneumonia studies published in [ , ] . all patients older than days admitted to sibu or kapit hospitals and diagnosed with pneumonia by an attending physician were considered for study eligibility. a medical officer (mo) evaluated eligible subjects for inclusion and exclusion criteria, including confirmation by chest radiography within hours of hospitalization (see supplementary table ). adults years of age or older provided written consent, whereas children ages to provided written assent along with written parental or guardian consent. written consent was obtained from all parents or guardians of children under the age of . the study received a scientific review, and all procedures followed were in accordance with the ethical standards of the although this pilot study had sparse sarawak baseline virus prevalence data from which to calculate sample size, we approximated sample size based upon an estimated prevalence of influenza a (iav) causing % of pneumonias. hence, if we enrolled pneumonia patients, we could be confident to calculate an estimated prevalence within . % of the true prevalence of iav. from june to july , , the study team relied on convenience sampling to enroll as many patients as possible. for the remaining months of the study, mos enrolled patients on of randomly selected days of the week, which were communicated to them by a study coordinator. after obtaining written assent and/or consent, mos administered a brief questionnaire. the questionnaire captured demographic information (age, gender, ethnicity) along with household size (number of cohabitants) and contact with animals within the last days. in addition, all pre-existing health conditions and current medications were self-reported by the subject or their parent/guardian during the questionnaire, then confirmed by the mo through a review of the patient's medical records. the mo then used a flocked swab to collect nasopharyngeal (np) swab from the subject's nose, which was quickly placed into a viral transport tube containing ml sterile viral transport medium (bd universal viral transport; becton, dickinson and company, franklin lakes, nj). all specimens were stored at − °c at the sibu hospital clinical research center (shcrc) until ribonucleic acid or deoxyribonucleic acid extraction was performed using the qiamp cador pathogen mini kit (qiagen, hilden, germany). specimens collected in kapit were stored at − °c until they could be transported to sibu for processing. real-time reverse-transcription polymerase chain reaction (rrt-pcr) or real-time pcr (rpcr) was conducted on similar biorad cfx c touch thermal cycler real-time systems at shcrc, duke-nus in singapore and at duke university in durham, north carolina. all np swabs were examined for molecular evidence of influenza a (iav), ibv, icv, and idv, human adenovirus (adv), human enterovirus (ev), human coronavirus (cov), rsv subtype a (rsv-a) and rsv-b, and piv types - (piv- , - , - , and - ). primer and probes sequences for targeted pathogens are recorded in supplementary table . a positive control and a no-template control were included in each run. all specimens were first run at shcrc. one-milliliter aliquots of these specimens were later shipped on dry ice to either duke-nus or duke university for validation. laboratory staff at duke-nus and duke were blind to the results of the assays at shcrc. cycle threshold (ct) values < were considered positive, and ct values to were considered suspect to acknowledge that positivity could be the result of cross-reactivity or nonspecific amplification. cycle threshold values > were considered negative. all discrepant assays were noted and repeated at both shcrc and either duke or duke-nus, using the same original assays, and discrepancies were thus resolved. partial genome sequencing was also performed for several specimens to validate discrepant results. questionnaire data and molecular results were entered into redcap version . and verified at shcrc and at duke. data were imported into stata version . (statacorp, college station, tx), cleaned, and categorized for statistical analyses. we categorized continuous variables based on the distribution of the counts for household size (quartiles) and for age (quartiles). after examining age quartiles, we rounded age categories into approximate age quartiles so that age was treated as a whole number. demographic and clinical risk factors were examined for bivariate associations with the most prevalent positive molecular assays. pearson's χ test or fishers exact test were used for bivariate work. risk factors with a bivariate test statistic p ≤ . were included in stepwise, manual, backward-elimination, unconditional logistic regression models. risk factors with p < . were retained in final models, and odds ratios (ors) and % confidence intervals (cis) were calculated. a total of hospitalized pneumonia patients were enrolled at sibu and kapit hospitals between june , and may , , with of the subjects enrolled at sibu hospital ( . %) and enrolled at kapit hospital ( . %). of the enrolled subjects, ( . %) were male. a total of ( . %) enrolled subjects were children years of age or younger and ( . %) were of age years and younger. the majority of participants identified as iban, with ( . %) iban subjects enrolled at sibu hospital and ( . %) iban subjects enrolled at kapit hospital (table ) . of the np swabs collected, were run using rrt-pcr/ rpcr; np swab collected from a pediatric patient at sibu hospital was accidentally destroyed before molecular screening. one or more viruses were detected by rrt-pcr/rpcr in . % of the samples testing positive or suspect positive for either iav, ibv, icv, idv, adv, ev, cov, rsv-a, rsv-b, piv- , piv- , piv- , or piv- . the prevalence of each pathogen out of the total number of patients enrolled by month is shown in figure . we detected coinfections in of the patients with evidence of viral infection ( table ) . of the coinfected specimens, adv was detected in approximately % (n = ) with the most common coinfection combination being adv and rsv ( adv/ rsv-b coinfections and adv/rsv-a coinfections) followed by adv/ev coinfections. respiratory syncytial virus subtype b was the second most prevalent virus among coinfections (n = ); in addition to coinfections with adv-positive specimens, rsv-b was also detected in specimens found positive by rrt-pcr for rsv-a, piv- , ev, iav, and ibv. one pediatric patient's specimen was positive for viruses (rsv-b, adv, and ev). overall, the most prevalent virus detected was rsv (table ) , with samples testing positive for either rsv-a or rsv-b (overall prevalence of . %; prevalence of . % among children < years). a total of specimens tested positive by rrt-pcr for rsv-a for an overall prevalence of . %. an additional specimens were suspect-positive for rsv-a (ct values ranged . - . ); however, suspect-positive specimens were not included in the final analyses. eighty-two of the rsv-a-positive samples were from children ≤ years age , totaling a prevalence of . %. a total of ( . % prevalence) specimens were positive for rsv-b by rrt-pcr, with additional suspect-positive specimens (ct values ranged . - . ). thirtyfive of those specimens were collected from children < years ( . % prevalence). after rsv, adv and iav were the most prevalent, each with positive specimens detected by rpcr and rrt-pcr, respectively, for an overall prevalence of . %. fifty-seven of the adv specimens were collected from children < years ( % prevalence), and of the iav specimens were collected from children < years ( . % prevalence). a lower prevalence ( . %) of ibv was detected, with ibv-positive specimens, of which were collected from children < years of age. twenty-five specimens were positive for ev with a . % prevalence overall and . % prevalence among children < years. six specimens were positive by rrt-pcr for cov. among the piv types, piv- was the most prevalent, with specimens testing positive for piv- , followed by piv- detections, piv- detections, and piv- detection. no specimens were determined to be positive for icv or idv; however, there were suspect-positive idv samples (ct values ranged . - . ), which we were unsuccessful at isolating at duke university. one patient of the enrolled was pregnant and tested positive for iav. three severe adverse events were reported to the malaysian ethics board for participants who died after enrollment. all deaths were pediatric patients under year of age with negative blood cultures. human adenovirus was detected in the np swab specimens of of those patients, of whom had an endotracheal tube culture that grew enterobacter aerogenes before death. respiratory syncytial virus subtype a was detected in the third patient's np swab. no coinfections were detected among these patients. due to low counts, cov, icv, idv, and piv - disease outcomes were not included in the risk factor analysis. across the disease outcomes examined (rsv-a, rsv-b, iav, ibv, ev, and adv), gender was not found as a statistically significant risk factor in the initial bivariate screenings. additional potential risk factors such as pre-existing diseases, treatment history, and animal contact defined as touched or come within meter in the last days. c other animals include the following: cow, rats, rabbits, snake, and monkey. ethnicity were eliminated in the stepwise, backward-elimination multivariate modeling. the month of enrollment was a statistically significant risk factor for most virus outcomes, including rsv-a, rsv-b, iav, and adv (tables and and supplementary tables and ). respiratory syncytial virus subtype a was most prevalent during the first month of enrollment, june-july with an adjusted or of . ( % ci, . - . ) compared with rsv-a detection by rrt-pcr in november-december (table ). in contrast, there was a very low detection of rsv-b in june-july (see supplementary figure ). compared to june-july , rsv-b had an increased adjusted or beginning mid-february, with an adjusted or of . ( % ci, . - . ) between april and may , (table ) . we detected adv in over % of the specimens collected from april to may , . compared to the month of october-november , there was an increased adjusted or of . ( % ci, . - . ) of adv infection during the month of april-may. the only disease outcome for which location of hospitalization (kapit versus sibu) was statistically significant was ev; patients with specimens found positive for ev had a . higher or ( % ci, . - . ) of being enrolled at kapit hospital compared with sibu hospital (see supplementary table ) . age was a statistically significant risk factor for rsv-a, rsv-b, and adv, with pediatric patients ages month to year and to years having increased adjusted or compared with patients > years of age. detection of rsv-a and rsv-b was associated with quartiles of household size (number of additional cohabitants) (tables and ). the only animal exposure that was statistically associated with a disease outcome was cat exposure for ibv, with those patients reporting coming into contact with a cat within meter in the last days having an or . times higher ( % ci, . - . ) than those patients who did not have contact with a cat. sarawak, located on the northwest side of the island of borneo, has an equatorial climate with a high relative humidity that rarely drops below % and temperatures ranging from °c to °c (see supplementary figure ). both sibu ( . °n, . °e) and kapit ( . °n, . °e) are approximately degrees north of the equator (supplementary figure ) . the rainy season in this region typically falls between november and february, with december to march seeing the most rain. a drier season typically falls between may and september, with june to august seeing the least rain. our previous studies have investigated the relationship between relative humidity or absolute humidity and influenza virus transmission, suggesting that increased levels of humidity are linked with decreased transmission efficiency; however, the prevalence of iav in sibu and kapit hospitals suggest the high humidity associated with the equatorial climate in this region may not constrain iav transmission [ , ] . our findings regarding the prevalence of rsv support the existing literature that the antigenic subgroups a and b can cocirculate but typically differ by season [ ] . unlike iav, we saw seasonal variation of rsv-a and rsv-b during the drier months (see supplementary figure ) . the year-long data found a lower prevalence of rsv overall than an earlier analysis of the data collected during the first months of the study, june and july ; the logistic regression model from the pilot study also found that hospital location was a risk factor for rsv-a infection, with patients at kapit hospital having a higher adjusted or (adjusted or = . ; % ci, . - . ) of testing positive for rsv-a compared with patients hospitalized at sibu hospital [ ] . the finding that age was a statistically significant risk factor for rsv infection is consistent with the epidemiology of this virus. in the year-long study, we found a slightly elevated odds ratio of rsv-a and rsv-b infection among children ages to years (rsv-a adjusted or = . after the initial statistical analysis, pediatric data were stratified and analyzed for the outcome of rsv-a (see supplementary table ). in the stratified analysis, the same risk factors, including age quartile, household size, and month of enrollment, were found to be risk factors for rsv-a infection. we speculate that the high or ( . ; % ci, . - . ) observed for the association between cat exposure and ibv (see supplementary table ) may have occurred by chance. children < years adults ≥ years denominator is total number of specimens examined by rrt-pcr and rpcr for viruses, n = . when considering the number of cohabitants in the household of a subject testing positive for rsv-a, q (≥ ) had a slightly increased or compared with q ( to cohabitants). the same was true when the analysis was run on the stratified data for pediatric subgroups (see supplementary table ). in contrast, for rsv-b infection, q ( to cohabitants) and q ( to cohabitants) had slightly increased or compared with q ( . [ % ci, . - . ] and . [ % ci, . - . ], respectively). the mean household size among all enrolled subjects was . people with a range of to persons. household size was self-reported and did not capture the type of household (ie, single-family home or traditional longhouse). the study had a number of limitations. although the study offered the questionnaire in different languages to ensure comprehension, it is possible that questions about behavior were not accurately understood. after the first months of study, patients were supposedly recruited on randomly selected days of the week; however, we cannot eliminate the possibility that mos selected the sicker patients in the ward for this study. in addition, this study was limited to hospitalized patients and therefore excluded milder cases of pneumonia not requiring hospitalization. although we used rigorously validated real-time pcr assays as the gold standard for virus detection, the study was limited to a panel of viruses and we therefore likely missed other important pathogens present in specimens, including human metapneumovirus, rhinovirus, and bacteria. specifically, this study would benefit from an understanding of the prevalence of bacterial mono-or coinfections within the patient population. this study provides data on year of pneumonia admissions at district government hospitals in sarawak, malaysia; however, prevalence of the viruses investigated can vary between years. nevertheless, this study is one of the largest viral pneumonia etiology studies of its kind conducted in southeast asia. the findings led investigators to extend the study for an additional year, and a subset of samples will be analyzed at duke university for rhinoviruses a, b, and c. through this study we found a viral etiology for a relatively high proportion ( . %) of pneumonia cases, demonstrating the need for these hospitals to gain clinical diagnostics for viral pathogens. this will help hospital medical staff appropriately administer antiviral treatment for illnesses, such as iav and ibv, and avoid inappropriate use of antibiotics for pneumonia with a viral etiology. the findings from this study may assist the hospitals in their preparedness for future pneumonia admissions when new antivirals and vaccines are more readily available. whereas current therapies for rsv infection are largely supportive, as of there are more than ongoing rsv vaccine trials and rsv antiviral drug trials currently being evaluated, suggesting that new prevention and treatment mechanisms may be on the horizon [ ] . the risk factor analysis of age categories and rsv-a detection also provides evidence to support and encourage breastfeeding among newborns. in a commentary on pneumonia published in the lancet, watkins and sridhar [ ] describe the multifold factors limiting global action on pneumonia, including the challenges that arise from the complexity of pneumonia due to its multiple etiologies and consequentially diverse treatments. accurate diagnosis of pneumonia will not only allow clinicians to prescribe better treatment for patients, but it will also contribute to knowledge regarding the respiratory viruses most likely to cause illness in various age groups and communities. given the high prevalence of viruses detected among the patients enrolled in this study, routine surveillance and more sensitive molecular-based assays for respiratory viruses are recommended for hospitals in sarawak, malaysia and similar equatorial climates. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. potential conflicts of interest. t one pediatric patient specimen destroyed, assay results out of n = . surveillance for emerging respiratory viruses global epidemiology of non-influenza rna respiratory viruses: data gaps and a growing need for surveillance addressing the public health burden of respiratory viruses: the battle against respiratory viruses (brave) initiative estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory tract infections in countries: a systematic analysis for the global burden of disease study global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in : a systematic analysis global burden of childhood pneumonia and diarrhoea clinical and economic burden of community-acquired pneumonia amongst adults in the asia-pacific region the bacterial aetiology of adult community-acquired pneumonia in asia: a systematic review assessing the burden of pneumonia using administrative data from malaysia, indonesia, and the philippines epidemiology and seasonality of respiratory viral infections in hospitalized children in kuala lumpur, malaysia: a retrospective study of years surveillance for respiratory syncytial virus and parainfluenza virus among patients hospitalized with pneumonia in sarawak community-acquired pneumonia requiring hospitalization among u.s. children community-acquired pneumonia requiring hospitalization among u.s. adults humidity as a non-pharmaceutical intervention for influenza a absolute humidity modulates influenza survival, transmission, and seasonality respiratory syncytial virus-a comprehensive review pneumonia: a global cause without champions we thank the medical officers of sibu and kapit hospitals (namely, nga-hung ngu, khai-fatt chao, cheng-ing kong, zhen-hao chin, edmund kwang-yuen wong, tiana ti, and hilary hon-yun kueh) for enrolling patients. we thank the laboratory staff at kapit hospital (namely, cornelius jambol, goh hieng hua, and velarie bill) and tiing-tiing chua at sibu hospital for processing specimens. we thank dr. cheesan lee for helping us to begin this collaboration. we thank jessica choi, sarah philo, kerry mallinson, sarah paust, calvin wang, and christine wang for laboratory support. we thank dr. larry park for his support in the statistical analysis. this work was conducted in partnership with duke university, the duke global health institute, sibu hospital clinical research center, and segi university sibu clinical campus. we thank the director general of health, malaysia for his permission to publish this paper.disclaimer. the views expressed in this article are those of the author(s) and do not necessarily reflect the official policy or position of the department of the navy, department of defense, or the united states government.financial support. this work funded by the us naval medical research center-asia and vysnova partners (sc- -saber- - , sc- -saber- - ) and professor gregory gray's discretionary funds from duke university's global health institute. key: cord- -jky jlrl authors: cellai, michele; o’keefe, james b title: characterization of prolonged covid- symptoms in an outpatient telemedicine clinic date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: jky jlrl we identified patients with coronavirus disease (covid- ) in a telemedicine clinic who requested ongoing follow-up calls weeks after symptom onset. in this group, respiratory symptoms are the most common complaints, asthma and lung disease are frequent comorbidities, and patients often have not returned to work or usual activity. while the clinical course of ambulatory patients with coronavirus disease (covid- ) is described in early reports [ ] [ ] [ ] [ ] , persistent symptoms beyond weeks are not yet well characterized. data illustrating delayed recovery are available from the severe acute respiratory virus disease (sars) outbreak in [ ] as well as community-acquired pneumonia [ ] , but these reports are limited to post-hospitalization cohorts. anecdotally, some patients with covid- report delayed return to routine activity, even with mild illness. the emory clinic virtual outpatient management clinic (vomc) is a telemedicine program for the care of adults with covid- during isolation at home. the vomc follows patients with confirmed covid- with regular telephone calls for a duration of - days depending on patient symptom severity, comorbidities, and age [ ] . the calls may be continued beyond days for ongoing symptom monitoring at the request of the patient and/or provider (registered nurse or advanced practice provider). we seek to describe the persistent symptoms experienced by patients with mild covid- by reviewing records of those who requested follow-up vomc care for greater than the planned days and more than weeks beyond symptom onset. we hypothesize that specific comorbidities may be associated with prolonged symptom duration in comparison to the overall vomc population. a c c e p t e d m a n u s c r i p t we conducted a search of the patients enrolled in the vomc between march and may , who received their final vomc follow-up call greater than weeks after symptom onset date. exclusion criteria were: ( ) unclear onset date, ( ) vomc follow-up call duration of less than weeks, and ( ) hospitalization prior to entering vomc. charts were reviewed through june , at which time all eligible patients had been discharged from vomc. chart review included: ( ) verification of patient demographics and comorbidities documented at vomc intake visit, ( ) verification of symptom onset dates, ( ) review of follow-up notes during the th week of symptoms, ( ) review of return to work advice/disability letters, and ( ) review of final notes for health status at time of vomc discharge. we obtained data from standardized lists of symptoms and comorbidities coded in the vomc notes, but allowed for specified "other" symptoms and comorbidities specifically denoted in provider narrative portion(s) of the note to be coded as "other" for later analysis. for patients who required additional medical evaluation after the acute period (defined as an in-person or telemedicine visit at least weeks into illness), we reviewed evaluation notes, diagnostics, and final diagnoses (including "alternate diagnoses" and "contributing diagnoses" based on provider documentation). delayed return to activity was coded as present only if a provider note during the th week of symptoms specifically noted less ability to perform physical activity (e.g. walk, jog, or run errands) compared to activity status immediately before illness. all chart review data were entered into a standardized template capturing all elements that we have reported in results. data for specific comorbidities were available for the overall vomc cohort[ ], extracted by data pull and available for comparison to the comorbidities for our "prolonged symptom" a c c e p t e d m a n u s c r i p t subset in this study. for the comparison of comorbidities, we used the same data source (intake note) for the overall cohort and the prolonged symptom subset. we included additional comorbidities in our chart review template if identified in or more charts (prolonged group only). results were analyzed in microsoft excel using descriptive statistics. a total of patients were identified as being monitored by vomc during the study period. of these, were confirmed to have covid- by nasopharyngeal pcr and enrolled in vomc care. we identified ( . %) as receiving calls > weeks after symptom onset and arrived at a total of ( . %) "prolonged cases" after exclusions: we removed patients due to unclear start dates ( reporting symptom onset > months before local transmission suspected, with negative testing at symptom onset and retesting positive > month later), patients due to total symptoms < weeks (dates clarified in chart review), and patients due to receiving fewer than days of vomc calls (for example, an initial vomc visit in the th week of illness, followed for week and discharged). due to the presence of persistent symptoms, ( . %) of patients delayed return to work at least five weeks from symptom onset, ( . %) delayed return to activity. the most common reasons cited for delayed return to work or activity was fatigue or weakness. the majority of patients ( %) underwent further evaluation at one or more sites at least weeks after symptom onset, either in emergency room (n= , . %), respiratory clinic (n= , %), or telemedicine visit with specialist (n= , %) or primary care provider (n= , %). common tests included chest x-ray (n= ), chest ct (n= ), labs (n= ), and echocardiogram (n= ). an alternate non-covid- diagnosis was reached only for patient (exacerbation of heart failure). a contributing diagnosis (to delayed improvement in covid- ) was suspected for patients ( %), most commonly allergic rhinitis (n= , . %), followed by asthma (n= , . %) and bronchiectasis in patients ( . %). a c c e p t e d m a n u s c r i p t our data demonstrate that a subset of outpatients with mild covid- will experience persistent symptoms, here defined as a period greater than weeks. while the majority of patients identified in this study experienced impairment that limited usual activity, we found that most patients ( . %) had an improving symptom course in the th week of symptoms, though long-term duration of symptoms is still unknown. a smaller proportion ( . %) reported a return to baseline health by the time of discharge from vomc. in this cohort, the majority of patients sought further evaluation for their symptoms, with only one patient identified to have a non-covid- alternate diagnosis. importantly, in patients evaluated for persistent symptoms, a contributing atopic diagnosis or chronic lung disease was often suspected, which led to specific directed treatments. this possible association is also suggested by comparison of comorbidities between the prolonged symptom group and the overall vomc cohort (table ); the incidence of asthma and chronic lung disease (prospectively coded at intake visit) appear more frequent in the patients identified in the persistent symptom cohort for this study. anecdotally, we note that many providers report that inhaled bronchodilators and corticosteroids are effective for prolonged covid- symptoms (see video: https://youtu.be/ecpjhdvf k) and our findings in this report strengthen the case for further research. while respiratory symptoms (cough, dyspnea on exertion, and other) are most common, a variety of symptoms may present across organ systems including neurologic, cardiac, and m a n u s c r i p t gastrointestinal. these manifestations merit further investigation as possible evidence of organ-specific dysfunction caused by "mild" covid- in outpatients. our data represent a specific population of patient who enrolled in a telemedicine program at a single center and may not be generalizable to other populations. additionally, the request for ongoing follow-up calls was not standardized across the cohort so we cannot be certain which symptoms or functional status concerns prompted the continuation of care. it is therefore likely that our data does not capture all patients with persistent symptoms. in a separate phone-call survey project / ( . %) non-hospitalized patients who were called after vomc discharge (median symptom day ) reported significant symptoms requiring ongoing medical care by primary care providers [ ] . the study period (march-may ) overlapped with the spring pollen season in georgia, which could explain the occurrence of contributing atopic diagnoses in this study. the peak pollen counts, however, occurred march to april , and the dates of discharge of our prolonged symptom cohort from vomc were april to june (median date: may ); the median dates of the th week of symptoms used for our analysis were may to may . furthermore, the provider documentation used in our analysis attributed the symptoms to covid- as the primary active diagnosis in all care plans except for a single "alternate diagnosis" case. a c c e p t e d m a n u s c r i p t for a subset of patients with covid- ( . % in our cohort), symptom duration is more than weeks and impacts their ability to return to work and activity. the most common persistent symptoms are respiratory in nature. these patients may be more likely to have underlying allergic and lung conditions than in the general telemedicine vomc follow-up cohort. further research is needed to determine the long-term effects of covid- in patients with persistent symptoms. m a n u s c r i p t the study was approved by the emory university institutional review board (study ), which granted a waiver of consent and a waiver of health insurance portability and accountability act authorization. the study was carried out in accordance with the principles embodied in the declaration of helsinki. clinical features of covid- patients with outpatient management in the greater paris: the covid-call study clinical characteristics and reasons for differences in duration from symptom onset to release from quarantine among patients with covid- in liaocheng clinical findings in a group of patients infected with the novel coronavirus (sars-cov- ) outside of wuhan, china: retrospective case series symptoms of covid- outpatients in the united states impact of severe acute respiratory syndrome (sars) on pulmonary function, functional capacity and quality of life in a cohort of survivors long-term symptom recovery and health-related quality of life in patients with mild-to-moderate-severe community-acquired pneumonia initial experience in predicting the risk of hospitalization of outpatients with covid- using a telemedicine risk assessment tool. medrxiv risk factors for long-term persistent symptoms in covid- in an outpatient cohort we would like to thank david tong, md mph for his assistance with comorbidity data extraction and david roberts, md for the creation of standardized vomc note templates. both authors contributed to the concept and design of the study. jo performed the primary chart review and mc performed a secondary review. both authors were involved in data interpretation. jo drafted the primary manuscript and both authors revised the manuscript critically for important intellectual content, and approved the final version of the manuscript.nding none the authors have no conflicts of interest to declare. all authors have submitted the icmje form for disclosure of potential conflicts of interest. 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 a c c e p t e d m a n u s c r i p t ( %) - ( . %) or more ( . %) *these symptoms identified from "other" category on chart review key: cord- -p cb idp authors: kanwar, anubhav; selvaraju, suresh; esper, frank title: human coronavirus-hku infection among adults in cleveland, ohio date: - - journal: open forum infect dis doi: . /ofid/ofx sha: doc_id: cord_uid: p cb idp background. human coronaviruses (cov) have been long recognized as a common cause of respiratory tract disease including severe respiratory tract illness. coronavirus-hku has been described predominantly among children less than years of age in the united states with few studies characterizing the disease spectrum among adults. methods. nasopharyngeal specimens of patients with respiratory symptoms were analyzed for cov-hku by nxtag respiratory pathogen panel multiplex assay from february , to april , . epidemiologic, clinical, and laboratory data were collected on adults (patients > years) whose samples screened positive. results. of adult respiratory specimens screened, ( . %) cases of cov-hku were identified. adults age ranged between and years and ( %) were males. all of whom had or more respiratory symptoms, and ( %) also reported or more gastrointestinal symptoms. eleven ( %) reported history of smoking and ( %) used inhaled steroids. seven ( %) required hospitalization, ( %) of these needed supplemental oxygen, and ( %) were admitted to intensive care. median length of hospitalization was days. eight ( %) received antibiotics despite identification of cov-hku . infectious work-up in patient who died did not reveal any other pathogen. in ( %) cov-hku -positive adults, the only viral coinfection detected was influenza a. conclusions. coronavirus-hku accounted for . % of adult respiratory infections and should be considered in differential diagnosis of severe respiratory illnesses among adults. coronavirus-hku has been predominantly reported in children in united states [ , ] but less commonly among adults [ ] [ ] [ ] . silva et al [ ] found case ( . %) among adults presenting with flu-like symptoms over a -month period, and gorse et al [ ] reported patient with cov-hku among adults ( . %) with history of copd. in this study, we report one of the largest case series of cov-hku infections among adults presenting with respiratory tract illness and describe their clinical characteristics. wards, and emergency department (ed) at the discretion of the on-service physicians. samples were placed in m -rt viral transport media (remel, lenexa, ks) and transported to the laboratory where they were frozen until testing. testing was performed using the nxtag respiratory pathogen panel ce-ivd assay kits (luminex, austin, tx) per the manufacturer's guidelines (package insert, nxtag respiratory pathogen panel assay; luminex). in brief, µl of extracted nucleic acid were added directly to nxtag respiratory pathogen panel preplated, lyophilized reagents. multiplexed reverse-transcription polymerase chain reaction and bead hybridizations were performed in each plate well under a single cycling program per manufacturer's instructions. the sealed plates were placed directly on the magpix instrument (luminex) for data acquisition. raw signals generated by the magpix instrument were subsequently analyzed by the assay-specific software accessory package using synct software to establish the presence or absence of each pathogen in each sample. for detection of covs, the nucleocapsid protein gene (n) was used to identify covs e, oc , and nl . the open reading frame aboratory region of the ribonucleic acid polymerase was used to identify cov-hku . the limit of detection titer for cov-hku was . e+ genome copies/ml (package insert, nxtag respiratory pathogen panel assay). sample collection and data analysis were approved by the metrohealth medical center institutional review board (irb - ). clinical data analysis for adults (patients > years of age) included the following: age, gender, hospitalization status, length of hospitalization, clinical features, discharge diagnosis, outcome (death or survived), comorbidities (smoking, lung disease), laboratory and radiology results, intensive care unit (icu) stay, oxygen use and duration, treatment provided, and exposure history. clinical data were collected using redcap software (redcap . . , vanderbilt university). coronaviruses detected from all respiratory specimens during the study period is summarized in table . of these, originated from adult patients (> years) with ( . %) screening positive for covs. thirteen ( . %) samples tested positive for cov-hku and represented % of all cov species detected among adults. median age of adult patients was years (range, to years). eleven cov-hku -positive adults ( %) had an underlying respiratory comorbidity, predominantly history of smoking, with ( %) being current smokers (table ) . five patients ( %) reported use of inhaled corticosteroids. one patient was on systemic immunosuppression (prednisone, azathioprine). in addition, patients had underlying gastrointestinal comorbid conditions. all adults with cov-hku infection had respiratory symptoms ( table ). shortness of breath was the most common respiratory complaint ( %) followed by cough ( %) and rhinorrhea ( %). however, fever, wheezing, and chest pain were less common ( %, %, and %, respectively). upper or lower gastrointestinal symptoms were reported in ( %) adults. other symptoms included myalgias ( %) and sore throat ( %). seven patients ( %) required hospital admission, ( %) of whom were diagnosed with pneumonia by the on-service team. among hospitalized adults, ( %) were admitted to the icu. both patients were male. three patients ( %) were diagnosed with sepsis, of whom developed septic shock and died. this individual had a history of smoking ( -pack years) and copd. another individual admitted to the icu developed pancreatitis, pericarditis, peritonitis, and altered mental status during hospitalization and recovered. all blood, urine, and sputum cultures from these individuals were negative for other bacterial, fungal, and viral infections. laboratory findings (table ) were obtained in ( %) of the cov-hku adults. of these, leukocytosis (white blood cell count [wbc] > cells/µl) was observed in ( %), with an average of cells/µl (range, - cells/µl). of these, neutrophilic predominance (neutrophil count > cells/µl) was seen in ( %) and bandemia (> % bands) was seen in ( %). one ( %) adult had leukopenia (wbc of cells/µl). twelve ( %) adults had chest radiography performed with ( %) showing infiltrative disease. the chest imaging findings included prominence of interstitial markings with a reticulonodular pattern, ground-glass opacities, patchy consolidation, interlobular and intralobular septal thickening, basilar atelectasis, small pleural effusions, and hyperinflated lungs ( figure ). eight ( %) received antibiotics, and ( %) received oseltamivir, despite identification of cov-hku as the table eighty-three percent of all cov-hku -positive samples occurred within a -week period between february and march ( figure ). this period included ( %) of the adult cases. coronaviruses oc and nl had a more prolonged circulation but also predominated during these same weeks. our report describes the largest number of cov-hku infections among the general adult population in the united states to date. we find that . % of adults screened for respiratory viruses have evidence of cov-hku . previous studies in north america have reported lower rates during a typical viral respiratory season [ - ]. on the other hand, cov-hku infection among adults outside the united states have been reported with rates ranging between . % and . % [ ] [ ] [ ] [ ] [ ] . our rate of . % is similar to these findings. we hypothesize that the overall rate might change if surveillance occurred throughout the year. it is likely that the study period represents peak cov-hku circulation in our community. we identified smoking as the predominant comorbid condition ( % of all cov-hku -positive adults). smoking has been found to be an independent predictor of mers-cov acquisition in saudi arabia [ ] and among % of smokers with cov-hku pneumonia in hong kong, china [ ] . increased respiratory infections are hypothesized to be secondary to continuing parenchymal trauma and suppression of host resistance over time [ ] . in our study, smoking was identified commonly among all age groups of adults with cov-hku disease irrespective of the age of onset of smoking. we found a high rate of cov-hku infections ( %) in patients using inhaled corticosteroids. although inhaled steroids have been accepted as safe agents with no or minimal systemic absorption, the effects on local cell-mediated immunity is unclear. they have been shown to be a risk factor for bacterial pneumonia in patients with asthma and copd, as well as influenza in copd patients [ , ] . in a recent meta-analysis by dong et al [ ] , there was an increased but nonsignificant trend towards influenza infection among patients taking inhaled fluticasone. further studies are needed to confirm any relationship between respiratory illness due to cov-hku and other cov with inhaled corticosteroids use. all patients we identified with cov-hku infection had respiratory symptoms with dyspnea, cough, and rhinorrhea being the most common. this is not unexpected due to our study design. similar studies describing hku in pediatric and adult patients have also found an association with upper and lower respiratory tract illness [ , , , , ] . however, cov-hku has also been reported in patients presenting with nonrespiratory symptoms [ ] . we identified gastrointestinal symptoms in % of cov-hku -positive adults, consisting of diarrhea and nausea and/or vomiting. the mechanism for gastrointestinal symptoms seen in cov-hku disease remains unclear. vabret et al [ ] and esper et al [ ] have isolated cov-hku from stool samples in patients with diarrhea and nausea and/or vomiting. non-cov, such as influenza [ ] , and other covs, such as sars-cov [ ] and mers-cov [ ] , have also been detected in stool specimens among patients with and without gastrointestinal symptoms. further studies are needed to determine whether cov-hku detection in stools is part of gastrointestinal disease versus asymptomatic viral shedding and whether it plays any role in disease transmission. it is interesting to note that adults identified with cov-hku had higher than expected severity of disease in our study, with increased occurrence of hospital admissions, oxygen use, and icu admission. this is in contrast to other studies in which at-risk patient populations had lower morbidity and hospitalization with cov-hku infections [ , , ] . looking at other covs, the rates of hospitalization and morbidity were relatively similar in combined pediatric and adult studies [ ] . our finding of % hospitalization and % icu admission could be accounted for by selection bias of the sample population (screening those presenting to the ed or hospitalized with respiratory tract illness). studies focusing on outpatient and asymptomatic adults will provide a better understanding of disease severity. however, this study does demonstrate cov-hku 's potential for severe illness. a -year-old with no history of immunosuppression died due to shock while meeting clinical criteria for sepsis and negative infectious work-up. it remains unclear what, if any, role cov-hku played in this patient's demise. most studies of cov-hku have demonstrated lower mortality [ ] . in the deaths reported by woo et al [ ] , both patients were immunocompromised with history of cancer, diabetes mellitus, advanced age, and lymphopenia. another death linked to cov-hku was reported in a severely immunocompromised patient lymphodepleted by conditioning for autologous hematopoietic stem cell transplantation [ ] . in this case, cov-hku was isolated from his lung tissue and bronchoalveolar lavage with autopsy revealing bronchopneumonia, organizing pneumonitis, and diffuse alveolar damage. in our study, hku -positive adults who did not require hospitalization had a normal chest x-ray, whereas % among inpatients with cov-hku had chest infiltrates. garbino et al [ ] reported interstitial and alveolar infiltrates in % of hospitalized patients with respiratory samples positive for cov-oc , cov-nl , cov- e, and cov-hku . given paucity of chest imaging data, complete characterization of radiographic findings in cov-hku infections is incomplete. approximately % of all patients with cov-hku infection in our study received antibiotics. this is similar to other studies in which up to % of patients with cov-positive bronchoalveolar lavage received antibiotics [ ] . antibiotic use after a positive respiratory pathogen panel for viral pathogen was observed for median duration of days in our study. this is consistent with other studies suggesting that mere disease diagnosis with respiratory pathogen panel might not alter antibiotic prescribing practices among healthcare providers for viral respiratory illnesses [ ] . such practices are concerning for unnecessary antibiotic exposure and the potential to aid the development of multidrug-resistant organisms [ ] . this highlights the need for education of providers to consider cov-hku as a pathogen associated with upper and lower respiratory tract infections and de-escalate antibiotics with negative bacterial cultures and antigen [ ] . among all cov-positive adults, % had coinfections, the most common being influenza a and rhinoviruses. these findings are comparable to other studies [ ] . higher coinfections with cov and other viruses could suggest common reservoirs, overlap in seasonality, and persistence of virus or viral genome in respiratory secretions [ ] . among our adults with cov-hku and influenza a coinfection, it was unclear whether symptoms were due to cov-hku or influenza or both. the clinical relevance of respiratory viral coinfections is not fully understood. higher severity of respiratory disease has been reported in certain pathogen coinfection combinations, including influenza a with covs [ ] . in other studies, there was no increased severity of illness in cov-associated coinfections [ , , ] . gaunt et al [ ] showed that a quantitative viral load for cov was unchanged in cases of coinfection with rsv and monoinfection. further investigation on the role viral coinfections play in alteration of respiratory disease severity should be undertaken. our study has several limitations. by evaluating only symptomatic patients, we could have missed asymptomatic or subclinical infections. this could lead to an underestimation of the disease prevalence in the adult population and an overestimation of disease severity. the retrospective aspect of our study is insufficient to establish causality. larger study periods will also be required to establish a complete understanding regarding seasonal distribution patterns of this virus in our community. however, the majority of cov-hku studies in the literature are single-center experiences occurring over season [ , ] . our study provides needed insight into clinical characteristics and severity associated with cov-hku infection in adults in the northeast region of the united states. we opine that cov-hku infection should be considered in differential diagnosis of community-acquired pneumonia in adults, including those that require hospitalization. more studies are needed to fully understand the seasonality, risk factors, incidence, and epidemiology of cov-hku . potential conflicts of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. history and recent advances in coronavirus discovery identification of a new human coronavirus isolation of a novel coronavirus from a man with pneumonia in saudi arabia characterization and complete genome sequence of a novel coronavirus, coronavirus hku , from patients with pneumonia coronavirus hku infection in the united states coronavirus infection and hospitalizations for acute respiratory illness in young children human coronavirus and acute respiratory illness in older adults with chronic obstructive pulmonary disease human rhinovirus and coronavirus detection among allogeneic hematopoietic stem cell transplantation recipients human respiratory coronaviruses detected in patients with influenza-like illness in arkansas united states census bureau website clinical and molecular epidemiological features of coronavirus hku -associated community-acquired pneumonia coronavirus hku and other coronavirus infections in hong kong human coronavirus infections in rural thailand: a comprehensive study using real-time reverse-transcription polymerase chain reaction assays human respiratory coronavirus hku versus other coronavirus infections in italian hospitalised patients characterization of human coronavirus etiology in chinese adults with acute upper respiratory tract infection by real-time rt-pcr assays risk factors for primary middle east respiratory syndrome coronavirus illness in humans, saudi arabia smoking, alcohol consumption, and susceptibility to the common cold inhaled corticosteroids and the increased risk of pneumonia: what's new? a updated review salmeterol and fluticasone propionate and survival in chronic obstructive pulmonary disease use of inhaled corticosteroids in patients with copd and the risk of tb and influenza: a systematic review and meta-analysis of randomized controlled trials. a systematic review and meta-analysis of randomized controlled trials etiology and clinical characterization of respiratory virus infections in adult patients attending an emergency department in beijing detection of the new human coronavirus hku : a report of cases human coronaviruses are uncommon in patients with gastrointestinal illness prevalence of gastrointestinal symptoms in patients with influenza, clinical significance, and pathophysiology of human influenza viruses in faecal samples: what do we know enteric involvement of severe acute respiratory syndrome-associated coronavirus infection viral shedding and antibody response in patients with middle east respiratory syndrome coronavirus infection epidemiology and clinical presentations of the four human coronaviruses e, hku , nl , and oc detected over years using a novel multiplex real-time pcr method use of a novel virus detection assay to identify coronavirus hku in the lungs of a hematopoietic stem cell transplant recipient with fatal pneumonia a prospective hospital-based study of the clinical impact of non-severe acute respiratory syndrome (non-sars)-related human coronavirus infection antibiotic discontinuation rates associated with positive respiratory viral panel and low procalcitonin results in proven or suspected respiratory infections impact of antibacterials on subsequent resistance and clinical outcomes in adult patients with viral pneumonia: an opportunity for stewardship access to a polymerase chain reaction assay method targeting respiratory viruses can reduce antibiotics: a randomised, controlled trial the role of infections and coinfections with newly identified and emerging respiratory viruses in children rate and influence of respiratory virus co-infection on pandemic (h n ) influenza disease detection of four human coronaviruses in respiratory infections in children: a one-year study in colorado key: cord- -p qchjva authors: alghamdi, abdulaziz; hassan, ahmed m; tolah, ahmed m; alamari, sawsan s; alzahrani, abdulrahman a; alsaaidi, ghaleb a; abujamel, turki s; azhar, esam i; hashem, anwar m title: molecular evidence of influenza a virus circulation in african dromedary camels imported to saudi arabia, – date: - - journal: open forum infect dis doi: . /ofid/ofz sha: doc_id: cord_uid: p qchjva little is known about influenza a viruses in dromedaries. here, we detected influenza a viral rna in specimens ( . %) out of nasal swabs collected from dromedaries between and in saudi arabia. positive samples were detected only in imported camels from sudan and djibouti but not local ones. partial genome sequencing indicates a close relationship to – human/swine influenza a h n isolates from different countries, suggesting possible interspecies transmission. taken together, dromedaries could represent a potentially unrecognized permissive host for these viruses, highlighting the need for enhanced surveillance in animals to aid implementation of one-health strategies. for centuries, camels have played a significant role as a major human companion and a key contributor to the livelihood of mankind. despite the known role of camels in zoonosis, many aspects of their health have not been studied before the emergence of the middle east respiratory syndrome-coronavirus (mers-cov) in [ ] [ ] [ ] [ ] . in fact, the possibility of spreading known and unknown zoonotic pathogens from camels to humans or other animals represents major public health and economic concerns [ ] [ ] [ ] . these concerns are exaggerated further because of the inevitable close contact between camels and humans during ranching, milking, feeding, and riding, raising the need for enhanced surveillance in these animals as a one-health approach. although data on influenza viruses circulation in camels are very scarce, some existing evidence suggests the viruses' ability to infect and cause disease in these animals. several outbreaks of severe respiratory diseases in bactrian camels have occurred between and in mongolia and were suspected to be due to influenza viruses [ ] . serum samples obtained from sick camels during these outbreaks had positive hemagglutination inhibition titers against influenza a/ ussr/ / (h n ) human vaccine strain [ ] . genetic and antigenic analyses of these isolates confirmed their relatedness to influenza a/ussr/ / (h n ) which is a reassortant vaccine strain obtained by reassortment between two h n strains (a/ pr/ / and a/khabarovsk/ ), possibly through transmission from vaccinated humans to camels [ ] . interestingly, experimental infection of bactrian camels with these isolates resulted in productive infections and antibody responses, indicating that camels are a potentially unexplored permissive host for influenza a viruses [ ] . further active and enhanced surveillance of bactrian camels in mongolia also resulted in the isolation of influenza a h n viruses that are phylogenetically related to equine influenza a viruses, suggesting possible interspecies transmission [ ] . although the existence of influenza viruses in dromedary camels has not been investigated properly, previous studies provided limited serological evidence of circulation of all influenza types (a, b, c, and d) among dromedaries in several african countries [ ] [ ] [ ] . it is clear that the potential role of camels in interspecies and zoonotic transmission of influenza as well as the ecology of these viruses in camels are poorly understood, highlighting the need for active and enhanced surveillance. here, we expanded our surveillance for influenza a viruses to include local and imported dromedary camels in saudi arabia, especially as thousands of camels are annually imported from african countries, such as sudan, djibouti, kenya, somalia, and eritrea, in addition to the large number of local camels. a total of and nasal swabs were collected from imported and local camels in saudi arabia, respectively. local camels were sampled form local farms in jeddah (western saudi) and riyadh (central saudi), whereas imported camels were sampled on incoming ships arriving from sudan ( samples) and djibouti ( samples) at jeddah islamic seaport (table ) before disembarking the vessels. all swabs were collected, immersed in viral transport media, transported in a cold container, and stored at - ˚c until studied. samples were collected upon ethical approval from the unit of biomedical ethics in king abdulaziz university hospital. extracted viral rna was screened for influenza a virus rna by one-step real-time reverse transcription polymerase chain reaction (rt-pcr) using single-step x quantifast rt-pcr master mix kit (qiagen, hilden, germany). targeting a bp fragment in the matrix (m) gene (infa-f: ′-gaccratcctgtcacctct gac- ′; infa-r: ′-agggcattytggacaaakcgtcta- ′; infa-p: ′-fam-tgcagtcctcgctcactgggcacg-mgb- ′), rt-pcr was conducted with consensus degenerate primers and probes according to world health organization protocol [ ] . viral rna from known influenza a isolates as well as no template controls were included in each run as positive and negative controls, respectively. samples with cycle thresholds (ct) values < were considered positive. precautions were taken to avoid cross-contamination of samples during all steps and all positive and some negative samples were re-extracted and retested independently to confirm the results. extracted rna from positive samples was used for one-step conventional rt-pcr using the superscript iii one-step rt-pcr high fidelity kit (invitrogen, foster city, ca) according to the manufacturer's instructions using the infa-f and infa-r primers. the resulting amplicons were analyzed on % agarose gel and bands with expected size (~ bp) were purified and sequenced using cycle sequencing on an abi automatic sequencer (applied biosystems, foster city, ca) using infa primers and the bigdye terminator v . reaction cycle kit (applied biosystems, usa) according to the manufacturer's instructions. sequences were assembled and analyzed for homology using the national center for biotechnology information (ncbi) blastn (nucleotide basic local alignment search tool), and the top hits with the highest alignment scores for each contig were kept and summarized in a tabular format. the viral genome was amplified directly from positive samples using the superscript iii one-step rt-pcr high fidelity kit according to the manufacturer's instructions by using the universal influenza a primers (fwuni and rvuni ) as previously described [ ] . purified rt-pcr amplicons were randomly fragmented and used for indexed metagenomic library construction utilizing the illumina truseq nano kit (illumina inc., foster city, ca between and , a total of nasal swabs were collected through active surveillance of imported and local camels ( from imported camels and from local camels). out of the tested samples, samples ( . %) were positive for influenza a virus by rt-pcr (table ) . viral rna was detected only in imported camels from sudan ( samples) and djibouti ( samples) but not local animals (table ). viral rna was detected in both male ( samples) and female ( samples) camels as well as from juvenile camels between to years ( samples) and those older than years ( samples) ( table ) . viruses could not be isolated from any of the positive samples in madin-darby canine kidney cells even after consecutive passages most probably due to the low viral load as shown by the high ct values, which varied from . to . (table ) . these results were confirmed for samples by conventional rt-pcr using the same primers used in the real-time rt-pcr targeting a conserved ~ bp fragment in the m gene of all influenza a viruses. query blastn of the obtained partial sequences of the fragments from these specimens further confirmed these results with > % sequence identity with at least or mismatches to multiple influenza a viruses subtypes (supplementary table s ). this analysis did not result in any definitive determination of the circulating subtypes as expected, because the used primers target a highly conserved region in all influenza a viruses (supplementary table s ). the obtained sequences were identical for samples spc , spc , and spc collected from djibouti in march with and mutations in the other samples (spc and spc ) obtained from camels from sudan and djibouti, respectively, at different time points (figure and table ). unfortunately, other trials to amplify other targets failed to generate products for sequencing possibly due to rna degradation and low viral load as well as the inability to use subtype-specific primers, especially as the exact subtypes were unknown. therefore, positive swab samples (spc and spc ) were analyzed by ngs for further confirmation. upon metagenomic sequencing of the samples, a total of out of and out of high quality reads that matched influenza a sequences in the influenza virus database by blastn were obtained from samples spc and spc , respectively. de novo assembly of these reads resulted in and contigs from samples spc and spc , respectively. query blastn of these contigs returned closely related viruses that belonged mostly to human and swine influenza a h n strains isolated between and from different countries (supplementary table s ). however, some strains from other subtypes such as h n , h n , and h n also were observed at lower frequencies (supplementary table s ). the pb contig ( bases) from both samples were identical and matched a fragment in the pb gene corresponding to the region between nucleotide to with > % identity and a minimum of mismatches. out of the top matches, were h n strains and were h n strains (supplementary table s ). blasting of the bases contig from segment in the spc sample showed > % identity match to residues to in the m gene of influenza a viruses with a minimum of mismatches with h n , h n , and h n strains out of the top matching sequences. the de novo assembled reads from segment of spc sample resulted in contigs ( and nucleotides) that matched regions corresponding to - and - in the ns gene of influenza a viruses, respectively. although the first contig ( nucleotides) matched h n , h n , and h n strains with > % identity, the second contig ( nucleotides) showed > % identity match to h n , h n , and h n strains as well as unknown or mixed influenza a isolates (supplementary table s ). emerging and re-emerging pathogens are potential pandemic threats that are often originate from animals and spread to humans [ ] . such threats could have a global impact on the public health and the economy. therefore, it is crucial to implement early detection, prediction, and risk assessment of pathogens in their animal reservoirs as a one-health approach for proper preparedness to minimize their potential spread to humans. we provide the first molecular evidence of influenza a virus circulation in dromedary camels imported from african countries (sudan and djibouti) but not in local camels from saudi arabia. our data suggest that dromedary camels could represent a potential unknown permissive host and zoonotic source for influenza a viruses. although the partial sequencing data obtained in this study point towards strains closely related to human and swine influenza a h n isolates obtained between and , it is clear that use of short fragments from highly conserved regions of internal genes are not definitive. unfortunately, we were not successful in isolating any virus from the collected samples for better characterization or able to obtain long genome sequences to accurately determine the subtype of these viruses. furthermore, the identical partial influenza rna sequences from different camels arriving from the same origin on the same day as well as the detection of viral rna from animals arriving from different countries at multiple time points over years reduces the possibility of environmental contamination or simple respiratory exposure to infected humans or animals. however, such evidence is not sufficient, and more studies are needed to confirm whether the detected viruses in camels are a result of a natural self-sustained infection or cross-species spillover from humans or pigs. nonetheless, previous productive experimental infection of camels with influenza a h n virus and their seroconversion, in addition to the detection of neutralizing antibody in farm and free ranging camels, clearly provide convincing evidence of the permissiveness of camels to influenza a viruses [ , , ] . although there is no report of human influenza infection due to contact with camels, the role of camels in human infections cannot be excluded, especially in high risk individuals who are in continuous contact with these animals directly or indirectly. the possible risks involved in interspecies transmission of influenza viruses and the odds of reassortment and coinfections in camels are also a big concern. the transmission of these viruses from camels to humans or pigs or vice versa cannot be confirmed and requires further studies to enhance our understanding of influenza ecology and epidemiology in camels and their role in influenza emergence. future studies should focus on virus isolation, full genome sequencing, and using hemagglutinin inhibition assays in order to determine accurately the possible circulating influenza a subtypes in dromedary camels. it is of note that the detected influenza a viruses were from asymptomatic animals, and the pathogenesis and transmission of this virus in camels are not known apart from previous experimental infection in bactrian camels [ ] . in conclusion, we provide the first molecular evidence of influenza a virus infection in dromedary camels, suggesting a possible role for dromedaries in influenza zoonosis or infection to other livestock. our data as well as previous reports suggest that influenza a virus could cause a sustained infection in these animals, highlighting the need for enhanced field surveillance for influenzas viruses as well as other pathogen in dromedary camels to help implementing better preventative one-health plans and programs. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. trypanosomiasis of camels (camelus dromedarius) in algeria: first report camelus dromedarius brucellosis and its public health associated risks in the afar national regional state in northeastern ethiopia molecular and immunological characterization of hyalomma dromedarii and hyalomma excavatum (acari: ixodidae) vectors of q fever in camels middle east respiratory syndrome coronavirus infection in dromedary camels in saudi arabia middle east respiratory syndrome coronavirus infection in non-camelid domestic mammals outbreaks of middle east respiratory syndrome in two hospitals initiated by a single patient in daejeon a reassortant h n influenza a virus caused fatal epizootics among camels in mongolia equine influenza a(h n ) virus isolated from bactrian camel detection of influenza antibody in animal sera from kassala region, sudan, by agar gel diffusion test preliminary survey for antibodies against respiratory viruses among slaughter camels (camelus dromedarius) in north-eastern nigeria serologic evidence for influenza c and d virus among ruminants and camelids world health organization. who information for the molecular detection of influenza viruses single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza a viruses public health. pathogen surveillance in animals we thank king abdulaziz city for science and technology for their generous funding and support.finanacial support. this work was supported by king abdulaziz city for science and technology through the mers-cov research grant program (number - ), which is a part of the targeted research program.potential conflicts of interest. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -sspcz t authors: chen, shi; robinson, patrick; janies, daniel; dulin, michael title: four challenges associated with current mathematical modeling paradigm of infectious diseases and call for a shift date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: sspcz t mathematical models are critical tools to characterize covid- dynamics and take action accordingly. we identified major challenges associated with the current modeling paradigm (seir) that hinder the efforts to accurately characterize the emerging covid- and future epidemics. these challenges included ( ) lack of consistent definition of “case”; ( ) discrepancy between patient-level clinical insights and population-level modeling efforts; ( ) lack of adequate inclusion of individual behavioral and social influence; and ( ) allowing little flexibility of including new evidence and insights when our knowledge evolved rapidly during the pandemic. therefore, these challenges made the current seir modeling paradigm less practical to handle the complex covid- and future pandemics. novel and more reliable data sources and alternative modeling paradigms are needed to address these issues. the covid- pandemic has swept the globe with unprecedented health, social, and economic consequences [ ] . we have used an array of state-of-the-art science and technology breakthroughs to understand this pandemic, including nextgeneration sequencing to rapidly sequence the genome of sars-cov- virus, deep learning to identify covid- patients from computed tomography scans, and big data to track human movements and predict hotspots of outbreaks. researchers, clinicians, and public health officials rely on mathematical models to characterize and predict the covid- epidemic, derive critical epidemiological metrics (eg, the basic reproduction number r ), evaluate various intervention strategies, and optimize resource needs [ ] . as of july , , > articles of covid- modeling have been peer-reviewed and published, with many more available on preprint archives. more than % of the current efforts adopt the susceptible-exposed-infectious-recovered (seir) paradigm, which is expressed in ordinary differential equations. seir models are mechanistic models developed almost a century ago [ ] . we have identified substantial interrelated limitations of this modeling paradigm that make it inadequate to address the current covid- and future pandemics. therefore, we advocate for a modeling paradigm shift for emerging and re-emerging epidemics. first, there is a substantial discrepancy between current molecular diagnosis of covid- and definition of "case" based on host symptoms in the original seir model. the original definition of "case" was not imagined in light of caveats of today's molecular techniques. for covid- , the lag between testing and reporting, variability of reliability and access to testing across time and regions, and lack of accurate accounting of asymptomatic/presymptomatic patients all contribute to the "iceberg" phenomenon [ , ] . these issues have a massive bearing on seir model formulation and consequently undermine their application to accurately characterize the covid- pandemic and provide evidence-based support for decision-makers. in addition, the lack of consistency of input across regions and among various model formulations makes cross-model comparison and validation extremely difficult. second, seir models are formulated at the population level. an important discrepancy exists between patient-level clinical information and population-level modeling for public health. especially, exposed (e) and infectious (i) states characterize the epidemic at the population level, ignoring important clinical variations among individual patients. a single and universal e state is assumed to be unable to infect others. similarly, a single i state does not reflect varying clinical severity and prognosis of individual patients (eg, asymptomatic, presymptomatic, mild, severe, and critical stages). current molecular diagnosis based on quantitative reverse transcription polymerase chain reaction (qrt-pcr) and antigen tests has already been able to provide much more detailed, patient-level quantitative pathogen load information. seir models cannot quantify the potential role of super-spreading patients who cause a disproportionately large number of new cases. superspreading can be the consequence of individual clinical characteristics (eg, supershedding of virus, which can be identified by qrt-pcr) and/or behavioral aspects (eg, supercontacting), neither of which are properly addressed in the population-level seir models. third, there is a lack of adequate inclusion of individual behavioral and social influence in seir models. infectious disease epidemics have a substantial social aspect and public health implication. it is imperative to include varying degrees of interventions such as social distancing, stay-at-home, and shelter-in-place orders at different times and across different regions. the assumption of homogenous mixing of s with i state individuals in the seir model is therefore invalid during covid- . even with more spatially explicit metapopulation models [ ] , homogeneous mixing at smaller spatial scales (eg, within a state, county, or city level) is still questionable, as some people can stay home and some are essential. in addition, the regional variability of individual sentiment and behavior, for example, whether to obey or enforce these orders, is essential to determine in order to predict the trajectory of the covid- pandemic, but is generally not included in the seir models. fourth, our understanding of the interrelated clinical, public health, and social system of covid- has rapidly evolved. in the original paper describing the seir approach, the model was applied retrospectively when the epidemic had ended, revealing most clinical and epidemiological information [ ] . seir-type mechanistic models allow little flexibility for new evidence and insights without substantially changing model structure and estimation of r . compared with other alternative approaches, it is especially difficult to characterize the beginning of the ongoing covid- pandemic with the seir model, given that many aspects of the disease remain unclear (eg, asymptomatic transmission, superspreading, and zoonotic transmission pathway) and reported data are vastly underestimated [ , ] . estimation of the r value has been raised several iterations from to . over the course of the epidemic [ ] . as this is an exponential growth term, any small change of r value can lead to vastly different public health consequences. this variability may lead to incorrect conclusions for decision-makers who rely on r to evaluate situations and take actions such as reopening. additionally, the conclusion that an epidemic will die out when r < holds true only for deterministic seir models, but is not necessarily valid for stochastic models. given the complexity of the covid- pandemic, formulating covid- as a deterministic system is an oversimplification. therefore, the lack of a comprehensive understanding of the covid- pandemic and accurate data makes current modeling efforts inconsistent, contradictory, and confusing. in addition, few studies publish the accompanying codes, undergo rigorous external appraisal, and revisit the original model with updated knowledge. unlike other aspects of covid- , which are less directly related to the public, numbers in epidemic trajectory often appear on headlines in major news outlets and social media and lead to unintended social consequences such as confusion, fear, and anger. worse still, inconsistency in modeling efforts is an easy and vulnerable target for political spin [ ] . we have made tremendous progress in the diagnosis, treatment, and prevention of covid- . however, the near -year-old seir model is a rusty weapon in our arsenal against this unprecedented pandemic. the seir modeling paradigm is less practical to handle the complicated clinical, public health, and social system of the covid- pandemic. in addition, relying on a single r value to summarize such a complicated system is fraught. in response, we suggest the following strategies. first, seir model assumptions should be carefully evaluated before deployment. second, alternative modeling frameworks and novel data sources are required to accurately characterize and respond to the covid- pandemic. these alternative frameworks include cross-scale models that incorporate both the pathogen and hosts, agent-based models that explicitly incorporate individual-level characteristics, and currently underexplored data-driven machine learning and deep learning models that are not prone to manmade biases in model hypotheses. furthermore, mechanistic models (such as the seir model) complement data-driven models. ensemble models across different types of models can provide a less biased characterization of the covid- epidemic. new data sources such as social media, electronic health records, and molecular "-omics" can identify possible asymptomatic patients, infer human behavioral aspects, and facilitate tracking transmission chains. we urge our colleagues to consider the challenges in the current seir modeling paradigm, to carefully evaluate a model's effectiveness in the covid- and other pandemics, and to consider the complicated clinical, behavioral, and social aspects. coronavirus disease (covid- ) situation report nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china: a modelling study a contribution to the mathematical theory of epidemics substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov ) antibody surveys suggesting vast undercount of coronavirus infections may be unreliable the reproduction number of covid- is higher compared to sars coronavirus conservatives who detest climate models add a new target: coronavirus models potential conflicts of interest. s.c., p.r., d.j., and m.d. have no conflicts of interest to declare. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed.patient consent. there were no human subjects involved in this study. key: cord- - z wnj authors: spellberg, brad title: alignment with market forces: the “re-whithering” of infectious diseases date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: z wnj given constant emergence of new infectious threats, infectious diseases (id) should be one of the most attractive medical specialties to students and trainees. yet, id fellowship programs continue to not fill in the match, and id remains among the lowest paid specialties. approximately years after dr. petersdorf first asked the question, we find ourselves once again wondering, “whither infectious diseases?” to answer this question, and align with predominant us market forces, id experts should push for the following: ( ) restrictions regarding utilization of id diagnostics and antimicrobial agents; ( ) pay-for-performance measures regarding antimicrobial prescribing rates; and ( ) healthcare reform as called for by the american college of physicians to move away from fee-for-service medicine. einstein said, “continuing to do the same thing over and over and expecting a different result is the definition of insanity.” we must move towards alignment with market forces, to benefit our patients, society, and our colleagues. the last several decades have continually reminded the world of how important infectious diseases (id) remain to the health and welfare of people all over the planet. anthrax scared americans in . severe acute respiratory syndrome (sars) terrified the world in . in , west nile virus became a global problem, from seemingly out of nowhere. in the first decade of the st century, id experts brought forth astounding advances in diagnostics and therapeutics that converted human immunodeficiency virus (hiv)/acquired immune deficiency syndrome from a death sentence to a manageable, chronic disease. meanwhile, the world was in the midst of a burgeoning crisis of rising antibiotic resistance and a collapse of new antibiotic development. in the years that followed, the h n influenza pandemic struck. new therapies became available that made hepatitis c virus curable. ebola once again terrified the world in , followed by the zika scare in . moreover, years of intensive id effort on the antibiotic resistance front have begun to pay off, with promising very recent declines in antibiotic resistance rates, combined with a surge of new antibiotics becoming available [ ] [ ] [ ] . and then of course, the once-ina-century global coronavirus (covid- ) pandemic struck [ ] [ ] [ ] . within weeks, diagnostics became available for sars coronavirus , within months therapeutics began to become available, and we anticipate a vaccine within to years. infectious diseases experts once again became media celebrities. history has shown us that new infectious threats continually emerge, and successes have continually followed. surely then, the id community must be now basking in the glow of recognition and the public need for top talent to come into the id field. indeed, some might speculate that the covid- pandemic alone would lure top talent into the field, as hiv did years earlier-or not. after decades of failed efforts to change, id remains very near the bottom of the renumeration ladder amongst physicians [ ] . this poor remuneration is in an era of ever-worsening, crushing medical student debt, the average of which has doubled since [ ] . indeed, id practitioners are of only subspecialties remunerated below general internists in the united states [ ] , raising the obvious questionwhy should top talent choose to spend or more additional years in training to end up making less money? whether students and residents are interested in the concepts of id or not, the ratio of debt to income for id relative to other specialties is a substantial deterrent to top talent entering the field [ ] . in , despite years of effort to reverse the trend, more than one third of us id fellowships did not fill, and % did not match any candidates at all [ ] . what has gone wrong? the answer is very simple. the field of id has never adapted to the reality of market forces. in , dr. robert petersdorf, legendary id physician and luminary of internal medicine, published an article in the new england journal of medicine in which he predicted the end of id as a specialty. his exact quote was, "even with my personal loyalty to infectious diseases, i cannot conceive of the need for more infectious disease experts [ie, graduating fellows] unless they spend their time culturing each other" [ ] . nearly a decade later, dr. petersdorf expanded on this theme in an incredibly prescient keynote lecture at the annual meeting of the infectious diseases society of america titled, "whither infectious diseases? memories, manpower, and money" [ ] . he said, "in a fee-for-service environment…infectious disease practitioners have difficulty in making a living. there are few or no procedures. there is a lot of uncompensated phone time, and there is the need to visit several hospitals and spend a good deal of time traveling. in academic medical centers, infectious disease divisions are almost invariably loss leaders, and i know of few that are not heavily supported by university salaries, hospital salaries, and grants. infectious disease divisions do not earn enough in practice to make a go of it and also require subsidies from the higher-earning divisions in their parent departments" [ ] . these realities called out by dr. pedersdorf years ago remain just as true today, leading us to again ask in , whither infectious diseases? some years ago, drs. liise-anne pirofski and arturo casadevall pointed out to me another flash of insight. one of the predominant handicaps of the id clinical specialty is that there is nothing we do that no one else can do. only oncologists prescribe cancer chemotherapy. only cardiologists do cardiac caths. only surgeons take patients to the operating room. what is it that only id practitioners do? we know antibiotics better than anyone, but anyone, up to and including the nurse practitioner at the walk-in clinic in the pharmacy on the corner, can prescribe them. we understand how to establish a microbial etiology of infections, and distinguish them from colonization, but there is little financial pressure on health systems to value this skill. we know hiv care better than anyone, but hiv fellows can be generalists, not subspecialists. viral pandemics may be infections, but they hit emergency medicine, hospitalists, critical care doctors, and primary care doctors harder than they hit the id specialists. there are no diagnostic tests or therapeutic options that only we can prescribe. add to this realization the fact that in a fee-for-service environment, the operating budgets of hospitals are highly dependent on high margin procedures [ ] [ ] [ ] , not cognitive encounters. infectious diseases practitioners may be better at diagnosing and treating infections than those who practice other specialties, but to what financial advantage to healthcare systems that hang on by their fingernails with operating margins under % [ , ] ? health systems have little room for expansion of costs into low return-on-investment service lines. how can the advantages id experts bring be monetized to justify higher id salaries? i am the chief medical officer of a large public hospital. like my colleagues in the c suite, i am responsible for ensuring that our hospital stays as close to within budget as is humanly possible [ ] . running deeply in the red threatens hospital closure, harming the hundreds of thousands of patients per year we serve, and putting out of work people. so, even though i am an id expert and love my clinical and research work, is it realistic to think that i can artificially inflate id salaries at my hospital above the level the market will bear? no, it is not. and if you cannot convince me to do that, good luck convincing anyone else. infectious diseases practitioners simply do not bring in revenue in a way that makes them a priority to health system operating margins in a fee-for-service environment. the encounter-based, fee-for-service healthcare payment model inherently cripples cognitive specialties' remuneration relative to proceduralists. cognitive services will never compete with the value that procedural encounters bring in a fee-for-service healthcare system. market forces are intrinsically against us. dr. petersdorf understood this nearly years ago. for years, id representatives have lobbied for better reimbursement for id practitioners through the medicare relative value scale (rvs) update committee (ruc). these efforts are meritorious and should and will continue. nevertheless, they would be likely much more effective if the lobbing efforts were backed by and aligned with market forces. for example, only an orthopedic surgeon can implant an artificial hip; they have a monopoly, with no competition. if their reimbursement fell such that the specialty became less attractive, and the number of trained orthopedic surgeons fell, patients would demand access, and the imbalance of supply-demand for hip surgeries would intrinsically drive up reimbursement. however, all licensed practitioners function as competition for id. if the number of id specialists decline, we may argue that quality of care will decline, but there will be plenty of other practitioners who can do what the id practitioners can do. there is no market-forces alignment with lobbying for higher rvu reimbursement. it is just an argument of merit and quality, with no economic market force behind it. are there data that support this assertion? absolutely. a recent analysis underscored how few id specialists there are across the united states to handle the covid- pandemic [ ] . years of lobbying for rvu increases have not led to changes in relative reimbursement or reversed the decline in fellowship applicants and trained id physicians. in the absence of id specialists, many other types of providers care for patients with covid- . the covid- pandemic has not led to reversal of the problem, but rather it further exposed this inequity. what we must do is change the interaction between our specialty and the healthcare system such that id work becomes aligned with market forces. there are practical solutions at hand, but they will require legal and/or regulatory changes. therefore, they will require a shift in emphasis of our specialty lobbying efforts. these solutions would allow our specialty to work in concert with market forces rather than against them. first, id practitioners have unique expertise in the diagnosis and treatment of infections, which can lead to less antimicrobial resistance and superinfections, better outcomes, and lower cost for patients and health systems. unfortunately, that unique expertise is hard to monetize. anyone can read the result of a diagnostic or antimicrobial susceptibility study in the electronic medical record. in addition, anyone can prescribe an antimicrobial agent. however, only an expert understands whether further diagnostics (eg, molecular studies) are necessary to benefit the patient and/or public health. it also takes an expert to know specifically what to prescribe and, perhaps more importantly, when not too. nevertheless, nothing stops nonexperts from doing this work now, leaving id practitioners unable to monetize that hard-earned expertise. granting the ability to any licensed practitioner, with no specialty training, to interpret complex diagnostic or susceptibility results, or prescribe powerful, new antimicrobial agents, seems antithetical to health of the public [ ] . only those who have undergone specialized id training, whether by accredited training or certification course, should be allowed (eg, via law, regulation, or medical staff credentialing) to interpret diagnostic/ susceptibility results or prescribe newly approved antimicrobial agents [ ] [ ] [ ] . this change would have the potential to improve prescriptions, decrease antibiotic abuse, diminish selective pressure driving antibiotic resistance, and decrease cost. all of this would be of great advantage to our patients and to public health. it would also have the effect of finally granting to id practitioners alignment with market forces, by providing us something that only we can do, much as oncologists and proceduralists have long had. second, we must push to mandate public reporting of antimicrobial prescriptions at the system level and linking pay for performance measures to such reporting [ , ] . systems that use at the highest end of antimicrobial agents, adjusted for disease severity, should receive payment penalties, whereas systems at the lower end receive payment bonuses. this construct is built upon the success of infection prevention, in which public reporting and pay-for-performance measures have successfully driven down hospital-acquired infection rates. as national-level financial penalties and rewards come into play, they will motivate health system c-suites to prioritize hiring and funding id experts to lead and staff antibiotic stewardship programs to improve the financial situation of the health systems [ ] . we would finally achieve true alignment with id expertise and market forces governing health system operating margins. moreover, society would benefit from diminished selective pressure driving resistance, prolonging the efficacy of life-saving therapies (including future biological therapies such as phage or immune modulatory therapy). third, we should be pushing for true reform to the payment structure of our healthcare system. the us healthcare system is by far the most expensive in the world, by any measure, and for that cost it delivers bad outcomes, including higher mortality rates and shorter life spans than peer nations [ ] . the fee-forservice basis of payment is a core driver of this high cost and bad value. paying for each episode of care, and in particular paying more for expensive, potentially dangerous procedures, encourages excess care delivery, which drives the operating margins of healthcare delivery entities [ ] . expensive, high volume, dangerous procedural-based, fee-for-service encounters may be bankrupting the united states as a whole, but they make money for hospitals and health systems. that market force discrepancy between societal and health system advantage is not in the best interests of patients, doctors, or society as a whole. in contrast, payments that are made for population-based healthcare favor judicious use of resources to maximize benefit to society. cognitive specialists become the gatekeepers of precious limited resources available for healthcare in the latter model. therefore, in the reformed model, cognitive specialists who keep people from becoming sick and minimize waste and harm become more valuable to healthcare payers than those who conduct expensive procedures on patients who are already sick. the american college of physicians has recently called for fundamental healthcare reform in the united states based on just this principle [ ] [ ] [ ] [ ] . our specialty has been unfortunately silent in the aftermath of this call for change, to our own detriment. infectious diseases will always plague the world. the question is, how will our subspecialty evolve over time when our work and remuneration are in opposition to the predominant feefor-service market forces that govern us healthcare? years of pressing for incremental tweaks to physician reimbursement in this system have thus far not worked to change the equation. after so many years of effort, continuing to lobby without alignment with market forces seems unlikely to change reimbursement. if we want to fundamentally change the equation of id practitioner value in the us healthcare system, we need to change id work and remuneration to become aligned with market forces. this situation can be remedied with advocacy and lobbying, and it must be. furthermore, once having mustered the political will to do so, the case should be easy to make to the public, because it is clearly in the public's and our patients' best interest to have id experts as the stewards of infectious-related diagnostic and therapeutic modalities. we can limit waste and improve precision, which improve patient and population outcomes, and at lower cost to the system at large. however, thus far, we have lacked the will to make this case. it is time to do so. ensuring sustainability of needed antibiotics: aiming for the dart board sustainable discovery and development of antibiotics -is a nonprofit approach the future? multidrug-resistant bacterial infections in u.s. hospitalized patients covid- -new insights on a rapidly changing epidemic coronavirus infections-more than just the common cold covid- -navigating the uncharted average student loan debt for medical school charting the future of infectious disease: anticipating and addressing the supply and demand mismatch id-fellowship-match-results-slight-declinesfrom-last-year/id the doctors' dilemma whither infectious diseases? memories, manpower, and money sb -operating-room-procedures-united-states- . pdf. accessed the list is in: hospitals' most profitable specialties factors of u.s. hospitals associated with improved profit margins: an observational study operating margins stabilize, but not-for-profit hospitals still vulnerable moody's finds how to pitch an antibiotic stewardship program to the hospital c-suite where is the id in covid- ? new societal approaches to empowering antibiotic stewardship the future of antibiotics and resistance seven ways to preserve the miracle of antibiotics bankrupt, and dying: how to solve the great american healthcare rip-off the american college of physicians' endorsement of single-payer reform: a sea change for the medical profession medical practice and quality committee of the american college of physicians. envisioning a better u.s. health care system for all: health care delivery and payment system reforms health and public policy committee and medical practice and quality committee of the american college of physicians. envisioning a better u.s. health care system for all: a call to action by the american college of physicians engel ls; health and public policy committee of the american college of physicians. envisioning a better u.s. health care system for all: coverage and cost of care key: cord- -qdehf rb authors: yun, heather c.; young, adam n.; caballero, manuel y.; lott, lisa; cropper, thomas l.; murray, clinton k. title: changes in clinical presentation and epidemiology of respiratory pathogens associated with acute respiratory illness in military trainees after reintroduction of adenovirus vaccine date: - - journal: open forum infect dis doi: . /ofid/ofv sha: doc_id: cord_uid: qdehf rb background. adenovirus (ad) has long been the predominant cause of acute respiratory illness (ari) in military trainees. in , live oral ad vaccines for serotypes and were reintroduced into us basic military training populations. this study evaluated the impact on clinical presentations and other respiratory pathogens. methods. the center for advanced molecular detection at joint base san antonio-lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among air force trainees presenting for care of ari. results. from june to august , trainees enrolled and were tested for selected respiratory pathogens. post-vaccine introduction (vi), reported systemic symptoms were less frequent, including fever ( % vs %) and myalgia ( % vs %; p < . ). median temperature and heart rate decreased ( . vs . °f, vs beats per minute; p < . ). ad detection decreased for all ad ( % vs %), ad ( % vs %), ( % vs %), ( % vs %), and ( . % vs %); p < . ). rhinovirus and cases with no pathogen identified increased in frequency ( % vs %, % vs %; p < . ). conclusions. acute respiratory illness in military trainees post-vi is associated with decreased severity of systemic symptoms and reduced fever and heart rate. marked reductions in frequency of ad serotypes are seen, including those in the vaccine, with no serotype shift. however, detection of several other respiratory pathogens, most notably rhinovirus, is observed in increasing proportions, and a majority are now undiagnosed clinical syndromes. reduction in fri due to ad [ ] . however, the military was the only purchaser of vaccine, which was produced by a sole manufacturer, and vaccine production ceased in when funding requirements for updating manufacturing facilities were not met. attempts by the department of defense to find an alternative solution were unsuccessful, and existing vaccine stocks were depleted in . ad quickly re-emerged as the major cause of morbidity, causing numerous outbreaks with both vaccine and nonvaccine serotypes, and directly resulting in approximately death per year [ ] [ ] [ ] [ ] [ ] . from to , ad ( primarily serotype ) caused % of all fri in the basic training environment [ ] . it is estimated that associated medical care and time lost from training resulted in costs of $ -$ million per year [ , ] . in , the us food and drug administration's (fda) newproduct approval process was initiated for resumption of production of ad and ad vaccines by a new manufacturer [ ] . phase vaccine trials demonstrated ( ) % efficacy for ad and ( ) ad (which was not circulating at the time) seroconversion rates of % [ ] . in , the vaccines were approved by the fda and reintroduced nearly simultaneously at all us military basic training locations in october/november of that year. since then, surveillance reports have consistently demonstrated great reductions in fri and ad-related illness. early data indicated a % decrease in fri, and proportions of collected specimens positive for ad decreased from % to % in the months surrounding vaccine introduction (vi) [ ] . nearly all of this was attributable to ad , with rare detections of serotypes , , , and , and cases involving vaccine-type p. follow-up data published in late , evaluating surveillance data from to , reported reductions in ad disease burden from . to . cases/person-week [ ] . the authors estimated that the current vaccines prevent cases of fri, - hospitalizations, and death per year. after vi, ad became the most prevalent circulating serotype, although actual number of cases detected decreased from approximately per year to in . this large study reported comprehensive surveillance data for overall ad and fri, but clinical data were not captured. whether the clinical presentation of those trainees who do present for care with a respiratory illness has changed post-vi is unclear. because respiratory illness remains a leading cause of presentation for care among military trainees, understanding of trends in clinical presentation and emerging, non-ad respiratory pathogens in the post-vi era requires evaluation. the purpose of this study was to evaluate ( ) changes in clinical presentations of ari pre-and post-vi, and ( ) reductions in proportions of disease due to ad. we also sought to further evaluate for evidence of nonvaccine type serotype shift and to determine whether the frequencies of common non-ad respiratory pathogens have changed after vi, in trainees presenting for care of ari, which have not previously been described in the published literature. joint base san antonio (jbsa)-lackland, texas, is the sole basic military training site for the us air force. training lasts . weeks, with - recruits present at any given time, and approximately training per year. units consisting of - individuals train together and live in open bay dormitories. the population is approximately % male. ill or injured trainees present for care at an outpatient medical clinic; those with respiratory illness and fever are then cohorted until well enough to return to training. those requiring hospitalization are admitted to the local military tertiary care hospital. vaccines, including ad vaccine beginning week of , and influenza vaccine seasonally, are administered during the first week. in , influenza vaccine against pdm h n influenza was available and administered after december , . oseltamivir was used for prophylaxis of close contacts of confirmed influenza cases throughout the study period. prophylaxis for streptococcus pyogenes is also administered to all trainees during the first week, consisting of benzathine penicillin, or azithromycin for penicillin allergic individuals. since , the center for advanced molecular detection ( th medical wing/science and technology, air education and training command) has prospectively evaluated epidemiology of respiratory pathogens and novel technologies for detection. for the purposes of this substudy, data were evaluated from june to august . ill recruits presenting for clinical care of ari at the outpatient clinic or hospital were approached by study personnel regarding participation. inclusion criteria were met if the trainee was ≥ years of age and endorsed any symptom of respiratory infection, including cough, coryza, sore throat, or nasal or sinus congestion. for those consenting to enroll in the study, demographic information was collected, along with a symptom questionnaire, including self-reported stress levels, and clinical signs, including vital signs and physical examination findings recorded during the medical encounter. provider diagnoses given at the time of the visit were also recorded when available. provider clinical diagnosis extracted from the note, if any, associated with the visit, was also explored with reference to diagnoses of upper respiratory tract infection (urti) vs lower respiratory tract infection (lrti). the diagnoses, "rhinitis, conjunctivitis, otitis, sinusitis, pharyngitis, sore throat" were considered to be representative of urti, and the terms "bronchitis, pneumonia" were representative of lrti. terms including "common cold", "viral syndrome", "fever", or "cough" were not included in the urti vs lrti analysis given their lack of anatomical description. nasal washes and throat swabs were collected for polymerase chain reaction (pcr) assays. duplicate presentations for multiple ari-related visits were excluded; each case represents an individual subject. specimen processing was performed as previously described [ ] . respiratory specimens were characterized daily by pcr on applied biosystems (abi) and htfast (applied biosystems, ca) and the viia real-time pcr systems. specimens were tested for ad ( panad and serotypes , , , , , , , and ); rhinovirus; influenza a, including h and h ; influenza b, enterovirus, human coronaviruses oc and e, bocavirus, human metapneumovirus (hmpv), parainfluenza virus type (hpiv), s pyogenes, streptococcus pneumoniae, mycoplasma pneumoniae, and chlamydophila pneumoniae. all primer and probe sequences used have been previously reported (association of public health laboratories guidelines for realtime reverse transcription-pcr assays of influenza respiratory viruses; non-influenza respiratory viruses from clinical respiratory specimens; respiratory bacterial pathogens) [ , ] . influenza a and b, enterovirus and rhinovirus thermocycling conditions were minutes at °c, minutes at °c, followed by seconds at °c and seconds at °c for ×. coronaviruses, hmpv, and hpiv thermocycling conditions were minutes at °c, minutes at °c, followed by seconds at °c and minute at °c for ×. streptococcus pneumoniae, s pyogenes, and bocavirus thermocyling conditions were minutes at °c followed by seconds at °c and seconds at °c for ×. thermocycling conditions for m pneumoniae and c pneumoniae were minutes at °c, minutes at °c, followed by seconds at °c and minute at °c for ×. analyses were performed using spss (spss, version . , spss). dichotomous variables were compared using χ or fisher's exact test as applicable. continuous variables were analyzed using mann-whitney u test for nonparametric data. all reported p values are -tailed with statistical significance set at <. . subjects provided voluntary, written informed consent in the presence of ombudsmen, and the study was approved by the jbsa-lackland institutional review board. this research was conducted in compliance with all applicable international and federal regulations regarding protection of human subjects. from june to august , trainees enrolled and had specimens tested for respiratory pathogens. ad vi took place week , ; % of this cohort enrolled pre-vi vs % post-vi. none of the pre-vi subjects received ad vaccine, vs % post-vi. overall, % were male, with a median age of years. enrollments ranged from to a peak of in for years with a complete calendar-year of data. trainees reported a perceived stress level of on a -point likert scale. post-vi, the male predominance of enrolled subjects decreased from % to % (p < . ) (see table ). clinical characteristics are presented in table . before vi, % of subjects had a recorded oral temperature > . °f, vs % afterward. one or more diagnoses representative or uri, lrti, or both, were present in . % pre-vi and . % post-vi. terms associated with lower respiratory tract infection (lrti) were more commonly included post-vi ( . % vs . %, p < . ) and terms associated with uri were less commonly included post-vi ( . % vs . %, p < . ). those with the diagnosis of "pneumonia" in the post-vi period were predominantly afebrile ( . %). supporting radiographs, if performed, were unavailable. the term "allergic" or "allergy" was included in none of the diagnoses pre-vi, but was included in . % post-vi (p < . ); % of these were listed in combination with some other diagnosis of uri or lrti. clinical signs and symptoms specifically associated with ad vs rhinovirus were also compared, with similar findings as those seen in general for pre-and post-vi (data not shown). the exceptions were the loss of statistical significance between those describing malaise and with abnormal tympanic membrane examinations. those with ad vs rhinovirus also more often described sore throat ( . %, . %, p < . ) and had more documented tonsillitis ( . % vs . %, p < . ). influenza a detections were less frequent post-vi; h accounted for the majority of the pre-vi detections, and these were all in . in subjects with documented fever post-vi (n = ), rhinovirus accounted for the largest proportion of abbreviations: iqr, interquartile range; vi, vaccine introduction. a abnormal examination: any of the following: "decreased breath sounds, rales, crackles, rhonchi, wheezes" for lungs, "abnormal, dull, erythematous, effusion" for tympanic membranes; "gallop, murmur, abnormal rhythm" for cardiac; "abnormal bowel sounds, distended, tender" for abdominal. these (n = ), with influenza detected in cases and any ad in ( serotype , serotype ). twenty-one of these had no pathogen detected the rate of detection of rhinovirus doubled in the post-vi period; an increase in raw numbers of rhinovirus positive enrollments per month was also seen despite lower enrollments in general (see table ). pre-vi, there were . rhinovirus positive cases per week, and . enrolled/week; post-vi, . / week were rhinovirus positive, among . enrolled/week. reintroduction of the ad vaccine in basic training populations has again been extraordinarily successful in reducing the burden of both ad-related respiratory illness and the burden of respiratory illness with fever. % reductions in fri have been demonstrated by others, including at joint base san antonio-lackland where this study was conducted, against the backdrop of a . % reduction in the weekly rate of ad-related illness [ , ] . sustaining the commitment to prevention of ad-related illness in uniquely susceptible trainees will be necessary if history is not to repeat itself. however, prevention of respiratory illness in this population is a complex task. risk factors for transmission of respiratory pathogens will continue to be present in conditions inherent to basic military training. adenovirus, despite its preeminence as a pathogen of interest in this group, has never been the entire story, and large outbreaks of non-vaccine serotype ads have occurred even while vaccine serotypes were circulating [ ] . influenza causes annual epidemics which, in the context of an effective vaccine program, are typically limited in this population, but which can have considerable impact when new strains emerge. in summer and fall of , influenza was responsible for % of fri in those who were tested [ , ] . large outbreaks of pharyngitis caused by s. pyogenes, complicated by acute rheumatic fever, pneumonia, necrotizing skin and soft tissue infections, and other suppurative and immunologic complications, have been reported throughout the past century, prompting widespread use of antimicrobial prophylaxis at training sites [ ] [ ] [ ] . pneumococcal outbreaks have also occurred despite such prophylaxis, including pneumonia and fatal meningitis [ , ] . others, including neisseria meningitidis, bordetella pertussis, m. pneumoniae, and c. pneumoniae, have been well-described in this population [ ] . horizontal efforts at respiratory infection prevention, such as promoting hand hygiene, environmental including gas mask disinfection, cohorting of ill trainees, and respiratory etiquette, will require continued emphasis, even with near-elimination of ad-related illness. however, vertical measures targeting specific organisms have also been demonstrated to have significant impact, with ad vaccine as the prime example, and ongoing exploration into post-vi causes of illness will be necessary to direct further interventions. furthermore, although widespread efforts exist to monitor fri rates and conduct surveillance for common respiratory viruses, not all acute respiratory illness is febrile. clearly, trainees are still presenting for illness, but those without fever, which now represent > % of those presenting for care, will not have respiratory pathogen analysis via dod-directed surveillance mechanisms. few prior data inform clinical differences between those presenting with ad vs other respiratory pathogens. recent comparisons of pdm( )h n influenza and ad, including an analysis from this cohort, corroborated a predominance of coryza and cough presentations for influenza, vs pharyngitis for ad [ , ] . this evaluation again emphasizes a classic presentation of ad-related illness: fever, systemic complaints, and pharyngitis, distinct from the afebrile, coryza/ cough presentations of those presenting post-vi and with rhinovirus. interestingly, documentation of abnormal lung examination findings increased post-vi, as did use of clinical diagnostic terms suggesting lrti, including both bronchitis and pneumonia. it is likely that most of those labelled "pneumonia" were never confirmed with radiographs, and absence of fever with these argues against that diagnosis in this young, otherwise healthy population. the predominant organism identified among these was rhinovirus, which, while not classically associated with lower respiratory disease in healthy adults, has been described including within military training populations [ , ] . nevertheless, the combination of increased lrti diagnoses, and the increase in cough as well as physical exam findings of the same, provide signal of an increase in lrti post-vi which should be explored with targeted research. it is also considerable that, despite a relatively broad panel of respiratory pathogens targeted with molecular methods, > % post-vi had no pathogen detected. some of these may have been noninfectious, as suggested by the increase in clinical diagnostic terms relating to allergies, but this represents a significant research gap. the nature of respiratory illness itself in basic military trainees has changed after reintroduction of ad vaccine, transitioning from a febrile pharyngitis marked by systemic signs and symptoms, to an afebrile, cough and coryza predominant illness. the ecologic niche occupied by vaccine-serotype ad in this population was remarkable, causing approximately % of all fri historically and with % of trainees infected by the end of training [ , ] . during ad vi in , molecular methods for pathogen surveillance were not available; despite this, serotype shift was observed. initially, ad was the only serotype included in the vaccine program, but ad was later added after this emerged and replaced ad as the predominant cause of fri [ ] . since that time, dozens of additional ad serotypes and other respiratory viral pathogens such as bocavirus and human metapneumovirus have been identified. respiratory pathogens cause outbreaks, which may come and go independently of a vaccine program's effect, so changes in frequency must be interpreted with caution. however, it is reassuring that ad has not yet reemerged in this population and, in fact, decreased in frequency since vi, a finding which has been corroborated by others, and potentially related to crossprotection with ad immunity [ , ] . the decrease in frequency of influenza a was driven by the unusually high number of influenza a cases in , which contributed to the total of during the entire study. the trend toward a decrease in s. pyogenes (with no changes in antibiotic prophylaxis during the study period) is potentially biologically plausible with viral coinfection increasing the likelihood of streptococcal illness, although specific associations between ad and s. pyogenes have not been established, and rates of s. pyogenes illness are not known to have changed during the first iteration of the ad vaccine program. the small increases seen in detection of m. pneumoniae, bocavirus and coronavirus oc may be due to chance alone or natural variation, but bear further observation. most significant was the increase seen in detections of rhinovirus, which increased as a proportion of detected pathogens, in rates of positive tests among those tested for rhinovirus, and in raw numbers despite fewer overall enrollments. rhinovirus may be associated with decreased probability of detecting other respiratory viral pathogens, including ad. an evaluation of virus pairs in a pcr-based analysis of co-detections demonstrated a negative association between ad and rhinovirus. while multiple additional respiratory viruses also demonstrated a negative association with rhinovirus, no others correlated either positively or negatively with ad [ ] . a negative interaction between these pathogens has previously been reported in military recruits with and without symptoms of respiratory illness, and with ad, but not rhinovirus, clearly associated with illness [ ] . the most significant strength of the study is the collection of a wide array of respiratory pathogen data alongside a detailed collection of clinical and demographic data, allowing thorough evaluations for ecologic niche replacement, as well as changes in clinical illness, throughout a major change in vaccine administration, in > trainees. others include the high uptake of ad vaccine, and the consistency in access to care, living and training conditions, and preventive medicine measures throughout the study period. the study also has a number of limitations. this is a single center which, although spanning several years, cannot account for natural variability of respiratory pathogens here or at other training sites, and some pathogens were tested for only from a subset of samples. these represent a convenience sample of the overall burden of trainees presenting to medical care for respiratory illness. trainees, for a number of reasons, may be reluctant to self-identify when ill and present for care. while we have no reason to believe this limitation changed over the course of the study, this limits the ability to extrapolate frequencies of detection to rates of disease. since asymptomatic subjects are not captured, it also limits the ability to determine colonization vs correlation with clinical illness. however, study procedures and approaches to enrolling trainees were unchanged over the course of the study period. there may have been increases in healthcare-seeking behavior in during the influenza pandemic, and this year saw the highest number of enrollments over the course of the study. finally, comorbidities in this group were not captured, although significant known comorbidities are typically disqualifying for military accession. in conclusion, reintroduction of ad vaccine in military trainees has markedly reduced the frequency of ad detection in trainees presenting for care of respiratory illness, and been associated with a -fold reduction in the proportion presenting with objective fever. acute respiratory illness has transitioned away from a febrile pharyngitis with systemic signs and symptoms to a predominantly afebrile coryza and cough illness. no evidence of ad serotype shift has been demonstrated, but rhinovirus is emerging as a potential pathogen of importance, and despite a broad array of tested viruses and bacteria, a majority now results with no pathogen identified. respiratory infections are no longer the leading cause of medical encounters among military recruits; now they are the second-leading cause [ ] . their ongoing importance epidemiologically requires continued surveillance and research into additional preventive measures. surveillance snapshot: illness and injury burdens among u.s. military recruit trainees psychological stress and susceptibility to the common cold transmission dynamics and prospective environmental sampling of adenovirus in a military recruit setting epidemiology of adenovirus respiratory infections in military recruit populations control of respiratory disease in recruits with types and adenovirus vaccines adult adenovirus infections: loss of orphaned vaccines precipitates military respiratory disease epidemics. for the adenovirus surveillance group adenovirus transmission-worthy of our attention large epidemic of respiratory illness due to adenovirus types and in healthy young adults outbreak of severe respiratory disease associated with emergent human adenovirus serotype at a us air force training facility in adenovirus-associated deaths in us military during post vaccination period surveillance snapshot: adenovirus among u.s. military recruit trainees prevention of adenoviral acute respiratory disease in army recruits: cost-effectiveness of a military vaccination policy cost-effectiveness analysis of reacquiring and using adenovirus types and vaccines in naval recruits history of the restoration of adenovirus type and type vaccine, live oral (adenovirus vaccine) in the context of the department of defense acquisition system a phase , randomized, double-blind, placebo-controlled study of the safety and efficacy of the live, oral adenovirus type and type vaccine dramatic decline of respiratory illness among us military recruits after the renewed use of adenovirus vaccines evaluation and validation of a real-time pcr assay for detection and quantitation of human adenovirus from clinical samples pring-akerblom p. rapid and quantitative detection of human adenovirus dna by real-time pcr human coronavirus infections in rural thailand: a comprehensive study using real-time reverse-transcription polymerase chain reaction assays retrospective analysis of demographic and clinical factors associated with etiology of febrile respiratory illness among us military basic trainees pandemic influenza virus h n and adenovirus in a high risk population of young adults: epidemiology, comparison of clinical presentations, and coinfection epidemic streptococcal disease among army trainees outbreak of group a streptococcal pneumonia among marine corps recruits-california acute rheumatic fever among army trainees-fort outbreak of pneumonia in the setting of fatal pneumococcal meningitis among us army trainees: potential role of chlamydia pneumoniae infection halting a pneumococcal pneumonia outbreak among united states marine corps trainees respiratory diseases among u.s. military personnel: countering emerging threats frequency of detection of respiratory viruses in the lower respiratory tract of hospitalized adults atypical pneumonia in young men with rhinovirus infections do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections? respiratory illness post ad vaccine • ofid • broad spectrum respiratory pathogen analysis of throat swabs from military recruits reveals interference between rhinoviruses and adenoviruses surveillance snapshot: illness and injury burdens among u.s. military recruit trainees we express our gratitude to dr. sandra valtier and the research coordinators at the camd for recruiting the subjects and assisting in the study logistics. we are also grateful to the trainees who participated in the study.disclaimers. the opinions or assertions contained herein are the private views of the authors and are not to be construed as official or reflecting the views of the department of the army, department of the air force, department of defense or the us government. this work was prepared as part of their official duties and, as such, there is no copyright to be transferred. financial support. the work was supported by the united states air force, th medical wing/science and technology, air education and training command.potential conflicts of interest. all authors: no reported conflicts. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -n yj zdy authors: huang, dayong; shu, wen; li, menglong; ma, juntao; li, ziang; gong, jiajian; khattab, nourhan m; vermund, sten h; hu, yifei title: social media survey and web posting assessment of the covid- response in china: health worker attitudes towards preparedness and personal protective equipment shortages date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: n yj zdy background: understanding health worker awareness, attitudes, and self-confidence in the workplace can inform local and global responses towards emerging infectious threats, like covid- pandemic response. availability of accessible personal protective equipment (ppe) is vital to effective care and prevention. methods: we conducted a cross-sectional survey from february - , to assess covid- preparedness among health workers. in addition, we assessed trends from search engine web crawling and text-mining data trending over the sina weibo platform from january to march , . data were abstracted on chinese outbreak preparedness. results: in the survey, we engaged , persons, of whom , agreed to participate and after an eligibility logic check, , participated ( . %). we accessed internet posts as to ppe availability. health workers satisfied with current preparedness to address covid- were more likely to be female, to obtain knowledge about the sars-cov- outbreak from government organizations, and to consider their hospital prepared for the outbreak management. health workers with more confidence in their abilities to respond were those with more faith in their institution’s response capacities. elements of readiness included having airborne infection isolation room, visitor control procedures, training in precautions and ppe use. both survey and web post assessments suggested that health workers in need were unable to reliably obtain ppe. conclusion: health workers’ self-confidence depends on perceived institutional readiness. failure to maintain available ppe inventory for emerging infectious diseases preparedness suggests a failure to learn key lessons from the - sars outbreak in china. according to the coronavirus disease (covid- ) situation reports of the world health organization (who), sars-cov- infections had been reported from countries, territories, or international conveyances (ships) by august , . china has been classified from a level country for community viral transmission, the highest level of concern based on clusters of cases. who had urged nations to prepare for the threat of autochthonous transmission, noting that emerging cases from secondary transmission now typically lacked a direct link to the original china epicenter. the u.s. centers for disease control and preparedness (cdc) define a pandemic as a global disease outbreak (i.e., multicontinent) in its all-hazards preparedness guide and pandemic infectious threats is health professional preparedness. in the who influenza pandemic plan in , who urged the global community for plans to address "infectious diseases: global alert, global response" . this plan was eerily prescient as to the sars pandemic just four years later. the roles and responsibilities of the who and national authorities in preparing for and responding to an influenza pandemic are identical to what would be needed for other respiratory pandemic threats. health workers are critical for building societal confidence during epidemic outbreaks. they cannot function effectively if they lack personal protective equipment (ppe), essential to ensure continuity of healthcare services during a public health emergency and to avoiding nosocomial acquisitions a c c e p t e d m a n u s c r i p t as of april , , chinese health workers have died, of whom ( . %) were confirmed dead of covid- , according to reports by china central television. at least , medical staff from medical institutions across the country were infected with sars-cov- , including , confirmed cases, , clinically diagnosed cases, and suspected cases. in hubei province alone, , infected cases (> % of the national total) in health workers were reported by february , (no further update was released officially since hospital burdens were eased after a large national-wide medical taskforce was dispatched to hubei province for assistance). we sought to study health worker self-perception of preparedness and ppe availability in , over two decades after the who call for pandemic influenza readiness. our mixed methods study was a two-part effort consisting of: ( ) an online cross-sectional survey using an online electronic questionnaire and ( ) a mining of web text via data crawling of ppe-related postings (fig ) . data crawling is a technique for data extraction from the internet using a crawling agent (automated script) that helps gather publicly available data in very large quantities. our survey was based on the who and cdc preparedness checklists and we targeted licenced health workers, evaluating awareness of, and confidence in covid- preparedness and response at their institutions. we also reviewed policy changes on provision of ppe in china related to the - sars-cov- outbreak. a c c e p t e d m a n u s c r i p t our survey targeted health workers based in hospitals, including physicians, nurses, and others. eligible participants were licensed health workers in practice; given our hubei province focus, this including workers at the front-line of care provision in the midst of the covid- crisis. while we did not indicated exclusion criteria in the recruitment poster (supplemental fig ) , we specified our research aims regarding self-perception of health worker preparedness. online consent was obtained for participation. participants were recruited using two methods. the first was an online advertisement on a the second means of recruitment was engagement via wechat "moments sharing". wechat is a comprehensive package of online services, equivalent to combining apps such as facebook  , whatsapp  , and paypal  . eligible recruited persons providing consent were given a self-administered structured questionnaire online using https://www.wjx.cn/. this "wjx" is similar to surveymonkey  and is more popular and accessible in china. we developed a poster with a qr code to link people to the questionnaire (suppl. fig ) . both the physician service app and the wechat moments sharing methods promoted the poster a c c e p t e d m a n u s c r i p t and encouraged interested health workers to identify the qr code and enter the online survey system. the first page of the questionnaire assessed eligibility and obtained informed consent for those who were eligible. no incentive was provided for survey participation. we studied three main outcome indicators using or - text mining of the weibo announcement searched (in chinese) for "(help or support or donate) and ppe" . weibo is a twitter  -like social media platform in china. people share social, cultural, and historical insights or comments on trending topics via the platform. we crawled text data or scripts of the video of needed ppe including "求助" (help) or "防护服" (gown)or "口罩" (facemask) from https://weibo.com/ from jan , through march rd, using python tm . . . after manually verifying and cleaning the raw data, we the survey data were exported into microsoft excel ® and then manually labelled with the level of the capability of the hospital according to the -tier category in china. through dynamic ip address and the name of the local hospital, we identified the geo-location of the participants and generated two variables of the location as "city" and "province" for each participant. in the case of a conflict between ip address and hospital, we chose the affiliated hospital for location classification. completed databases were analysed after data cleaning using statistical analysis system  (v. . ; sas institute inc, cary, nc, usa). we used univariate and multivariable logistic regression analysis to identify the association between a respondent's current confidence in coping with covid- suspected/confirmed cases and his/her sociodemographic characteristics. crude and adjusted odds ratios (cor and aor) with % confidence interval ( %ci) were calculated for the association of the covariates with the outcome (self-confidence). the variables with p value of < . in univariate analysis were entered into the multivariable backward regression models and only variables with twosided p value of < . or less were considered statistically significant in the final model. a c c e p t e d m a n u s c r i p t the study was approved by capital medical university ethics review board ( sy ). the study protocol, contents, and procedure were explained before survey inception. online consent was obtained for participation. non-identifiable data from the app was collected or analysed per the study protocol. the web-based questionnaire was uploaded february , and taken offline on fig b) . doctors accounted for . % of the respondents, nurses representing . %, and others . %. fewer than half ( %) of participants were satisfied with the protective equipment in the hospital to cope with the covid- epidemic, and . % of respondents were very dissatisfied. nearly three-quarters ( %) of health workers expressed selfconfidence in coping with persons under investigation (pui) or known patients. about half ( %) of the participants expressed confidence in institutional preparedness and its ability to respond to eids in the future (table ) . a c c e p t e d m a n u s c r i p t there were posts of ppe request announcements from our weibo crawl during january to march , . for posts, we were able to do manual city-labelling, narrowing the focus of the request for ppe and mapping respondents' locations (fig ) . weibo posts calling for help or donations of ppe, including gowns, facemasks, and goggles, increased sharply from january to january , and the number of cities that posted requests for urgent help for medical supplies online increased drastically, and then levelled after the lockdown of the city of wuhan, policy guidance was gradually put into place. health workers who were infected were seen in the early stages of the epidemic, correlating with the time of acute shortage of ppe. after centralized management and emergency response protocols and the action of ppe manufacturers to accelerate production and supply mobilization to the hubei province epicenter, the number of health workers being infected decreased significantly (fig ) . a c c e p t e d m a n u s c r i p t suppl. table presents predictors of health workers' satisfaction with current readiness of ppe in their hospitals during the outbreak. multivariable analysis suggested that health workers who were more satisfied with the readiness of the affiliated hospitals were more likely to be female (aor= . , % ci: . - . ), obtain knowledge /information of the sars-cov- outbreak from government sources (aor= . , % ci: . - . ), have airborne infection isolation rooms in their hospital (aor= . , % ci: . - . ), and to think their hospital is prepared for the outbreak (aor= . , % ci: . - . ). suppl. table presents predictors with a sense of confidence in treating patients and confidence in current institutional readiness during the outbreak. those who tended to have higher current confidence to deal with suspected patients were more likely to be male health self-discipline to exercise in order to increase immunity ( %), and rotating the shift times since wearing ppe accelerated a sense of exhaustion in the medical workplace ( %). over half of them recommended compulsory training on self-protection standards. some respondents suggested the need for attention to gender-related vulnerability in crises. one example was for female health workers to be allowed to take breaks during their menstruation due to inconvenience with gowning and consequent potential of increasing infection risks. over % of the respondents complained about an amateurish style of hospital leadership, for instance, exhibiting managerial incompetent to achieve effective responses as well as exhibiting a lack of health care knowledge and professionalism (suppl. preparedness of their hospitals than in their personal readiness. since hospital level preparedness requirements are intensive and complex to battle outbreaks, our finding echoed an ebola virus preparedness report from the u.s. compulsory training on precautions and the application of universal standard guidelines, including ppe use, can reduce occupational infection and increase confidence during a crisis , . health emergency responders should consider integrating grass-root level simulation training for staff (primary and undetermined hospitals, clinics) to increase the capacity and readiness for patient management . we also found that health workers had more trust in the source of information when it was from the government than from other channels. this may be true in china, but could plausibly be the opposite in other nations. chinese health authorities' timely disclosure of epidemic information likely increased a sense of security through viable up-to-date information in late january , , . better hospital infrastructure, worker satisfaction with ppe, and a worker's current sense of confidence in the hospital's current readiness seem to increase self-confidence of health professional staff in addressing eids . outbreaks and epidemics mean that hospitals and frontline care facilities need products in unprecedented quantities . alongside the significant spike in product demand, health care workers can experience fear and panic, devastating the confidence of the public and health workers alike. this occurred when ppe distributors and manufacturers were unable to fill early orders for the sars-cov- programs . hospitals and governments must address the needs for surging supply and stock via tiered advanced planning to cope with different epidemic scenarios , . this phenomenon can also be seen in a c c e p t e d m a n u s c r i p t study strengths were the ability to draw conclusions from mixed methods results. that we could do the study in such proximity to the epidemic's geometric rise ensures the freshness of opinions of our respondents, minimizing recall bias. our study has some limitations. data crawling text information was gathered retrospectively. it may underestimate the actual quantity of postings asking for ppe help since some information that was shared by the institutions may have been taken down when their needs were met. some information over the internet (such as criticisms of local responses) are more likely to be removed than other responses, making the current data an under-estimate of gaps in preparedness. changes in the trend of numbers may reflect either true product shortages or difficulties in supply chains over time. our survey was a convenience web-based sample with a comparatively low response rate, limiting generalizability. however, this method was the only feasible way to avoid intra-person contact in data gathering during the pandemic crisis in china. since our survey was conducted after the ppe supply need was almost met after extreme scarcity, the satisfaction rate of the ppe supply may have been an overestimate. ensuring ppe supply for health workers is an essential inventory component for effective health emergency response, and ppe should be an integrated element in all-hazards emergency preparedness procedures. ppe availability increases a sense of confidence among health workers and reduces nosocomial infection. tiered management, reasonable rotation, specified inventory of ppe for stockpile, and inventories that are ready-for-use for health workers are all vivid lessons from china for consideration by other global infection control fighters. who. coronavirus disease (covid- ) situation report - covid- ). who. rolling updates on coronavirus disease (covid- ) web site all-hazards preparedness guide infectious diseases : global alert, global response approach to prioritizing respiratory protection when demand exceeds supplies during an influenza pandemic: a call to action potential demand for respirators and surgical masks during a hypothetical influenza pandemic in the united states rolling update of those died for combatting covid- evolving epidemiology and impact of non-pharmaceutical interventions on the outbreak of coronavirus disease lessons learned from hospital ebola preparation health care provider knowledge and attitudes regarding reporting diseases and events to public health authorities in tennessee ebola in the netherlands, - : costs of preparedness and response ebola outbreak preparedness and preventive measures among healthcare providers in saudi arabia developing a simulation-based training program for the prehospital professionals and students on the management of middle east respiratory syndrome attitudes towards zika virus infection among medical doctors in aceh province the sars, mers and novel coronavirus (covid- ) epidemics, the newest and biggest global health threats: what lessons have we learned? straining the system: novel coronavirus (covid- ) and preparedness for concomitant disasters personal protective equipment supply chain: lessons learned from recent public health emergency responses what us hospitals should do now to prepare for a covid- pandemic. website: clinicians' biosecurity news implementation of mitigation strategies for communities with local covid- transmission monitoring pharmacy and test kit stocks in rural mozambique: u.s. president's emergency plan for aids relief surveillance to help prevent ministry of health shortages cdc's evolving approach to emergency response the asia pacific strategy for emerging diseases -a strategy for regional health security strategy for emerging infectious disease control and prevention[卫生 部关于印发《突发急性传染病预防控制战略》的通知 national health commission; . . national health and family planning commission c. guidance on strengthening the standardized construction of health emergency work《关于加强卫生应急工作规范化建设 的指导意见》 addressing maternal health during cdc's ebola response in the united states considerations for u.s healthcare facilities to ensure adequate supplies of personal protective equipment (ppe) for ebola preparedness accessed. . ministry of finance c. hospital financial measures 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 a c c e p t e d m a n u s c r i p t key: cord- -qnxj d l authors: hueston, linda; kok, jen; guibone, ayla; mcdonald, damien; hone, george; goodwin, james; carter, ian; basile, kerri; sandaradura, indy; maddocks, susan; sintchenko, vitali; gilroy, nicole; chen, sharon; dwyer, dominic e; o’sullivan, matthew v n title: the antibody response to sars-cov- infection date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: qnxj d l background: testing for sars-cov- -specific antibodies has become an important tool, complementing nucleic acid tests (nats) for diagnosis and for determining the prevalence of covid- in population serosurveys. the magnitude and persistence of antibody responses are critical for assessing the duration of immunity. methods: a sars-cov- -specific immunofluorescent antibody (ifa) assay for igg, iga and igm was developed, and prospectively evaluated by comparison to the reference standard of nat on respiratory tract samples from individuals with suspected covid- . neutralizing antibody responses were measured in a subset of samples using a standard microneutralization assay. results: individuals were eligible for the study ( nat positive, prevalence · %). the median ‘window period’ from illness onset to appearance of antibody was · days (range · – · ). the sensitivity and specificity of either sars-cov- igg, iga or igm when collected days or more after symptom onset was · % ( % ci · - · ) and · % ( · - · ), respectively. the negative predictive value was · % ( · - · ). the positive predictive value of detecting any antibody class was · % ( · - · ); this increased to · % ( · - · ) for the combination of igg and iga. conclusions: measurement of sars-cov- -specific antibody by ifa is an accurate method to diagnose covid- . serological testing should be incorporated into diagnostic algorithms for sars-cov- infection to identify additional cases where nat was not performed, and resolve cases where false-negative and false-positive nats are suspected. the majority of individuals develop robust antibody responses following infection, but the duration of these responses and implications for immunity remain to be established. m a n u s c r i p t the acute respiratory tract disease covid- caused by the novel coronavirus sars-cov- emerged in hubei province, china in december . as of may , there were more than . million cases worldwide. diagnosis is primarily by detecting sars-cov- -specific rna by nucleic acid testing (nat), but this has limitations, including the possibility of false-negative results due to low virus load in patients with minimal disease, inadequate respiratory tract sampling or mutations in the target sequence, and false-positive results due to contamination or nonspecific amplification. assays for detection of sars-cov- -specific antibodies in serum or plasma can be used to confirm a diagnosis of covid- or to make a retrospective diagnosis in individuals who have already recovered from the acute illness and are no longer nat positive [ ] , which can be critical for outbreak investigations [ ] . such assays also permit estimates of the proportion of a population who have been infected by testing unbiased collections of sera in population-weighted serosurveys. in addition, serology assays are needed to establish the effectiveness and durability of immune responses to sars-cov- infection, for correlating humoral immune responses with disease severity [ ] , for facilitating studies of convalescent plasma and hyperimmune globulin as therapeutic or prophylactic interventions [ ] , and for investigating vaccine strategies. the objective of this study was to develop and evaluate an immunofluorescent antibody (ifa) test for sars-cov- -specific igg, igm and iga, and apply it to document the serological response in individuals with confirmed covid- . since the start of the epidemic in australia, the public health laboratory network recommended collecting acute and convalescent sera for serological assays on individuals being tested for sars-cov- infection, in addition to respiratory tract samples for nat, though this has not been universally adopted [ ] . individuals with suspected sars-cov- infection having both respiratory a c c e p t e d m a n u s c r i p t tract samples for nat and serum samples for serological testing referred to the public health laboratory at the nsw health pathology-institute for clinical pathology and medical research, westmead from th january to th may were prospectively included in this study. in addition, discarded blood samples collected for routine biochemistry from patients with nat-confirmed covid- managed at westmead hospital were utilised as individual seroconversion panels. a specificity panel consisting of samples positive for rheumatoid factor (n= ), human influenza a virus (n= ) or mycoplasma pneumoniae (n= ) antibodies collected during june to august were used to separately assess cross-reactivity. detection of sars-cov- rna was performed on respiratory tract samples and viral culture supernatant using established methods [ , ] . sars-cov- isolated from a sample collected on th january from an individual who acquired covid- in wuhan was utilised for the serological assays. the isolate belonged to sars-cov- linage a using the phylogenetic assignment of named global outbreak lineages tool (pangolin [ ] ) and the consensus genome sequence has been submitted to gisaid (accession epi_isl_ [ ]). the virus was inoculated into vero-e cells and examined daily for cytopathic effect (cpe) in a bsl- laboratory. growth of sars-cov- was confirmed by the presence of cpe and the detection of sars- samples positive for sars-cov- ifa underwent sars-cov and mers-cov ifa using commercially available slides (euroimmun, luebeck, germany) according to the manufacturer's instructions. neutralizing antibody titers were determined by microneutralization using established methods [ ] . samples from individuals with nat-confirmed sars-cov- infection that demonstrated seroconversion by ifa were used to determine the 'window period' for appearance of sars-cov- - positive reference cases were defined as persons with clinically suspected covid- who had sars-cov- detected by nat. positive reference cases with an ifa titer of < beyond the observed upper range of the serologic window period were classified as having false negative serology, otherwise they were classified as true positive if an ifa titer of ≥ was detected at initial or follow-up testing. negative reference cases were defined as persons with suspected covid- who had one or more negative sars-cov- nats. negative reference cases were classified as having false positive serology if an ifa titer of ≥ was detected on initial or follow-up serology, otherwise in these cases an ifa titer of < was classified as true negative. sensitivity, specificity, negative and positive predictive values and confidence intervals were calculated using medcalc (https://www.medcalc.org/). confidence intervals for mean 'window periods' were calculated using microsoft excel . of individuals with suspected covid- were included in the study (figure ), ( · %) were female, and the median age was years with an interquartile range of - . two thousand five hundred and seventy-seven individuals had a single serology test performed, had two or more. one hundred and twenty-six individuals were sars-cov- nat positive (prevalence · %). a c c e p t e d m a n u s c r i p t fifteen individuals had appropriately timed serum collections for calculation of the serological window period. the mean window period from symptom onset to seroconversion of one or more sars-cov- -specific antibody classes (igg, iga or igm) was · days ( % ci · - · ) with an upper range of · days. window periods for individual or combinations of antibody classes are shown in table . of nat-confirmed cases, had antibody from one or more classes detectable by ifa within days of illness onset (sensitivity · %%; % ci · - · ). the sensitivity and specificity, negative and positive predictive value of individual antibody classes and their combinations are shown in table . the cases classified as false negative serology results were predominantly from individuals with one positive and several negative nat tests (supplementary table s ). when the cases with only a single nat positive test were excluded, the calculated sensitivity of serology increased to · % ( · - · ). two individuals had multiple positive nats but no sars-cov- -specific antibody detected beyond the -day window period. one had severe covid- and died on day of illness, the second had mild disease with prolonged rna shedding to day of illness, no detectable antibody at day of illness but iga detected at a titer of on day . the median antibody titers in each of the four-day intervals up to days, followed by weekly intervals to weeks, after illness onset were used to plot the dynamics of the antibody response using samples from the sars-cov- infected individuals (figure ) . the peak antibody response was seen in the third week post-illness onset, with iga and igm titers declining after this time point, and igg titers declining in the sixth week after illness onset. by the seventh week, the proportion of individuals who still had detectable igg was %, but only % for iga and for igm. the maximum recorded igg titer was, on average, higher in those who were hospitalized ( , % ci - ) compared with those who were managed as an outpatient ( , % ci - , p= . ). there was no correlation between antibody titers and sex, age or duration of viral rna shedding (supplementary figures s -s ). we show that our in-house developed ifa is a reliable diagnostic method for the detection of anti-sars-cov- antibodies. the sensitivity of this assay is greater, and window period shorter, than those reported for many other sars-cov- serology assays [ , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . this may be because the antigen utilised in this ifa assay is whole virion-infected cells rather than one or two purified or recombinant viral proteins. complementing the high sensitivity is the high specificity of our ifa, with minimal cross-reactivity against other coronaviruses other than sars-cov (also described in other studies [ , ] ). the absence of reactivity in the vast majority of cases without sars-cov- infection also suggests that cross-reactivity with common endemic coronaviruses such as cov- e and cov-oc is minimal, as has been described for sars-cov [ ] . false-positive cases were associated with low titers of one antibody class only. the ifa assay has the advantage of being quantitative so changes in titer can be observed on paired samples which aids in interpretation of results and helps a c c e p t e d m a n u s c r i p t time the onset of infection. timing of sera collection after illness onset is important, and we recommend an acute sample in the first few days after illness onset and a second sample - days after illness onset to reliably detect seroconversion. there may be a small but important incidence of false-positive sars-cov- nat results, which are not always easily identified [ ] [ ] [ ] [ ] [ ] . this can be particularly significant in jurisdictions where the incidence of covid- cases is low. we recommend serological follow-up of unexpected nat positive cases in these circumstances in an attempt to confirm the diagnosis of covid- . we found that sars-cov- -specific iga provided better performance characteristics than igm with higher sensitivity, equivalent specificity and higher titers at all time points after illness onset. this is consistent with findings in other respiratory tract infections, and has been observed previously for we chose to report any reactivity as positive in the ifa test, since the best way to resolve falsepositive results is to collect a second sample to observe a rising titer. low antibody titers that are associated with true positive cases will generally demonstrate a rising titer on a second sample, c c e p t e d m a n u s c r i p t has occurred. as with sars-cov, the appearance of igg antibodies appears to be simultaneous with, or even occurs before, the appearance of iga and igm [ , ] . while the association between serological response, humoral immunity and protection from reinfection remains to be established for sars-cov- , it is concerning that the kinetics of the antibody responses demonstrated in this study suggest that antibody responses may be short-lived, at least when measured by ifa. whether this translates to early susceptibility to re-infection is a priority research area. the investigations into the association of antibody response with disease severity in sars-cov- , sars-cov and mers-cov infections have yielded inconsistent results. some studies have shown early, robust antibody responses to be associated with mild disease [ , ] , while others have indicated that severe disease is associated with higher antibody titers which may indicate a role for disease-enhancing antibodies in the pathogenesis of sars-cov- [ , [ ] [ ] [ ] . our study found that antibody titers were higher in individuals who were hospitalized for management of covid- . it is possible that certain antibody subsets are associated with protection against severe disease while others are associated with poorer outcomes [ ] . poorer immune responses may be associated with prolonged viral shedding, and the presence of antibody does not always correlate with viral clearance [ , ] . we were unable to demonstrate associations between age, sex or duration of viral shedding and antibody titer. this study has several limitations. nat was utilised as the reference standard for comparison to serology -false-positive and false-negative nats may have resulted in under-estimates of the sensitivity and specificity of ifa. antibody testing by neutralization is a more appropriate reference standard, but was only performed on a subset of samples due to the technical challenges associated with this method. furthermore, samples classified as reference standard negative may have been collected from individuals who had an earlier, undiagnosed sars-cov- infection but who were now presenting with a second, unrelated respiratory tract or febrile illness. such individuals may have a c c e p t e d m a n u s c r i p t had negative nat tests with persistent positive serology and would have been classified as false positive serology tests. we did not assess for cross-reactivity with other endemic coronaviruses, however, if this were to be significant we would have expected more false-positive results given that these other coronaviruses circulate commonly. the median age of participants was years, with those at extremes of age being under-represented so our results may not be readily generalizable to these age groups. ifa testing is a relatively specialised technique, and while robotic instruments can be utilised for slide preparation and incubation, the reading of results is a relatively manual process requiring well trained laboratory staff. commercially produced serology tests designed for high-throughput automated platforms such as chemiluminescent microparticle immunoassays and enzyme-linked immunosorbent assays may be more suitable than ifa for many laboratories settings, but will need to be subject to robust evaluation. measurement of anti-sars-cov- -specific antibody by ifa in serum is an accurate method for retrospective diagnosis of covid- . serological testing should be selectively incorporated into diagnostic algorithms for sars-cov- infection for use in identifying additional cases where nat was not performed, and to help resolve cases where false-negative and false-positive nats are suspected. ifa, along with neutralizing antibody testing, will serve as appropriate comparators for other sars-cov- -specific antibody assays. this includes for assessment of rapid point-of-care antibody tests, which have been shown to be less sensitive and specific [ ] . future research is awaited to further define the duration of the antibody responses to sars-cov- infection and to understand the serological correlates of protection from re-infection. antibody assays will play a major role in the understanding of covid- epidemiology, pathogenesis, immunity and immunotherapeutics. evaluation of the auxiliary diagnostic value of antibody assays for the detection of novel coronavirus (sars-cov- ) connecting clusters of covid- : an epidemiological and serological investigation the many faces of the anti-covid immune response convalescent plasma in covid- : possible mechanisms of action public health laboratory network (phln) guidance on laboratory testing for sars-cov- (the virus that causes covid- ) detection of novel coronavirus ( -ncov) by real-time rt-pcr molecular assays to diagnose covid- : summary table of available protocols a dynamic nomenclature proposal for sars-cov- lineages to assist genomic epidemiology global initiative on sharing all influenza data (gisaid) diagnostic procedures for viral, rickettsial, and chlamydial infections profile of igg and igm antibodies against severe acute respiratory syndrome coronavirus (sars-cov- ) profiling early humoral response to diagnose novel coronavirus disease (covid- ) antibody responses to sars-cov- in patients with covid- serological assays for severe acute respiratory syndrome coronavirus (sars-cov- ) antibody detection and dynamic characteristics in patients with covid- severe acute respiratory syndrome coronavirus −specific antibody responses in coronavirus disease evaluation of nucleocapsid and spike protein-based elisas for detecting antibodies against sars-cov- antibody responses to sars-cov- in patients of novel coronavirus disease serological responses in patients with severe acute respiratory syndrome coronavirus infection and cross-reactivity with human coronaviruses e, oc , and nl united states food and drug administration. false positive results with bd sars-cov- reagents for the bd max system -letter to clinical laboratory staff and health care providers public health laboratory network statement on nucleic acid test false positive results for sars-cov- interpret with caution: an evaluation of the commercial ausdiagnostics versus in-house developed assays for the detection of sars-cov- virus false-positive reverse transcriptase polymerase chain reaction screening for sars-cov- in the setting of urgent head and neck surgery and otolaryngologic emergencies during the pandemic: clinical implications real-time rt-pcr in covid- detection: issues affecting the results iga-ab response to spike glycoprotein of sars-cov- in patients with covid- : a longitudinal study persistence of antibodies against middle east respiratory syndrome coronavirus duration of antibody responses after severe acute respiratory syndrome longitudinal profile of antibodies against sars-coronavirus in sars patients and their clinical significance viral shedding and antibody response in patients with middle east respiratory syndrome coronavirus infection kinetics of serologic responses to mers coronavirus infection in humans mers-cov antibody responses year after symptom onset, south korea a comparison study of sars-cov- igg antibody between male and female covid- patients: a possible reason underlying different outcome between sex profile of specific antibodies to sars-cov- : the first report kinetics of sars-cov- specific igm and igg responses in covid- patients virological assessment of hospitalized patients with covid- long-term coexistence of sars-cov- with antibody response in covid- patients rapid point-of-care testing for sars-cov- in a community screening setting shows low sensitivity key: cord- - jd gn authors: karra, nour; dolinski, rina; akria, luiza; yampoulski, yevgeni; awad, jamal title: a case of hemophagocytic lymphohistiocytosis associated with mediterranean spotted fever in a healthy -year-old female date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: jd gn a -year-old female presented with fever, headache, and epigastric pain. though her initial presentation was benign and nonspecific, she soon developed a full-blown cytokine storm with disseminated intravascular coagulation. she was diagnosed with hemophagocytosis secondary to rickettsia conorii infection. a good outcome was achieved thanks to prompt diagnosis and proper treatment. hemophagocytic lymphohistiocytosis (hlh) is a rare, potentially life-threatening syndrome caused by excessive immune activation and cytokine storm [ , ] . cardinal features include fever, hepatosplenomegaly, cytopenias, and histological hemophagocytosis [ , ] . primary genetic hlh is caused by a mutation in a component of the perforin-mediated cytotoxicity pathway and may be either familial or associated with genetic immunodeficiency syndromes (chediak-higashi, griscelli type- , and x-linked lymphoproliferative disorder) [ ] . most commonly it affects infants, and it may also be triggered by a viral infection, particularly epstein barr virus (ebv) [ ] . secondary or acquired hlh may occur in adults sporadically, in association with many triggers, namely infectious, autoimmune, and malignant diseases [ ] . it is believed that the incidence of secondary hlh has been rising in recent years, perhaps due to increased awareness. in the absence of a proven relevant mutation, the henter criteria have been proposed and are commonly applied to diagnose hlh [ , , ] . we describe a case of acquired hlh secondary to mediterranean spotted fever (msf) caused by rickettsia conorii in a -year-old healthy female in the north of israel. the clinical manifestations, workup, differential diagnosis (dd), and outcome in this patient are described and discussed. a -year-old jewish female presented to the emergency room at the galilee medical center nahariya in northern israel with a -week history of headache and days of fever (> . °c). she had also complained of diarrhea lasting days at a prior presentation that had resolved spontaneously. she had been previously healthy with an uneventful medical history. at presentation, she was tachycardic ( bpm) with fever ( . °c). otherwise she was in a good clinical shape, with no alarming signs. her laboratory results were unremarkable (table ) . her beta hcg was negative. she was symptomatically treated with clinical improvement and subsequently discharged with a presumed diagnosis of a mild viral illness. two days later, she returned with persisting complaints of headache, fever, and chills. in addition, she mentioned epigastric pain, nausea, and vomiting. she had been self-medicating with ibuprofen for days. except for tachycardia ( bpm), her vital signs were normal. blood tests revealed a normal white blood cell count and hemoglobin (hb), but she now had thrombocytopenia (platelets [plt] × /ul), mild hyponatremia ( mmol/l), and hypokalemia ( . mmol/l) with a c-reactive protein of mg/l (table ) . chest and abdominal x-rays were unrevealing. due to persisting symptoms and abnormal labs, she was admitted for further evaluation. upon admission, she was tachycardic ( bpm) with a fever of °c. in repeated anamnesis, she denied any travels, exposure to unhealthy individuals, or contact with animals. on physical examination, there was only mild epigastric tenderness without rebound. blood cultures and viral serologies were drawn. due to increased hepatocellular enzymes and slightly increased bilirubin (table ) , the dd included viral hepatitis, acute cholecystitis/cholangitis, or a liver injury secondary to nonsteroidal anti-inflammatory drugs. an abdominal ultrasound showed only a normal size gallbladder with thickened walls ( cm). acute cholecystitis was the most likely diagnosis. ceftriaxone and metronidazole were initiated. twelve hours later, she began deteriorating: her blood pressure dropped, and lab tests showed metabolic acidosis, acute kidney injury, hepatocellular and cholestatic injury with rising bilirubin, prolonged pt, and low fibrinogen ( mg/dl). she had anemia (hb . g/dl), deteriorating thrombocytopenia ( × /μl), and leukocytosis with a left shift ( figure ). schistiyocytes were observed on a blood smear. a diagnosis of disseminated intravascular coagulation (dic) was made, and she was treated with fresh frozen plasma and cryoprecipitate. following blood product transfusion, the patient stabilized. she later developed skin necrosis on the dorsal side of her feet and was treated with intravenous heparin. an urgent computed tomography scan excluded emphysematous cholecystitis or visceral perforation as a cause of dic. significantly thickened gallbladder and periportal edema were demonstrated. re-evaluating the dd, a wide battery of serological tests was taken (table ) . sepsis was the most likely diagnosis. due to thrombocytopenia, hyponatremia, and headache, an atypical infection such as rickettsiosis was considered, and doxycycline treatment was empirically initiated. interestingly, ferritin levels were dramatically elevated ( ng/ml), and fibrinogen levels were still particularly low ( mg/dl). a bone marrow biopsy performed on day of admission exhibited evident hemophagocytosis ( figure ). natural killer (nk) cell activity was preserved ( %), but soluble il- receptor (sil- r) levels were elevated ( u/ml; normal: - u/ml). a diagnosis of hlh was established. as there was no family history of primary hlh, immune deficiencies, or perforin pathway mutations, a plethora of possible triggers was evaluated. rheumatologic and infectious serologies were all negative (table ) . adamts- antibodies and activity were within the normal range. blood, urine, and stool cultures were also negative. blood polymerase chain reaction (pcr) was positive for rickettsia conorii. the hlh- treatment protocol (dexamethasone and etoposide) was immediately initiated, in addition to doxycycline. subsequently, the patient gradually improved during the next few weeks, and her labs normalized ( figure ). an increasing number of acquired hlh cases have been reported in recent years [ ] . however, it has been suggested that hlh may go undiagnosed due to a varying clinical presentation, poor reproducibility of the henter criteria, and insufficient awareness in medical caregivers of this syndrome [ ] . indeed, several challenges might hinder diagnosis [ ] : first, the hlh- diagnostic criteria were initially developed based on pediatric familial cases, and even though widely applied, they have not been validated in adults or in secondary hlh. second, many diagnostic criteria are nonspecific (fever, cytopenias, hypofibrinogenemia) and may be encountered contrarily, hlh patients frequently exhibit findings other than those included in the diagnostic criteria (hypoalbuminemia, elevated liver enzymes, coagulopathy). the clinical overlap between hlh, sepsis, and multi-organ dysfunction syndrome may lead to hlh misdiagnosis, particularly in an intensive care unit setting. finally, without specific markers such as sil- r levels, nk cell activity, or histological hemophagocytosis, these syndromes could be clinically indistinguishable. needless to say, these markers are neither tested routinely nor readily available at medical centers [ , ] . in the present case, the clinical presentation was indeed nonspecific and dynamic. through the course of illness, the patient developed clinical and radiologic findings suggestive of acute acalculus cholecystitis. retrospectively, these findings could be explained by periportal and hepatic infiltration of macrophages and lymphocytes [ ] . upon deterioration, she was re-evaluated, and a comprehensive dd was considered. fever and multi-organ failure in a previously healthy individual are attributed with a high probability to sepsis. as already mentioned, sepsis is a great mimicker of hlh. padhi et al. previously reported that in out of reviewed cases of secondary hlh, a diagnosis of sepsis was initially presumed [ ] . in the present case, the dramatic rise in ferritin beyond ng/ml ("sky high" hyperferritinemia) was suggestive of hlh [ ] . microangiopathic hemolytic anemia and thrombocytopenia could also be attributed to hemolytic uremic syndrome (hus) or thrombotic thrombocytopenic purpura (ttp). however, the multi-organ failure combined with coagulopathy could not be well explained by hus or ttp. nevertheless, a normal admats activity ruled out ttp. although diagnosis of hlh is quite challenging, our patient eventually fulfilled of the henter criteria: fever, bicytopenia, hyperferritinemia, hypertriglyceridemia with hypofibrinogenemia, histologic hemophagocytosis, and elevated sil- r levels. when hlh diagnosis was established, a trigger was sought. pcr was positive for rickettsia conorii, although serologies were negative. this was attributed to the fact that serologies were examined early during the disease course (day / since initial symptom onset). early manifestations of msf commonly include fever, headaches, myalgias, and sometimes nausea and vomiting. a maculopapular rash usually follows, predominantly on the palms and soles, with rickettsia conorii. occasionally an inoculation eschar may be found [ ] . thrombocytopenia, leukopenia, hyponatremia, and increased hepatocellular enzymes are common findings [ ] [ ] [ ] [ ] . indeed, our patient presented with many of these symptoms. however, rash and eschar were not found. in a study by lecronier et al., in only out of msf cases was a rash not present [ , ] . in israel, the common variant is israeli spotted fever (isf) caused by rickettsia conorii subsp. israelensis. the clinical manifestations are similar to msf; however, tick exposure is reported in %, and an eschar is rarely observed ( %) [ ] . unfortunately, sequencing for the specific subspecies of rickettsia conorii was not performed in the present case. ramos-casals reported a total of identified cases of adult hlh in the literature, half of which were triggered by infections [ ] . most cases of bacteria-associated hlh were due to intracellular organisms, primarily tb. notably, < cases of hlh secondary to msf have been reported [ ] [ ] [ ] [ ] [ ] [ ] [ ] (table ) . most cases were reported in france [ , , ] , with others in spain [ ] , italy [ ] , and sri lanka ( table ) [ ] . in nearly all cases, patients presented with fever and a maculopapular rash. headache, nausea, vomiting, and myalgia were also prevalent. interestingly, of the earliest hlh cases caused by rickettsia conorii was reported in israel in [ ] . israel is an endemic country of rickettsia conorii [ ] . thus, in the present case doxycycline was initiated early and based on clinical suspicion only, even though the classical rash and exposure were absent. this clinical approach turned out to be life-saving. other pathogens from the rickettsia family have also been associated with hlh (table ) [ ] . in fact, hlh has been primarily reported with scrub typhus and ehrlichiosis and to a lesser extent with rickettsia conorii and rickettsia japonica (table ) [ , ] . a recent comprehensive review on scrub typhus-associated hlh identified cases, all in the far east [ ] . in adults, treatment mostly relied on rickettsia-specific antibiotics, while only in % were other treatments added ( table ) . as for ehrlichiosis-induced hlh, there are substantial reports [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] , mostly in the united states. ten cases in immunocompetent adults have been reported with a good outcome upon doxycycline treatment (table ) [ ] . the pathogenesis of rickettsia-induced hlh is not completely elucidated. the underlying common mechanism in both genetic and reactive hlh is a defective granule-mediated cytotoxicity. uncontrolled activation of t cells and antigenpresenting cells (macrophages and histyocytes) is thought to be caused by enhanced antigen presentation and continuous stimulation of toll like receptors by interferon-ɣ [ , ] . rickettsia is an intracellular pathogen. as such, following phagocytosis, it may trigger an inappropriate th- response, activating macrophages and significant cytokine release. concurrent deficient cytotoxicity of nk and cd cells may result in persistent lymphocyte and histyocyte activation and excessive levels of tumor necrosis factor-α, interferon-ɣ, macrophage colony-stimulating factor, interleukin (il)- , il- , il- , il- , and il- , all important markers of the cytokine storm seen in hlh [ ] . treatment of hlh is generally based on support measures, trigger elimination, and immunosuppressive therapy. however, currently, there are no randomized controlled table trial-based guidelines regarding the ultimate treatment protocol in adults. therapeutic decisions are practically based on clinical experience, expert opinion, and on a case-by-case approach [ ] . the hlh- protocol has been mainly established as a consensus for primary genetic hlh [ ] . in adults, treatment of secondary hlh should be tailored according to the underlying trigger. a treatment algorithm has been recently suggested by la rosée et al. [ ] : in clinically stable patients, it is acceptable to specifically target treatment to the underlying condition. however, in deteriorating patients, corticosteroids may be initiated with the possible addition of intravenous immunoglobulin (ivig). a clear indication for immediate etoposide administration is severe hlh presenting with imminent organ failure [ ] . upon trigger identification, several additional treatments are possible: in ebv-associated hlh, virostatics and rituximab may be added. in leishmaniasisassociated hlh, liposomal amphotericin b is suggested. cytokine-directed agents (anti-il , anti-il ) have emerged in recent years as add-on treatments in macrophage-activating syndrome (mas; ie, hlh secondary to rheumatologic conditions). conventionally, mas is treated with pulse steroids, with the possible addition of cyclosporin a and anakinra (anti-il ) [ ] . etoposide may be added in nonresponsive cases. tocilizumab (anti-il ) may be used in mas and druginduced hlh [ ] . tocilizumab has also been reported as an adjuvant therapy for hlh associated with visceral leishmaniasis [ ] and has been recently employed to treat the hlhresembling hyperinflammation associated with sepsis and covid- [ ] [ ] [ ] . there is a strong consensus that hlh induced by intracellular infections (tuberculosis, leishmaniasis, rickettsiosis) usually does not need hlh- treatment [ ] . notably, most reported cases of rickettsiosis-associated hlh have been successfully treated with only specific antibiotics (mostly doxycycline). however, in acutely ill deteriorating patients, treating the underlying infection may not always be sufficient. in a few reported cases, corticosteroids, ivig, and occasionally anakinra were added (table ) . although prognosis varies between studies, if left untreated, hlh is invariably fatal. in adults, prognosis is worse in those with an underlying malignancy (particularly lymphoma), alcoholism, g pd deficiency, age > years, neurologic involvement, and high ferritin with a slow decline [ , [ ] [ ] [ ] . specifically, the prognosis of msf-associated hlh may depend on the specific rickettsia subspecies, the delay in antibiotic treatment, and the use of immunosuppressive drugs [ ] . an excellent outcome has been reported in msf-associated hlh, in most cases without additional treatment other than antibiotics [ ] [ ] [ ] [ ] [ ] [ ] [ ] . nevertheless, as our patient presented with rapidly deteriorating multi-organ failure and dic, an aggressive treatment approach was opted for. dic is considered a severe complication and has been previously reported as an independent predictor of high mortality in hlh [ ] . here, dic was diagnosed early. skin gangrene in the lower extremities also indicated the severity of our patient's disease. cohen et al. reported a case of isf complicated by dic and purpura fulminans where the patient eventually died [ ] . similarly, a case of jsf complicated by hlh and dic was fatal despite maximal treatment [ ] . in contrast, a good outcome was achieved here. this may be attributed to the patient's young age, baseline well-being, early recognition and treatment of dic, and most importantly prompt initiation of doxycycline and the hlh- protocol. hlh is an elusive clinical syndrome. this case underscores the importance of having a high index of suspicion both for hlh and for msf as a triggering infection in endemic areas, even when the classical rash and exposure details are lacking. hypercytokinemia in familial hemophagocytic lymphohistiocytosis cytokine production regulating th and th cytokines in hemophagocytic lymphohistiocytosis adult haemophagocytic syndrome review of haemophagocytic lymphohistiocytosis hlh- : diagnostic and therapeutic guidelines for hemophagocytic lymphohistiocytosis how i treat hemophagocytic lymphohistiocytosis hemophagocytic lymphohistiocytosis: critical reappraisal of a potentially under-recognized condition diagnostic challenges of hemophagocytic lymphohistiocytosis clinical utility of soluble interleukin- receptor in hemophagocytic syndromes: a systematic scoping review autopsy findings in children with haemophagocytic lymphohistiocytosis highly elevated ferritin levels and the diagnosis of hemophagocytic lymphohistiocytosis update on tick-borne rickettsioses around the world: a geographic approach clinical and laboratory findings of boutonneuse fever in sicilian children ehrlichioses in humans: epidemiology, clinical presentation, diagnosis, and treatment mediterranean spotted fever in algeria-new trends two cases of israeli spotted fever with purpura fulminans q fever and mediterranean spotted fever associated with hemophagocytic syndrome: case study and literature review unusual pancytopenia secondary to haemophagocytosis syndrome in rickettsioses hemophagocytosis syndrome in mediterranean boutonneuse fever haemophagocytic syndrome secondary to mediterranean spotted fever severe rickettsia conorii infection associated with hemophagocytic syndrome haemophagocytic syndrome and rickettsial diseases transient histiocytic hemophagocytosis and pancytopenia in mediterranean spotted fever mediterranean spotted fever in israel: a tick-borne disease secondary hemophagocytic lymphohistiocytosis in zoonoses. a systematic review japanese spotted fever with hemophagocytic lymphohistiocytosis hemophagocytic lymphohistiocytosis due to rickettsia japonica in a -month old-infant hemophagocytic lymphohistiocytosis associated with scrub typhus: systematic review and comparison between pediatric and adult cases hemophagocytic syndrome: a cause of pancytopenia in human ehrlichiosis ehrlichiosis mimicking thrombotic thrombocytopenic purpura. case report and pathological correlation hemophagocytic lymphohistiocytosis secondary to ehrlichia chaffeensis infection: a case report ehrlichiosis presenting as hemophagocytic lymphohistiocytosis in an immunocompetent adult ehrlichia-induced hemophagocytic lymphohistiocytosis: a case series and review of literature human monocytic ehrlichiosis complicated by hemophagocytic lymphohistiocytosis and multi-organ dysfunction syndrome macrophage activation syndrome secondary to human monocytic ehrlichiosis ehrlichiosis presenting with toxic shock-like syndrome and secondary hemophagocytic lymphohistiocytosis hemophagocytic lymphohistiocytosis: an unreported complication of ehrlichiosis in adults diagnosis and treatment of hemophagocytic lymphohistiocytosis in an adult patient with ehrlichiosis hemophagocytic lymphohistiocytosis (hlh) secondary to ehrlichia chaffeensis with bone marrow involvement ehrlichia-induced hemophagocytic lymphohistiocytosis in two children use of extracorporeal support in hemophagocytic lymphohistiocytosis secondary to ehrlichiosis recommendations for the management of hemophagocytic lymphohistiocytosis in adults tocilizumab as an adjuvant therapy for hemophagocytic lymphohistiocytosis associated with visceral leishmaniasis cytokine release syndrome in severe covid- : interleukin- receptor antagonist tocilizumab may be the key to reduce mortality tocilizumab for the treatment of severe covid- pneumonia with hyperinflammatory syndrome and acute respiratory failure: a single center study of patients in hlh across speciality collaboration, uk. covid- : consider cytokine storm syndromes and immunosuppression prognostic factors of early death in a cohort of adult haemophagocytic syndrome: impact of triggering disease and early treatment with etoposide prognostic factors and outcomes of adults with hemophagocytic lymphohistiocytosis clinical characteristics, prognostic factors, and outcomes of adult patients with hemophagocytic lymphohistiocytosis potential conflicts of interest. there are no conflicts of interest to declare. all authors: no reported conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed.patient consent. the patient's consent was obtained. ethical approval. a local ethical committee approval does not apply in this case. key: cord- -bq ok h authors: belongia, edward a; king, jennifer p; kieke, burney a; pluta, joanna; al-hilli, ali; meece, jennifer k; shinde, vivek title: clinical features, severity, and incidence of rsv illness during consecutive seasons in a community cohort of adults ≥ years old date: - - journal: open forum infect dis doi: . /ofid/ofy sha: doc_id: cord_uid: bq ok h background: the epidemiology and burden of respiratory syncytial virus (rsv) illness are not well defined in older adults. methods: adults ≥ years old seeking outpatient care for acute respiratory illness were recruited from – through – during the winter seasons. rsv was identified from respiratory swabs by multiplex polymerase chain reaction. clinical characteristics and outcomes were ascertained by interview and medical record abstraction. the incidence of medically attended rsv was estimated for each seasonal cohort. results: rsv was identified in ( %) of enrollments ( of individuals), including rsv type a and rsv type b. the rsv clinical outcome was serious in ( %), moderate in ( %), and mild in ( %). serious outcomes included hospital admission (n = ), emergency department visit (n = ), and pneumonia (n = ) and were associated with lower respiratory tract symptoms during the enrollment visit. moderate outcomes included receipt of a new antibiotic prescription (n = ; %), bronchodilator/nebulizer (n = ; %), or systemic corticosteroids (n = ; %). the relative risk of a serious outcome was significantly increased in persons aged ≥ years (vs – years) and in those with chronic obstructive pulmonary disease or congestive heart failure. the average seasonal incidence was cases/ , and it was significantly higher in persons with cardiopulmonary disease compared with others (rate ratio, . ; % confidence interval, . – . ). conclusions: rsv causes substantial outpatient illness with lower respiratory tract involvement. serious outcomes are common in older patients and those with cardiopulmonary disease. over the past decade, respiratory syncytial virus (rsv) infection has been increasingly recognized as an important cause of acute respiratory illness in older adults. both influenza and rsv account for a substantial number of respiratory illness deaths among adults ≥ years of age in the united states. from to , influenza and rsv contributed to approximately and annual cardiorespiratory deaths, respectively [ ] . rsv is also an important cause of adult respiratory illness in both developed and developing countries, including tropical and subtropical regions [ ] [ ] [ ] . studies conducted in the s and s first identified rsv as a cause of acute respiratory illness in a variety of adult populations, including older adults, working-age adults, hospitalized patients, and residents of long-term care facilities [ ] [ ] [ ] [ ] [ ] . immunocompromised adults and those with advanced age and/or cardiopulmonary disease are at especially high risk for severe complications from rsv infection [ ] [ ] [ ] [ ] [ ] . the incidence and burden of rsv in adults are difficult to measure as clinical symptoms are nonspecific and physician awareness of rsv in adults is limited. most adult studies of rsv have been conducted in the hospital setting, where rsv accounts for about % to % of respiratory illness hospitalizations during the winter season [ ] [ ] [ ] [ ] . advanced age, radiographic pneumonia, ventilator support, and secondary bacterial infection are all associated with increased risk of death among hospitalized patients with rsv [ ] . few studies have assessed the incidence and clinical characteristics of adult rsv infections in the community and outpatient setting. a seminal prospective cohort study of adults ≥ years of age during winter seasons ( ) ( ) ( ) ( ) ( ) found that %- % developed symptomatic rsv infection each season [ ] . a -season study of adults ≥ years old with predominantly outpatient acute respiratory illness found that rsv was the third most common viral pathogen (after influenza and human rhinovirus) [ ] . advanced age, cough, nasal congestion, wheezing, and increasing interval from symptom onset to care-seeking were independently associated with rsv detection. the latter study was conducted in a wisconsin community cohort, and the overall seasonal incidence of medically attended rsv illness was estimated as episodes per individuals m a j o r a r t i c l e ≥ years old [ ] . the incidence of medically attended rsv increased with age, and it was highest ( episodes per ) among persons ≥ years of age. rsv vaccines and antivirals for older adults are currently in prelicensure clinical trials [ ] , and more detailed knowledge of rsv incidence and burden is needed to inform policy recommendations and evaluate cost-effectiveness. the objective of this study was to describe the clinical characteristics, severity, clinical outcomes, and long-term incidence of medically attended rsv illness in a community cohort of adults ≥ years of age from the - through - influenza seasons. this analysis significantly extends a previous report on medically attended rsv infections in adults ≥ years of age in the community cohort from - through - [ ] . the current report includes an additional seasons with more detailed clinical information based on medical record abstraction for rsv cases, including physical exam findings, management, and outcomes. the marshfield clinic research institute conducted prospective seasonal studies of influenza vaccine effectiveness in a wisconsin community cohort during the - through - seasons [ ] [ ] [ ] [ ] . before each influenza season, a community cohort was defined based on residency in or near marshfield, wisconsin, and receipt of care from the marshfield clinic. individuals in the community cohort were eligible to be recruited when seeking care for acute respiratory illness in outpatient clinics (all seasons) or in the hospital setting ( - through - ) . each season, recruitment began when influenza activity was detected in the community and usually continued for - weeks. symptom eligibility criteria varied by season but included fever/feverishness or cough during most seasons. for the - through - seasons, eligibility was based on the presence of acute respiratory illness with cough. the maximum duration of illness was days for the - through - seasons and days for all subsequent seasons. after obtaining informed consent, a midturbinate swab was obtained for influenza detection. symptoms and onset date were assessed during the enrollment interview. realtime reverse transcription polymerase chain reaction (rt-pcr) was performed each season to identify influenza cases. after testing was complete, aliquots of samples in viral transport media were frozen at - °c. this study was reviewed and approved by the marshfield clinic institutional review board. during each season, all study participants (or parents) provided informed consent for influenza testing. multiplex rt-pcr testing to detect additional viruses was subsequently approved by the institutional review board with a waiver of informed consent. archived samples were tested for the presence of respiratory virus nucleic acid using a multiplex respiratory virus panel (genmark dx esensor, respiratory viral panel). this is a food and drug administration (fda)-approved multiplex panel for detection of rsv a and b, human rhinovirus, human metapneumovirus, parainfluenza viruses - , influenza a (h , h , and h n pdm ) , influenza b, and adenoviruses b/e and c. nucleic acid was extracted from the swabs using the roche magnapure . system and was then amplified using rt-pcr with target-specific primers. target-specific signals were determined by voltammetry, a process that generates electrical signals from ferrocene-labeled signal probes. a published comparison of respiratory virus panels found that the genmark dx esensor assay had % sensitivity for rsv a and rsv b detection [ ] . samples collected from the - through - seasons were previously tested using the genmark multiplex assay in a separate study of rsv illness in adults ≥ years of age [ ] . a subset of these was retested in for validation as the original testing was performed before fda licensure of the genmark dx esensor assay. all samples collected from - through - were tested using the fda-approved genmark assay. for the - season only, funding for multiplex testing of respiratory swabs was provided by the us centers for disease control and prevention (cdc). electronic diagnosis codes, procedure codes, laboratory tests, and prescribing data were extracted from the medical record for all rsv-positive patients. trained research coordinators abstracted detailed clinical data for the initial respiratory illness visit, subsequent outpatient or ed visits, and hospital admissions within days for all participants with pcr-confirmed rsv illness. symptoms of acute respiratory illness and onset date were available from the original study enrollment interview. abstracted clinical data included additional symptoms not assessed during study enrollment, functional status, smoking status, physical exam findings, treatment, pulmonary function, and presence of specific comorbid chronic diseases. for each clinical encounter in the -day window, information was abstracted regarding diagnosis or suspicion of pneumonia, acute sinusitis, and acute otitis media. abstraction of laboratory results included hemoglobin, total leukocyte count, bun, creatinine, glomerular filtration rate, hemoglobin a c, procalcitonin, and brain natriuretic peptide (bnp). measures of cardiac and pulmonary function were abstracted, including peak flow, fev /fvc, oxygen saturation, and cardiac ejection fraction (from echocardiogram). additional abstractions were performed for participants who were hospitalized within days after pcr-confirmed rsv illness. abstracted data included admission and discharge diagnoses, hospital course, use of supplemental oxygen or ventilation support, intensive care unit (icu) admission, antibiotic or antiviral treatment, and disposition at discharge. all chest x-ray and chest computed tomography (ct) reports for participants with rt-pcr-confirmed rsv illness were independently reviewed by physicians to identify a new radiographic opacity or infiltrate within days after enrollment. chest x-rays obtained > hours after hospital admission were excluded as they may represent nosocomial rather than community-acquired illness. discrepancies in x-ray interpretation were adjudicated by consensus. for the purposes of this analysis, pneumonia was defined as an illness meeting all of the following criteria: ( ) clinical diagnosis or suspicion of pneumonia mentioned in the medical record; ( ) new opacity or infiltrate identified by chest x-ray or ct scan; and ( ) antimicrobial treatment. clinical outcomes for rt-pcr-confirmed rsv illness were classified as serious, moderate, or mild. a serious outcome was defined as acute care hospital admission, emergency department (ed) visit for acute illness, or pneumonia occurring within days after enrollment. a moderate outcome was defined as new antibiotic or antiviral therapy, new/increased bronchodilator therapy, or new/increased systemic corticosteroid therapy during the -day window after enrollment. individuals were classified as having a mild outcome if they did not meet criteria for serious or moderate rsv illness outcome. a physician independently validated all serious clinical outcomes. hospital admissions were reclassified to a nonserious outcome category if the reason for admission was unrelated to cardiopulmonary disease based on review of hospital records. at the time of initial presentation, participants with rt-pcrconfirmed rsv were classified as having moderate to severe lower respiratory tract disease (rsv-mslrtd) if at least of the following lower respiratory tract symptoms or signs were present: cough, wheezing (or worsening in baseline wheezing), new sputum production (or increase in baseline sputum), new (or worsening) shortness of breath, and tachypnea (≥ breaths/minute). the same criteria were used to define rsv-mslrtd in a phase iii clinical trial for rsv vaccine in older adults (clinicaltrials.gov identifier: nct ). for this descriptive analysis, we compared the demographic and clinical characteristics of study participants ≥ years of age with and without rt-pcr-confirmed rsv illness. among those with rt-pcr-confirmed rsv illness, we further assessed clinical and demographic characteristics and severity stratified by rsv subtype (a or b), as well as presence or absence of rsv-mslrtd during the initial clinical encounter. univariate comparisons were performed with the chi-square (categorical variables) or wilcoxon test (continuous variables), as appropriate; p values of <. were considered significant. seasonal incidence of medically attended rsv illness was estimated in the community cohort for individuals ≥ years of age for the period - through - . seasonal incidence is reported as episodes of medically attended rsv illness per population. a detailed description of the incidence estimation procedure was published previously [ ] . briefly, all estimates were standardized to a -week period from approximately early october through early may using wisconsin state laboratory of hygiene surveillance data. incidence calculations were based on assumptions: ( ) test results from enrolled patients can be extrapolated to nonenrolled cohort members with a respiratory illness visit during the enrollment period; and ( ) the number of rsv cases occurring outside the enrollment period in the cohort was proportional to the number of statewide cases occurring outside the enrollment period. poisson regression with analytic weights, offsets, and robust variance estimation was used to estimate seasonal incidence with corresponding % confidence intervals and test for linear trends in seasonal incidence. analyses were performed using sas . (sas institute inc., cary, nc). rsv was detected in ( %) of encounters (representing of individuals) for acute respiratory illness. rsv cases were equally represented by rsv a (n = ) and rsv b (n = ). of the rsv cases, ( %) had an additional viral target identified. influenza was detected in ( %), and (< %) were positive for both rsv and influenza. there were individuals with an episode of rsv during different seasons; none of the study participants had rsv episodes in the same season. among encounters negative for rsv and influenza by rt-pcr, the most common viral pathogens were coronavirus oc , nl , hku , e (n = ; %), human metapneumovirus (n = ; %), human rhinovirus (n = ; %), and parainfluenza virus types - (n = ; %); ( %) encounters were negative for all viral targets in the multiplex rt-pcr assay. patients with rt-pcr-confirmed rsv were similar to those with non-rsv respiratory illness in terms of age, gender, number of ed visits, and hospital admissions in the prior months ( table ). the mean (median) interval from symptom onset to study enrollment and swab collection was . ( . ) days for rsv-negative patients and . ( . ) days for rsv-positive patients (p = . ). chronic obstructive pulmonary disease (copd) was present in % of those with rsv illness, % of those with other viral respiratory infection, and % of those with no virus detected. rsv prevalence among adults with acute respiratory illness varied from a low of % common symptoms of rsv illness included sore throat, sputum production, cough, fever/feverishness, dyspnea, myalgia, and wheezing ( table ). the most common diagnosis codes on the date of enrollment for rsv-positive patients were cough ( %), acute upper respiratory infection ( %), acute bronchitis ( %), acute sinusitis ( %), and bronchitis, unspecified ( %). fifty-nine patients ( %) met the criteria for rsv-mslrtd during the enrollment encounter. the presence of rsv-mslrtd on enrollment was associated with a -fold higher risk of serious clinical outcome (relative risk, . ; % confidence interval [ci], . - . ) ( table ) . rsv-positive participants with mslrtd during the enrollment encounter had a higher prevalence of copd and congestive heart failure (chf) and a greater number of medical encounters in the days after enrollment (median, vs ; p = . ). the clinical outcome for rsv illness was serious in ( %), moderate in ( %), and mild in ( %). nearly half of serious outcomes occurred in patients ≥ years of age with rsv infection (table ) . serious outcomes were not mutually exclusive ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) - ( ) ( ) ( ) ( ) . no. of ed visits in the prior mo, median (min-max) b ( - ) ( - ) . ( - ) ( - ) . no. of hospital admissions in the prior mo, median (min-max) b ( - ) ( - ) . ( - ) ( - ) . no. of outpatient visits w/ provider in the prior mo, median (iqr) b ( - ) ( - ) . ( - ) ( - ) . abbreviations: chf, congestive heart failure; copd, chronic obstructive pulmonary disease; ed, emergency department; iqr, interquartile range; rsv, respiratory syncytial virus. a smoking status is missing for a larger proportion of non-rsv illnesses because these cases were not abstracted. b wilcoxon test was used for differences in medians. and included hospital admission (n = ), ed visit (n = ), and pneumonia (n = ). the ed visits included patients who were admitted and who were discharged. among patients with a moderate outcome, ( %) received a new antibiotic prescription, ( %) received bronchodilator or nebulizer treatment, and ( %) received new systemic corticosteroid therapy; ( %) were treated with an antiviral drug. the risk of a serious outcome was approximately double for patients with copd or chf compared with patients without these conditions (table ) . thirty-two participants with rsv infection were admitted to a hospital within days. three of these hospitalizations were for noncardiopulmonary conditions that were unlikely to be related to rsv infection, including incarcerated hernia, small bowel obstruction, and acute gastrointestinal illness. these hospital admissions were excluded from the serious outcome group. fifteen of the remaining hospitalized patients were enrolled in the inpatient setting. four of those were directly admitted from an outpatient clinic, whereas the remaining were admitted from the emergency department. seven patients were enrolled during an outpatient encounter on the same day as their hospital admission, leaving with hospital admissions or more days after enrollment. the median interval from symptom onset to admission for rsv-positive hospitalized individuals was days. preexisting chronic diseases were common among hospitalized patients with rsv, including copd (n = ; %), chf (n = ; %), asthma (n = ; %), and diabetes (n = ; %) ( table ). twenty-one ( %) received a discharge diagnosis of respiratory tract infection (eg, pneumonia, bronchitis, exacerbation of copd). only patient was recognized to have rsv at the time of hospital discharge. the mean (sd) duration of hospital admission was . ( . ) days. twenty-seven ( %) were discharged to home, and ( %) were transferred to a rehabilitation or long-term care facility; there were no deaths within days. the hospital course was uncomplicated for most patients. none required mechanical ventilation or icu admission. twenty-five ( %) received antimicrobials; ( %) were treated with antiviral drugs. to estimate the number of hospitalized rsv cases that were not included in this analysis, we extracted hospital diagnosis codes for community cohort members during periods of study enrollment. we identified an additional individuals ≥ years of age who were hospitalized during study enrollment periods with a diagnosis code for rsv but were not enrolled in the influenza vaccine effectiveness study. the median community cohort size for adults aged ≥ years was (range, - ) for the seasons from - through - . the overall seasonal incidence of medically attended rsv illness was cases per ( % ci, - ). the rsv incidence was cases per ( % ci, - ) among persons with chronic cardiopulmonary disease and ( % ci, - ) among those without cardiopulmonary disease (incidence rate ratio [irr], . ; % ci, . - . ). there was a significant decline in the incidence of medically attended rsv from - through - for the entire cohort (p = . , chi-square test for trend) and for those with cardiopulmonary disease (p = . , chi-square test for trend). the incidence of medically attended rsv was also higher in women compared with men (irr, . ; % ci, . - . ). the overall incidence rates of medically attended illness caused by rsv a and rsv b were nearly identical (irr, . ; % ci, . - . ), although or the other subtype was often dominant during a single season. the temporal trend in rsv incidence suggests an overall reduction among adults ≥ years of age after the - season (figure ). abbreviations: chf, congestive heart failure; copd, chronic obstructive pulmonary disease; ed, emergency department; iqr, interquartile range; mslrtd, moderate to severe lower respiratory tract disease; rsv, respiratory syncytial virus; rt-pcr, reverse transcription polymerase chain reaction; sob, shortness of breath. a high-risk comorbid conditions (except immune-compromised status, which was determined from electronic diagnosis codes), symptoms/exam findings from enrollment visit, and therapeutic interventions were obtained by medical record abstraction. b three additional hospital admissions occurred within days for incarcerated hernia, small bowel obstruction, and acute gastrointestinal illness. these conditions were considered unrelated to the preceding rsv infection. c wilcoxon test was used for differences in medians. d p-values not shown for characteristics which contributed to the mslrtd case definition. we compared the peak month for rsv and influenza positives during each season among study participants ≥ years old. in seasons, the rsv peak and the influenza peak occurred in the same calendar month. in seasons, the rsv peak occurred before the influenza peak, and in seasons, the rsv peak occurred after the influenza peak. we also compared the peak month for rsv detection among study participants with the peak month based on local clinical testing of children < months. in seasons, the peak calendar month was the same for enrolled adults ≥ years old and children; the pediatric peak occurred - months earlier in seasons and month later in seasons. in a longitudinal assessment over seasons in a single community, we found that rsv was a common cause of outpatient respiratory illness in adults ≥ years of age. rsv was detected in % of those with medically attended acute respiratory illness, and it was abbreviations: chf, congestive heart failure; ci, confidence interval; copd, chronic obstructive pulmonary disease; ed, emergency department; iqr, interquartile range; mslrtd, moderate to severe lower respiratory tract disease; rsv, respiratory syncytial virus; rt-pcr, reverse transcription polymerase chain reaction; sob, shortness of breath. a high-risk comorbid conditions (except immune-compromised status, which was determined from electronic diagnosis codes) and symptoms/exam findings from enrollment visit were obtained by medical record abstraction. the second most common viral pathogen in this age group. the number of rsv a and rsv b cases was similar overall, but subtype was usually dominant during any given season. the seasonal incidence of medically attended rsv was variable but was consistently higher in persons with preexisting cardiopulmonary disease. moderate or serious outcomes, including change in therapy, hospital admission, and pneumonia, occurred in > % of patients with laboratory-confirmed rsv infection. serious outcomes (hospital admission, ed visit, or pneumonia) occurred in nearly of every patients with rsv infection. patients with serious outcomes were significantly more likely to present with dyspnea and objective signs of lower respiratory tract involvement, including wheeze, rales, and rhonchi. hospital admission was the most common serious outcome, and the risk of a serious outcome increased with age. serious rsv illness was significantly associated with chronic obstructive pulmonary disease and congestive heart failure. the majority of outpatient rsv cases ( %) resulted in a moderate outcome, including a new prescription for antibiotics, antivirals, bronchodilators, or systemic corticosteroids. nearly half of individuals with rsv required a chest x-ray and measurement of oxygen saturation during the enrollment visit or follow-up period. overall, the most common therapeutic interventions included new antibiotic prescription and bronchodilator/nebulizer treatment. more than three-quarters of patients with rsv were treated with antibiotics. although this study did not evaluate bacterial coinfections, it is possible that many of these antibiotic courses were unnecessary. few studies have assessed the occurrence, clinical spectrum, and outcomes for rsv illness among older adults in the outpatient setting. a sentinel system in the united kingdom identified rsv in % of adults ≥ years old with medically attended acute respiratory illness [ ] . this is similar to the percent positive ( %) that we observed over seasons in adults ≥ years old. in a previous study over a shorter time period, we found that cough, nasal congestion, and wheezing were more common in adults ≥ years old with rsv compared with those with other causes of acute respiratory illness [ ] . prospective rsv illness surveillance in nearly healthy, working-age adults from to demonstrated that % of rsv infections were symptomatic [ ] . of the latter, % involved the lower respiratory tract (tracheobronchitis or wheezing). additional studies are needed in diverse populations to estimate the burden of adult rsv illness and the potential impact of future licensed vaccines. rsv-associated moderate to severe lower respiratory tract illness is a composite measure of lower respiratory tract illness that has been used as a proxy for serious respiratory disease outcomes in rsv vaccine clinical trials (clinicaltrials.gov identifiers: nct and nct ). in this study, we found that rsv-mslrtd at the time of enrollment was significantly associated with a serious clinical outcome. in particular, patients with rsv-mslrtd at enrollment were significantly more likely to require hospital admission and were also more likely to develop pneumonia during the follow-up period. the incremental risk (absolute risk difference) for each of these outcomes exceeded % when rsv-mslrtd was present at enrollment. these findings suggest that rsv-mslrtd may be a useful surrogate measure to identify individuals at risk for more serious clinical end points in trials of vaccines and antivirals. the strengths of this study include consistent prospective recruitment of patients with acute respiratory illness from a defined community cohort, inclusion of consecutive winter seasons, collection of standardized clinical data during the enrollment encounter, and detailed abstraction of outpatient and inpatient medical records for the -day follow-up period. abbreviations: bipap, bilevel positive airway pressure; chf, congestive heart failure; copd, chronic obstructive pulmonary disease; cpap, continuous positive airway pressure; icu, intensive care unit; mslrtd, moderate to severe lower respiratory tract disease; rsv, respiratory syncytial virus; rt-pcr, reverse transcription polymerase chain reaction. this observational study also has several limitations. recruitment was restricted to individuals who sought medical care for respiratory illness during periods of influenza transmission, and cough was required for enrollment during seasons after the pandemic. this study underestimated the occurrence of rsv hospital admissions as enrollment was restricted to primary care and urgent care outpatient clinics after . based on diagnosis codes, we identified an additional individuals ≥ years old in our community cohort who were hospitalized with a diagnosis of rsv but not enrolled in the vaccine effectiveness study. these patients were most likely admitted through the emergency department or subspecialty clinics where study recruitment did not occur. in addition, some rsv cases may have been missed by rt-pcr testing, as serology has been shown to improve the detection of rsv infection in adults with community-acquired pneumonia [ ] . finally, this study was conducted in a largely rural and racially homogenous population, and results may not reflect outpatient rsv occurrence and outcomes in urban and racially diverse settings. as new vaccines and antivirals are licensed for rsv prevention and treatment in adults, there will be a great need for data to estimate the population burden and the potential reduction in cases and serious outcomes. the potential impact on reducing antimicrobial use is another potential benefit that requires further evaluation. these data will be needed to increase awareness of rsv among adult health care providers and to inform cost-effectiveness analyses for public health planning and policy deliberations. in preparation for these decisions, additional research is urgently needed to estimate disease burden and outcomes in larger and more diverse populations. estimates of mortality attributable to influenza and rsv in the united states during - by influenza type or subtype, age, cause of death, and risk status respiratory viruses associated with patients older than years presenting with ili in senegal all chronic cardiopulmonary disease viral etiology of influenza-like illnesses in respiratory syncytial virus infection in guatemala a study of respiratory infections in the elderly to assess the role of respiratory syncytial virus isolation of respiratory syncytial and influenza viruses from the sputum of patients hospitalized with pneumonia an epidemic of respiratory syncytial virus in elderly people: clinical and serological findings noninfluenza respiratory virus infection in long-term care facilities respiratory syncytial virus infections on an adult medical ward nosocomial transmission of respiratory syncytial virus in immunocompromised adults an outbreak of respiratory syncytial virus in a bone marrow transplant center the natural history of respiratory syncytial virus infection in cancer and transplant patients: implications for management respiratory syncytial virus is not an important community acquired pathogen in adult hematological malignancy patients respiratory syncytial virus infection in elderly and high-risk adults respiratory syncytial virus is an important cause of community-acquired lower respiratory infection among hospitalized adults respiratory syncytial virus and other respiratory viral infections in older adults with moderate to severe influenza-like illness rates of hospitalizations for respiratory syncytial virus, human metapneumovirus, and influenza virus in older adults high morbidity and mortality in adults hospitalized for respiratory syncytial virus infections medically attended respiratory syncytial virus infections in adults aged ≥ years: clinical characteristics and outcomes seasonal incidence of medically attended respiratory syncytial virus infection in a community cohort of adults ≥ years old immunogenicity and safety of a respiratory syncytial virus fusion protein (rsv f) nanoparticle vaccine in older adults effectiveness of inactivated influenza vaccines varied substantially with antigenic match from the - season to the - season influenza vaccine effectiveness in wisconsin during the - season: comparison of interim and final results influenza vaccine effectiveness in the united states during - : variable protection by age and virus type influenza vaccine effectiveness in the united states by vaccine type comparison of the biofire filmarray rp, genmark esensor rvp, luminex xtag rvpv , and luminex xtag rvp fast multiplex assays for detection of respiratory viruses incidence of medically attended respiratory syncytial virus and influenza illnesses in children - months old during four seasons contribution of influenza and respiratory syncytial virus to community cases of influenza-like illness: an observational study medically attended respiratory syncytial virus infections in adults aged ≥ years: clinical characteristics and outcomes respiratory syncytial virus infections in previously healthy working adults serology enhances molecular diagnosis of respiratory virus infections other than influenza in children and adults hospitalized with community-acquired pneumonia the authors appreciate the contributions of the following individuals: elizabeth key: cord- -kc pev authors: cohen, adam l.; sahr, philip k.; treurnicht, florette; walaza, sibongile; groome, michelle j.; kahn, kathleen; dawood, halima; variava, ebrahim; tempia, stefano; pretorius, marthi; moyes, jocelyn; olorunju, steven a. s.; malope-kgokong, babatyi; kuonza, lazarus; wolter, nicole; von gottberg, anne; madhi, shabir a.; venter, marietjie; cohen, cheryl title: parainfluenza virus infection among human immunodeficiency virus (hiv)-infected and hiv-uninfected children and adults hospitalized for severe acute respiratory illness in south africa, – date: - - journal: open forum infect dis doi: . /ofid/ofv sha: doc_id: cord_uid: kc pev background. parainfluenza virus (piv) is a common cause of acute respiratory tract infections, but little is known about piv infection in children and adults in africa, especially in settings where human immunodeficiency virus (hiv) prevalence is high. methods. we conducted active, prospective sentinel surveillance for children and adults hospitalized with severe acute respiratory illness (sari) from to in south africa. we enrolled controls (outpatients without febrile or respiratory illness) to calculate the attributable fraction for piv infection. respiratory specimens were tested by multiplex real-time reverse-transcription polymerase chain reaction assay for parainfluenza types , , and . results. of sari cases enrolled, ( . %) tested positive for any piv type: ( . %) were type ; ( . %) were type ; ( . %) were type ; and ( . %) had coinfection with piv types. after adjusting for age, hiv serostatus, and respiratory viral coinfection, the attributable fraction for piv was . % ( % ci [confidence interval], . – . ); piv contributed to sari among hiv-infected and -uninfected children < years of age and among individuals infected with piv types and . the observed overall incidence of piv-associated sari was ( % ci, – ) cases per population and was highest in children < year of age ( [ % ci, – ] cases per population). compared with persons without hiv, persons with hiv had an increased relative risk of piv hospitalization ( . ; % ci, . – . ). conclusions. parainfluenza virus causes substantial severe respiratory disease in south africa among children < years of age, especially those that are infected with hiv. parainfluenza virus (piv) is a paramyxovirus commonly detected in patients with respiratory illness, such as upper respiratory tract infections, laryngotracheobronchitis (croup), or pneumonia. there are distinct types: , , , and . parainfluenza virus infection is most common in childhood, and serologic surveys have shown that nearly all children have antibodies to piv by years of age [ , ] . parainfluenza virus is associated with %- % of hospitalized respiratory tract infections in children and adults [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . parainfluenza virus infections occur throughout the year, but there are recognized patterns of seasonality associated with different types [ ] . the clinical significance of identifying piv infection among patients with respiratory illness does not necessarily imply causation because the virus may be found in individuals without respiratory symptoms [ ] . in south africa, human immunodeficiency virus (hiv) is prevalent, which impacts respiratory disease burden [ ] . in , the national hiv prevalence estimate among children < years was . % and decreased to . % by ; the hiv prevalence among adults ≥ years of age was approximately . % during the same time [ ] . a study from soweto prior to availability of antiretroviral therapy (art) found that hiv-infected children with piv-associated lower respiratory tract infection had greater morbidity and mortality than hivuninfected children [ ] . a more recent study from cape town found that piv was associated with % of viral-associated pediatric intensive care unit admissions [ ] . previous studies from our group have detected piv in . % of adults and . % of children hospitalized with severe acute respiratory illness [ ] [ ] [ ] . little is known about the epidemiology of piv infection, including its association with illness and its clinical manifestation among both hiv-infected and -uninfected children and adults in south africa, especially in the era of art management. in this study, we aimed to describe the epidemiological and clinical characteristics of hiv-infected and -uninfected children and adults hospitalized with piv-associated pneumonia in south africa. in addition, we compared the prevalence of piv detection with controls for better interpretation of surveillance data. we conducted surveillance for children and adults hospitalized with pneumonia through the severe acute respiratory illness (sari) program, an active, prospective, sentinel hospitalbased surveillance system in provinces in south africa, as described previously [ ] . in february , sari surveillance began in of the provinces of south africa (chris hani-baragwanath academic hospital [chbah] , an urban site in gauteng province; edendale hospital, a periurban site in kwazulu-natal province; and matikwana and mapulaneng hospitals, rural sites in mpumalanga province). in june , an additional surveillance site was introduced at the klerksdorp-tshepong hospital complex, periurban sites in north west province. we stopped enrolling at chbah in december of . in addition to sari cases, controls were enrolled from may at outpatient clinics serving the same population as of the sari sentinel sites: edendale hospital gateway clinic, kwazulu-natal province, and jouberton clinic, north west province. the case definitions used and enrollment procedures for both sari cases and controls are described fully in the supplementary material. this surveillance, including testing for influenza and hiv, received human subjects review and ethics approval by the universities of the witwatersrand, kwazulu-natal, and pretoria, all of south africa. the centers for disease control and prevention (atlanta, ga) deemed this a nonresearch, surveillance activity. nasopharyngeal aspirates from patients aged < years and nasopharyngeal and throat swabs from patients aged ≥ years were placed in viral transport media, kept at - °c, and sent to the national institute for communicable diseases (nicd) in johannesburg within hours of collection. respiratory specimens were tested by multiplex real-time, reversetranscription polymerase chain reaction (pcr) assay for respiratory viruses (piv types , , and ; respiratory syncytial virus [rsv]; influenza a and b viruses; enterovirus; human metapneumovirus; adenovirus, and rhinovirus) [ ] . we did not test for piv type during the study period. we did not test for adenovirus from august to october because of unavailability of reagents. streptococcus pneumoniae was identified by quantitative real-time pcr detecting the lyta gene from whole blood specimens [ ] . when available, hiv-infection status data were obtained through routine standard of care testing at the treating hospital. when not available, hiv testing was implemented at nicd through anonymized, linked dried blood spot specimen testing by hiv pcr assay for children aged < months and by enzyme-linked immunosorbent assay for those aged ≥ months. we conducted multivariable logistic regression models. in our first analysis, we implemented univariate and multivariable logistic regression models to determine the association of piv infection with sari (for all types together and for each viral type separately) compared with controls enrolled from may to december at the sites in kwazulu-natal and north west provinces. for the estimation of association with sari, we conducted an overall analysis adjusting for age, hiv serostatus, respiratory viral coinfection, and underlying illness and subanalyses stratifying by age and hiv serostatus and adjusting for respiratory viral coinfection and underlying illness. then, we estimated the attributable fraction (af) from the odds ratio (or) obtained from the multivariable model using the following formula: af = (or- )/or × . in our second analysis, univariate and multivariable logistic regression was used to determine factors associated with hiv infection among patients with piv-associated sari from january to december at all sari sites. in our third analysis, we used multinomial regression to compare and contrast demographic and clinical characteristics and severity among patients infected with the piv types. for the multinomial analysis, we used piv type as the baseline category because type is most common. the second and third analyses models were built using manual backward elimination in which nonsignificant variables were removed from the model one at a time starting with the variables with smallest magnitude of effect until all remaining variables had a p value of <. . covariates with a p value of <. at univariate analysis were assessed for significance with multivariable analysis; statistical significance was assessed at p < . for all multivariable models. two-way interactions were assessed by inclusion of product terms for all variables remaining in the final additive models. for each univariate analysis, we used all available case information. for important variables in the hiv association and af analyses that had substantial missing data, namely hiv infection status, we multiply imputed that variable as well as any variables that were incomplete and associated with hiv using chained equation multiple imputation over iterations. when adjusting for respiratory viral coinfection in our models, we evaluated coinfection with each virus separately and also as a combined variable of coinfection with any of the tested viruses. calculation of observed incidence and incidence adjusted for af of piv-associated sari hospitalizations was done for study site (chbah) where population denominators were available, as described previously [ ] . a complete description of the incidence calculation methods can be found in the supplementary material. . of the sari cases tested for piv, ( . %) tested positive for any piv type: ( . %) were solely type , ( . %) were solely type , and ( . %) were solely type . coinfection with types of piv occurred in ( . %) patients: ( . %) tested positive for both types and , ( . %) for types and , and ( . %) for both and . children < years of age were more likely to test positive for piv ( . %, of ) than individuals aged ≥ years ( . %, of , p < . ). males were slightly more likely to test positive for piv ( . %, of ) than females ( . %, of , p = . ). the sari patients who died in hospital were less likely to test positive for piv ( . %, of ) than those who did not ( . %, of , p = . ). there were no differences in percentage testing positive by race or surveillance site (data not shown). human immunodeficiency virus status was determined for ( . %) of sari cases, of which ( . %) were infected with hiv. most of the patients with missing hiv status were children < years of age ( . % [ of ], compared with . % [ of ] for individuals ≥ years of age). on univariate analysis, sari patients that were hivinfected were less likely to test positive for piv ( . %, of ) than those that were hiv-uninfected ( . %, of , p < . ). during the time period when controls were enrolled (may -december ), sari cases were enrolled. for controls, were screened and ( . %) were enrolled. overall, ( . %) of the cases and ( . %) of the controls tested positive for piv ( table ). the overall piv af was . % ( % confidence interval [ci], . - . ), after adjusting for age, hiv serostatus, respiratory viral coinfection, and underlying illness, suggesting that more than two-thirds of pivassociated sari cases could be attributed to piv infection. a statistically significant af was seen among both hiv-infected ( . %; % ci, . - . ) and hiv-uninfected individuals of any age ( . %; % ci, . - . ); although the point estimates are different, the cis overlap. the af was highest among young children and older adults, although it was only statistically significant among children < years of age (for < year, . %, % ci, . - . ; for - years, . %, % ci, . - . ); this same association among children < years of age was seen among both hiv-infected and -uninfected individuals. we then calculated the af for piv types , , and separately. the af was . % ( % ci, . - . ) for piv type , . % ( % ci, - . ) for piv type , and . % ( % ci, . - . ) for piv type . the age and hiv-status subgroup analysis results for piv types and separately were similar to those found for parainfluenza overall, except that some subgroup analyses involved smaller numbers of subjects and were not statistically significant (data not shown). we did not conduct the subgroup analysis for piv type because it was not found to be statistically associated with disease. most ( . %, of ) patients with piv-associated sari were < years of age, the group for which we found a statistically significant and substantial af. twelve percent ( . %, of ) of children < years of age with piv-associated sari were infected with hiv ( tables and ). on multivariable analysis among individuals ≥ years of age with piv-associated sari, hiv-infected individuals were more likely to be young adults - years of age (aor . , % ci, . - . ), compared with children and young adults ( - years of age), and less likely to have an underlying illness other than hiv (aor . , % ci, . -. ; table ). when we compared epidemiologic and clinical characteristics of the piv types, we found statistically significant differences in age, year of infection, and coinfection with other respiratory viruses (supplementary table ). on multivariable multinomial analysis, patients with piv type infection were more likely to be < year of age and patients with piv type infection were more likely to be - years of age, compared with patients with other piv types. compared with sari patients with piv type infection, patients with either type or infection were more likely to be coinfected with rsv (for type , aor . , % ci, . - . ; for type , aor . , % ci, . - . ). in addition, patients with piv type infection were more likely to be coinfected with rhinovirus (aor . , % ci, . - . ) or enterovirus (aor . , % ci, . - . ) than patients with type infection. the overall observed incidence of piv-associated sari in soweto from to was ( % ci, - ) cases per population ( table ). the observed incidence was highest in children < year of age ( [ % ci, - ] cases per population) and lowest in those - years of age ( [ % ci, - ] cases per ). in all age groups, the observed incidence was higher among hiv-infected compared with hivuninfected individuals. the subgroup with the highest incidence was hiv-infected infants < year of age ( [ % ci, - ] cases per ). the overall incidence adjusted for the af was cases per ( % ci, - ); the age-specific adjusted incidences followed the same trend as the observed incidences ( table ). the age-adjusted relative risk of piv hospitalization by hiv status was . ( % ci, the piv serotypes ( , , and ) were found to cocirculate throughout the year and differed from year to year; seasonal peaks were observed for piv- between september and november, which is spring in south africa (figure ). the percentage of specimens testing positive for any piv type varied by year, with a higher proportion of sari positive for piv in parainfluenza virus is associated with a significant amount of severe respiratory disease in south africa among children < years of age, especially those that are infected with hiv. the evidence for this is based on of our findings: the af and the observed incidence. among children < years of age, a substantial amount of sari is attributable to piv, particularly types and . the observed incidence of piv in soweto, south africa, is much higher among hiv-infected individuals and is similar to other respiratory viral pathogens such as influenza and human metapneumovirus [ , ] . clinicians should recognize piv as a common cause of respiratory illness in children during the spring season, especially among children that are infected with hiv, and interventions should be developed to prevent and treat piv disease. as we found in south africa, studies from across the globe have found that piv is associated with up to % of inpatient respiratory illness, particularly among the very young. this has been found in bangladesh [ ] , china [ , ] , thailand [ ] , the united states [ , ] , and in multiple countries across the african continent. in kenya, . % of individuals ≥ years of age hospitalized with pneumonia had piv types - detected [ ] . in ghana, . % of children hospitalized with acute lower respiratory tract infection had piv types - [ ] . in mozambique, . % of infants < year and . % of children < years of age hospitalized with acute respiratory illness tested positive for piv [ , ] . it can be difficult to attribute respiratory disease to a specific pathogen. molecular tests may identify viruses in respiratory specimens that may not be causing illness, and coinfection with other potentially pathogenic respiratory viral infections was common in our population. we found that a majority of sari was attributable to piv types and in children, even when controlling for viral respiratory coinfection, but not all studies have found that piv is pathogenic. in fact, very few studies have adequately evaluated piv in the context of controls. two studies from kenya that compared patients with respiratory illness to controls did not find a statistically significant attributable risk for piv [ , ] . however, a study comparing children < years of age from thailand hospitalized with pneumonia to controls found findings similar to ours, specifically that infection with piv types or was associated with disease [ ] . the lower incidence and nonsignificant af from our data among individuals ≥ years of age suggests that piv infection may not be associated with respiratory disease in older children and adults. we did not find a significant af for patients infected with piv type , but we may not have been powered to detect this because type was the least common type. we found differences among patients infected with different types of piv and between patients infected and uninfected with hiv. in children, patients with piv-associated sari who were hiv-infected were more likely to be older and to be coinfected with pneumococcus; however, the af among adults was not statistically significant. the association between respiratory viral and pneumococcal infection, although not described previously for piv infection, is well described for other pathogens such as influenza [ ] and rsv [ ] . pneumococcal conjugate vaccine was introduced in the south africa childhood immunization system in , so it was available and being used during the entire time of this study. the seasonality of piv in south africa is similar to that seen in other temperate countries such as the united states, where piv circulates during the northern hemisphere spring and winter seasons [ ] . in contrast, in tropical and subtropical countries in africa, such as cameroon, ghana, and kenya, piv does not appear to have distinct seasonality [ , , ] . this is one of few studies that describe the epidemiology of piv in both children and adults over a long period and in the context of controls. however, there were some limitations to our study. not all children were tested for hiv, and we did not analyze piv in cases of milder outpatient influenza-like illness, which includes common presentations of piv illness such as croup. although it is uncommon and uncommonly tested for, we did not test for piv type , so our incidence estimates would be a minimum estimate. we also did not test for all viral respiratory pathogens, such as coronavirus and bocavirus. the large number of patients from chbah ( %) may bias results toward the epidemiology at that one site. our calculation of incidence was for only site and the calculation of af was conducted at , so these analyses may not be representative of all regions in south africa. the incidence may be an underestimate if patients did not seek medical care for their illness or sought care at a hospital other than chbah or died before reaching the hospital. the increased incidence of hospitalization among individuals infected with hiv may be due to a lower threshold for hospitalization compared with hiv-uninfected individuals. lastly, we did not have data on steroid use, which is a common treatment for croup in children, and for patients with hiv infection, we did not have information on art nor cd cell count. in conclusion, based on years of respiratory disease surveillance, piv is a common cause of sari among children < years in south africa. among children, the observed incidence of piv is higher in the hiv-infected population than the hivuninfected population. a vaccine to protect against piv is not currently available, but vaccine candidates are in the clinical testing phase [ ] . the findings of our study accentuate the need to target children for piv prevention strategies including vaccination, should a vaccine against piv become available. abbreviations: ci, confidence interval sari, severe acute respiratory illness preparedness and response to avian and pandemic influenza in south africa (cooperative agreement number: u /ip - ), and the national institute for communicable diseases, south africa. potential conflict of interest. h. d. has received honoraria from msd-south africa and novartis-south africa, honoraria from pfizer-south africa for speaking engagements a study of the antibodies against parainfluenza viruses in childrens' sera half-life of human parainfluenza virus type (hpiv ) maternal antibody and cumulative proportion of hpiv infection in young infants parainfluenza virus infection of young children: estimates of the population-based burden of hospitalization human parainfluenza virus-associated hospitalizations among children less than years of age in the united states epidemiology and clinical presentation of the four human parainfluenza virus types etiology and incidence of viral and bacterial acute respiratory illness among older children and adults in rural western kenya respiratory viruses in children hospitalized for acute lower respiratory tract infection in ghana viral acute respiratory infections among infants visited in a rural hospital of southern mozambique community-acquired pneumonia among u.s. children community-acquired pneumonia requiring hospitalization among u.s. adults influenza and parainfluenza viral infections in children a preliminary study of pneumonia etiology among hospitalized children in kenya severe influenza-associated lower respiratory tract infection in a high hiv-prevalence setting-south africa severe lower respiratory tract infections associated with human parainfluenza viruses - in children infected and non-infected with hiv type an investigation into the prevalence and outcome of patients admitted to a pediatric intensive care unit with viral respiratory tract infections in cape town, south africa respiratory viral coinfections identified by a -plex real-time reverse-transcription polymerase chain reaction assay in patients hospitalized with severe acute respiratory illness-south africa epidemiology of severe acute respiratory illness among adults and children aged ≥ years in a high hiv-prevalence setting epidemiology of viral-associated acute lower respiratory tract infection among children < years of age in a high hiv prevalence setting evaluation and improvement of real-time pcr assays targeting lyta, ply, and psaa genes for detection of pneumococcal dna population-based incidence of severe acute respiratory virus infections among children aged < years in rural bangladesh viral etiologies of hospitalized acute lower respiratory infection patients in china hospitalization due to human parainfluenza virus-associated lower respiratory tract illness in rural thailand etiology and epidemiology of viral pneumonia among hospitalized children in rural mozambique: a malaria endemic area with high prevalence of human immunodeficiency virus incidence and etiology of acute lower respiratory tract infections in hospitalized children younger than years in rural thailand interaction between influenza virus and streptococcus pneumoniae in severe pneumonia association between respiratory syncytial virus activity and pneumococcal disease in infants: a time series analysis of us hospitalization data seasonal trends of human parainfluenza viral infections: united states viral etiology of influenza-like illnesses in cameroon progress in the development of human parainfluenza virus vaccines we thank the surveillance officers, severe acute respiratory illness programme team, and especially the patients. we also acknowledge dorothy supplementary material is available online at open forum infectious diseases (http://openforuminfectiousdiseases.oxfordjournals.org/). key: cord- -no ucyq authors: murkey, jamie a.; chew, kara w.; carlson, margrit; shannon, chelsea l.; sirohi, deepika; sample, hannah a.; wilson, michael r.; vespa, paul; humphries, romney m.; miller, steve; klausner, jeffrey d.; chiu, charles y. title: hepatitis e virus–associated meningoencephalitis in a lung transplant recipient diagnosed by clinical metagenomic sequencing date: - - journal: open forum infect dis doi: . /ofid/ofx sha: doc_id: cord_uid: no ucyq hepatitis e virus (hev) infection uncommonly causes chronic hepatitis and neurologic disease. we describe a case of genotype a hev meningoencephalitis diagnosed by metagenomic next-generation sequencing, illustrating the power of an unbiased molecular approach to microbial testing and the first reported case of hev infection presumably acquired through lung transplantation. the precision diagnosis of acute infectious diseases (pdaid) study for the diagnosis of hospitalized patients with suspected infectious causes of meningoencephalitis was launched in june . the goal of this multihospital, nationwide study is to evaluate the utility and cost-effectiveness of a clinical metagenomic next-generation sequencing (mngs) assay for pathogen detection as compared with conventional microbiological testing (supplementary methods). the mngs approach does not define targets a priori; rather, any and all viruses, bacteria, fungi, and parasites are identified in clinical samples on the basis of sequence homology to genbank microbial reference databases. the mngs assay has been validated in a clinical laboratory improvement amendments (clia) laboratory [ , ] , and results are relayed to the treating clinical team(s) and reported in the patient's electronic medical record. here we present a case of hev meningoencephalitis diagnosed by clinical mngs in an immunocompromised patient enrolled in the pdaid study. we demonstrate the power of clinical mngs in elucidating the cause of uncommon and unexpected infections and identify a case of chronic hev infection most likely transmitted through the transplanted lungs the patient had received years prior. the case patient is a -year-old woman with a history of idiopathic pulmonary fibrosis status post bilateral lung transplant in , migraines, hypercoagulability, and multiple sclerosis (ms) on chronic immunosuppression who was admitted to university of california, los angeles medical center in october with days of fever, headache, nausea, vomiting, neck stiffness, and photophobia. the patient had been hospitalized days prior to admission at an outside hospital complaining of the "worst headache of my life. " during that hospitalization, she was treated with a variety of abortive migraine medications with only partial response and diagnosed with tacrolimus toxicity (initial tacrolimus level of . ng/ml; . ng/ml on discharge) and acute kidney injury. of note, her symptoms occurred in the setting of > years of ms-attributed episodic leg pain and swelling, years of occasional word-finding difficulty and slurred speech, year of recurrent episodes of dizziness and falls, and month of lower extremity weakness. in addition, the patient had an acute episode of encephalopathy in and a first-time seizure of unclear etiology in march . the patient is a resident of orange county, california. she denied sick contacts, pets or other animal exposure, insect bites, and eating shellfish or game meats. she reported travel to the mountains in utah in august , the caribbean in , and throughout europe decades before admission. her outpatient medications included immunosuppressive medications (tacrolimus, mycophenolate mofetil, and prednisone for lung transplant; teriflunomide for ms), antimicrobial prophylaxis (trimethoprim/sulfamethoxazole and acyclovir), anticoagulation, and pain medications, including an intrathecal morphine pump. upon admission, the patient was noted to be sleepy but fully oriented and in moderate distress from pain; she had a fever of . °c but otherwise had normal vital signs. physical exam was remarkable for right leg tenderness from deep venous thrombosis. initial exams showed stable pancytopenia (white blood cell and platelet counts of . × /l and /l, respectively, and hemoglobin of . g/dl), elevated transaminases (alanine aminotransferase and aspartate aminotransferase of u/l and u/l, respectively), elevated international normalized ratio of . , and tacrolimus level of . ng/ml. magnetic resonance imaging revealed baseline periventricular, subcortical, and juxtacortical t /flair white matter intensities associated with her ms but no acute changes (table ) . empiric antimicrobials were initiated with vancomycin, ceftazidime, acyclovir, and voriconazole. tacrolimus was initially held but subsequently resumed. given the patient's ongoing symptoms, a lumbar puncture was performed on day , revealing a lymphocytic pleocytosis ( table ) . all clinical microbiologic studies returned negative (table ) . by day , the patient was clinically improved except for mild persistent headache. the differential diagnosis included viral meningoencephalitis or tacrolimus toxicity. the patient was identified as a possible pdaid case based on the unknown etiology of her meningoencephalitis. a cerebrospinal fluid sample from day of her hospitalization was analyzed by clinical mngs testing at university of california, san francisco. dna and rna sequencing libraries yielded and reads, respectively. analysis using the sequence-based ultra-rapid pathogen identification (surpi+) clinical bioinformatics pipeline detected hev. assembly yielded a . % complete viral genome with approximately % pairwise identity to the closest matched reference in genbank (supplementary figure a and b) . phylogenetic analysis assigned the genome to genotype a, most closely related to viral strains from japan and southeast asia (supplementary figure c) . the diagnosis of hev-associated meningoencephalitis was communicated to the patient. review of the patient's electronic medical record showed normal transaminase levels before lung transplantation, with persistent low-level elevations after transplantation in (supplementary figure a and b) . the patient was readmitted weeks after being discharged with new decompensated liver disease, encephalopathy, asterixis, ascites, and cirrhosis by abdominal ultrasound and liver elastography. the hev mngs results prompted immediate follow-up clinical testing demonstrating serum hev immunoglobulin m (igm) positivity, negative immunoglobulin g (igg), and plasma hev viremia ( international units [iu]/ml) ( table , supplementary figure c ), and treatment with ribavirin and low-dose diuretics. hepatitis e virus rna declined, transaminases normalized, and ascites, edema, and mentation improved, but the patient subsequently had readmissions for headache, nausea, and vomiting attributed to tacrolimus toxicity or side effects from ribavirin, necessitating multiple ribavirin treatment interruptions. the case was reported to the united network for organ sharing donor safety net. testing of stored donor serum was positive for hev igg and igm antibody but negative for hev rna. the donor was reported to be a -year-old woman with methamphetamine use from central california without clear risk factors for hev infection or abnormal transaminase levels. pretransplant samples from the case patient were not available. we present a case of genotype a hev infection in a lung transplant recipient with ms on immunosuppressive therapy. the patient's symptoms and lymphocytic pleocytosis on admission were consistent with acute viral meningitis. tacrolimus toxicity may have also contributed to her presentation because she improved rapidly after tacrolimus discontinuation. the patient's persistent low-level transaminitis for several years before admission and subsequent evidence of cirrhosis suggest that she was likely chronically infected with hev. although initial testing for hev igg was negative, serologies can be unreliable in immunosuppressed patients [ ] . her prior episodes in and of seizure and "encephalopathy" are also suggestive of chronic neuroinvasive hev disease with intermittent flares. although the development of chronic hev infection is infrequent in the general population, solid organ transplant (sot) recipients are at greater risk [ ] . in series of sot recipients with hev infection, > % developed chronic hepatitis [ ] . in some of these patients, cirrhosis can develop within several years [ ] . neurologic manifestations of hev infection, including inflammatory polyradiculopathy, encephalitis, and guillain-barré syndrome, have been seen in . % of cases [ ] . the timing of neurological manifestations after hev infection has not been well described, but ranged from - months in review of cases in immunosuppressed patients. in animal models, hev is able to cross the blood-brain barrier, replicate in the central nervous system, and cause neuronal necrosis and myelin degeneration [ ] . hepatitis e virus infection is infrequently considered as an infectious cause of meningoencephalitis and specific diagnostic testing is not routinely done, underscoring the benefit of an unbiased approach such as mngs for pathogen detection [ ] . hepatitis e virus infection may be detected through serological testing, but concurrent blood and stool hev rna testing is recommended, especially in immunosuppressed patients [ ] . clinicians should consider hev in the differential diagnosis for sot or other immunosuppressed patients with unexplained hepatitis, particularly those taking calcineurin inhibitors [ ] . the treatment of chronic hev infection includes reduction in immunosuppression, enabling viral clearance in approximately % of sot patients [ ] . ribavirin monotherapy has achieved sustained virologic response in approximately % of patients and was initiated in this patient [ ] . new antivirals such as sofosbuvir may have a future role in treatment [ ] . notably, our patient appears to have contracted hev from her donor. supporting evidence includes the positive anti-hev igg/igm testing of the donor's serum and the patient's persistent low-level transaminase elevations that began after transplant. of only published reports of donor-derived hev transmission, liver transplant recipient developed cirrhosis and death from septic shock within months of transplantation, and renal transplant recipients (with the same donor) developed cholestatic hepatitis at and months after transplantation [ , ] . this is the first report of presumptive hev transmission through lung transplantation. transplant centers and clinicians should be aware of the potential for hev infection in donors judged to be at elevated risk. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. hepatitis e virus and chronic hepatitis in organ-transplant recipients hepatitis e and pregnancy: understanding the pathogenesis hepatitis e virus in blood components: a prevalence and transmission study in southeast england professional practice committee and committee on laboratory practices of the microbiology resource committee of the college of american pathologists. validation of metagenomic next-generation sequencing tests for universal pathogen detection neurobrucellosis: unexpected answer from metagenomic next-generation sequencing hepatitis e virus reinfections in solid-organ-transplant recipients can evolve into chronic infections hepatitis e virus infection among solid organ transplant recipients, the netherlands factors associated with chronic hepatitis in patients with hepatitis e virus infection who have received solid organ transplants hepatitis e virus and neurologic disorders evidence of hepatitis e virus breaking through the blood-brain barrier and replicating in the central nervous system a cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples treatment of hev infection in patients with a solid-organ transplant and chronic hepatitis liver transplant from a donor with occult hev infection induced chronic hepatitis and cirrhosis in the recipient evidence of hepatitis e virus transmission by renal graft we would like to thank the patient for participating in the pdaid research study. permission to publish this case report was granted by the patient through written informed consent.financial support. this work was supported by the california initiative to advance precision medicine; an award from abbott laboratories, inc; and philanthropic grants from the sandler, bowes, and schwab foundations.potential conflicts of interest. c. y. c. is the director of the ucsf-abbott viral diagnostics and discovery center and receives research support from abbott laboratories, inc.all other authors report no conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -lhadzo o authors: lepak, alexander j; chen, derrick j; buys, ashley; stevens, linda; safdar, nasia title: utility of repeat nasopharyngeal sars-cov- rt-pcr testing and refinement of diagnostic stewardship strategies at a tertiary care academic center in a low prevalence area of the united states date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: lhadzo o background: multiple factors have led to an extremely high volume of sars-cov- rt-pcr testing. concerns exist about sensitivity and false-negative sars-cov- rt-pcr testing results. we describe a retrospective observational study examining the utility of repeat nasopharyngeal (np) sars-cov- rt-pcr testing at an academic center in a low prevalence setting. methods: all patients within our health system with > np sars-cov- rt-pcr test result were included. sars-cov- rt-pcr testing was performed according to one of four validated assays. key clinical and demographic data was collected including whether the patient was inpatient or outpatient at time of the test and whether the test was performed as part of a person under investigation (pui) for possible covid- or for asymptomatic screening. results: a total of patients had > np sars-cov- pcr test performed. the initial test was negative in . there were only negative-to-positive conversions ( . %). all were outpatients undergoing a pui work-up - days after an initial negative result. in > inpatients with repeat testing, we found no instances of negative-to-positive conversion including those undergoing pui or asymptomatic evaluation. conclusions: in a low prevalence area, repeat inpatient testing after an initial negative result, using a highly analytically sensitive sars-cov- rt-pcr, failed to demonstrate negative-to-positive conversion. the clinical sensitivity of np rt-pcr testing may be higher than previously believed. these results have helped shape diagnostic stewardship guidelines, in particular guidance to decrease repeated testing in the inpatient setting to optimize test utilization and preserve resources. the coronavirus disease (covid- ) pandemic has presented numerous unprecedented challenges. one challenge was the need for novel rapid and accurate testing methods in the context of regulatory, supply chain, and resource allocation hurdles. early reports demonstrated high accuracy and performance of real-time, reverse transcription polymerase chain reaction (rt-pcr) testing of nasopharyngeal (np) swabs [ ] [ ] [ ] . these were quickly adapted worldwide including numerous commercial iterations now available in the us. while this rapid development of testing methods was encouraging, it was overshadowed by the fact that massive quantities of tests would be necessary to diagnose, track, and attempt to contain the spread of the viral agent of covid- , sars-cov- . repeat testing of individuals has also contributed to the extremely high demand for testing. first, reports of low clinical sensitivity of the np rt-pcr testing in certain regions and case reports of falsenegative initial test results have fueled interest in repeat testing under certain clinical conditions . second, extensive and prolonged community transmission meant a high demand for testing . finally, repeated asymptomatic screening of individuals seeking care or undergoing procedures at health care facilities, as well as residents of congregate living facilities, such as skilled nursing facilities, was conducted to prevent nosocomial spread , . left completely unchecked, the repeat testing of patients could lead to diagnostic testing congestion, undue delays in results, and exhaustion of diagnostic testing resources. thus, diagnostic stewardship that is informed by clinical data is urgently needed. we have previously reported on the low rate of test positivity in asymptomatic outpatients getting tested before procedures or surgery . in this paper we report the findings of a retrospective observational study to examine results of repeat sars-cov- rt-pcr testing for patients who were suspected of having covid- (persons under investigation, or pui) and asymptomatic patients and how the results may inform diagnostic stewardship within our academic medical center in wisconsin. m a n u s c r i p t methods all patients, including adult and pediatric patients, in the university of wisconsin health system (uw health), which includes three hospitals, over clinics, and serves > , patients in the upper midwest, were eligible for inclusion in this study. those that had more than one sars-cov- rt-pcr testing from march , , to may , were included in the analysis. patients who were not cared for at our hospitals or clinics were excluded as reasons for testing and clinical information was not obtainable from medical records. uw health employees that were tested through employee health services were also excluded. advice on testing and/or re-testing was disseminated to all providers via daily emails and updated continuously on the institutional covid- resource website. outpatient testing was defined as specimen collection in an outpatient clinic encounter, an emergency room or urgent care encounter, or on admission as part of the initial admission work-up (i.e. within the first hours). inpatient testing was defined as specimen collection that was performed after the first hours during a hospitalization. pui versus asymptomatic screening designation was based on cdc pui criteria at the time of testing and was manually determined based on chart review for each patient in the dataset. in the initial stages of testing at our facilities, only puis were tested for sars-cov- . pui testing in the outpatient setting was performed according to early cdc criteria, which limited testing to moderately or a c c e p t e d m a n u s c r i p t severely ill patients; over time testing was liberalized to those with high risk conditions and symptoms compatible with covid- . repeat testing in the outpatient setting was performed if patients presented a second time and met the aforementioned criteria. no specific time to presentation was considered an exclusion to repeat testing in the outpatient setting. inpatient pui testing was mandated for those with symptoms consistent with possible covid- (e.g. unexplained fever, chills, cough, shortness of breath/hypoxia, loss of smell or taste, fatigue, vomiting or diarrhea, and/or sore throat). daily screening for respiratory symptoms was performed in the inpatient setting and repeat testing encouraged for those with changes in symptoms consistent with possible covid- disease. providers were advised, though, to only repeat pui testing on inpatients after discussion with, and verbal approval by, the on call covid- infectious disease physician, but this was not actively enforced. this meant most repeat pui tests for inpatients met clinical suspicion for high-risk or high likelihood of the patient actually having covid- despite a first negative test. on march , , we initiated pre-procedure testing for asymptomatic individuals undergoing procedures in which exposure to oral/respiratory secretions were possible. preprocedure screening was required to be completed within hours of a procedure, with repeat testing performed for subsequent procedures if they fell outside of hours of the first test or if the original procedure was rescheduled to more than hours after the test result. for example, a patient having surgery under general anesthesia on hospital days , , and would have separate tests, each occurring within hours of each surgery. advice on which procedures met criteria was circulated to all providers, but, as with repeat pui testing, proper test utilization was not actively enforced. finally, admission screen testing for all individuals admitted to certain units (e.g. nicu, pediatric and adult icu's) was performed routinely throughout the period and eventually expanded on april , , to every admission irrespective of reason or unit location. a c c e p t e d m a n u s c r i p t given that repeat screening of asymptomatic individuals was a much different clinical scenario than repeat testing of someone suspected to have covid- (i.e. pui), we separated the analysis for these two situations. also, it is important to note that a small subset of patients had more than tests performed and may have had both repeat pui testing and repeat asymptomatic screening over the study period. each subsequent test was considered a separate repeat test in the analysis and therefore the total number of tests is greater than the study population. we present descriptive statistics to summarize the data. the university of wisconsin institutional review board determined this study to be exempt. in the analysis population there were patients with > sars-cov- rt-pcr test ( children and adults) that were cared for in our health system. the results of repeat testing for the total population are shown in table . initial tests were positive in ( %) patients and negative in ( %) patients. in those initially positive, there were patients who converted from positive to negative on a repeat test. the median time between first test and repeat test for those that converted to negative was days (range - days), whereas for those that retested positive the median time between tests was days (range - days). of those that tested negative initially (n= ), there were only conversions to positive ( . % negative-to-positive conversion rate), which was noted on repeat tests done between to days after an initial negative test. repeat testing as part of a pui work-up numbered patients ( adult, pediatric). a repeat test (e.g. second, third, or rarely th test) for pui occurred in inpatients and outpatients. for inpatients, patients tested positive for sars-cov- on a repeat pui test and all were known to be positive from their first test that was done as part of an initial pui work-up (range of time to repeat testing was - days). the remainder of inpatients tested negative on repeat pui testing. within this cohort, we found instances in which an inpatient a c c e p t e d m a n u s c r i p t had a negative pui test following an initial positive test (range of time to repeat testing was - days). thus, of inpatients who tested initially negative for pui evaluation were negative on repeat testing. said another way, we found no cases of inpatients demonstrating conversion from a negative test to a positive test on repeat pui testing. the median time to repeat pui testing for inpatients was only days (range - days). it is also noteworthy that % of patients with repeat pui testing in the inpatient setting did not have a clear alternative diagnosis. out of outpatients with a repeat pui test, tested positive but only were known to be positive from prior testing. thus, outpatients converted from an initial negative test result to a positive test result ( table ). it is notable that of the had a testing interval > days between negative to positive conversion. similar to inpatient testing, we found patients had tested positive on an initial test and converted to negative on repeat testing in the outpatient setting, and the time between first test (positive) and second test (negative) was - days. those that had repeated negative pui testing results as outpatients had a median time to repeat testing of days (range - days). repeat pcr testing as part of asymptomatic screening (e.g. pre-procedure or admission screening) for sars-cov- was performed in patients. inpatient repeat screening was performed on patients with repeat screening tests ( had > screening tests for repeated procedures over a prolonged hospitalization), and all were negative on repeat screening. therefore, similar to pui testing we failed to demonstrate any inpatient negativeto-positive conversions for asymptomatic screening. the median time to repeat screen for asymptomatic inpatient testing was only days (range - days). outpatient asymptomatic screening, largely performed for planned procedures, occurred in patients. there were positives, both of which were known to be positive from an initial test. one patient was positive on asymptomatic screening days after previously testing positive and the second a c c e p t e d m a n u s c r i p t was positive on asymptomatic screening days after previously testing positive. for the remainder of outpatients that tested repeatedly negative on asymptomatic screen testing, the median time between tests was days (range - days). as part of the data analysis we examined the appropriateness of pui testing and asymptomatic screening in the context of institutional guidance that was conveyed at the time of testing. we found . % of repeat pui testing and . % of repeat asymptomatic screens likely should not have been performed based on institutional guidance. the most common reason for inappropriate pui repeat testing was provider judgement. the most common reasons for inappropriate screening included a pre-procedure screen performed for a patient that never had a procedure (n= ), a screen performed with inappropriate timing in relation to the procedure leading to additional screening (n= ), and a screen performed for a procedure that did not meet institutional guidelines to perform screening prior to said procedure (n= ). in this retrospective observational study, we demonstrated a number of important findings to inform ongoing utilization of sars-cov- rt-pcr testing resources at our institution. we believe the biggest lesson learned for our institution is that we found no cases of conversion from a negative to a positive result for inpatients undergoing a repeat pui test or a repeat asymptomatic screen test. other reports of the clinical sensitivity of rt-pcr testing for covid- have demonstrated a sensitivity range of - % for pui [ ] [ ] [ ] [ ] [ ] . these studies therefore suggest that a subset of patients may test negative when in fact they are positive, and consequently repeat testing may be warranted to identify these patients. however, in our study, we failed to find a single occurrence of negative-to-positive conversion in repeat tests in the inpatient setting. it is noteworthy that the median time to repeat testing was only days and repeat pui testing at our center was, in general, directed at those that a c c e p t e d m a n u s c r i p t were negative but had high risk or high likelihood based on clinical factors of having covid- disease. thus, we conclude that the pcr testing methods (e.g. specimen collection and testing platforms), combined with infection control measures, likely lead to higher sensitivity and lower likelihood of false-negative testing results in a low prevalence area than previously suggested. we acknowledge that the study design is not amenable to estimate the true sensitivity as not all patients were serially tested and there is no agreed upon gold-standard confirmatory test. a recent study by long and colleagues at two large academic centers in the us have recently published a similar study examining the rates of conversion from negative to positive np sars-cov- rt-pcr test results when performed within days of each other . out of patients, ( . %) converted from negative to positive. it is unclear the number of inpatients versus outpatients for the second test, but based on the initial test location it appears their dataset included mostly outpatients. therefore, it is possible ongoing community exposure could occur within the repeat testing window in the study. in our population, we had only patients convert from negative to positive out of patients. within those conversions, of those converted within a day window from the first test. when we limit our dataset to repeats within days, we had patients who had a repeat test within days of an initial test leading to a conversion rate of . %. differences in prevalence, infection control measures (inpatient and ambulatory) and/or compliance with those measures, and the number of asymptomatic screens done between the two studies likely explains the differences in rate of conversion. however, it is important to note that both studies suggest false negative np sars-cov- rt-pcr results may be much lower than previously believed. our results have important implications for improving diagnostic stewardship of sars-cov- rt-pcr testing at our facility. indeed, we continue to discourage repeat testing for pui in the inpatient setting unless it is discussed and approved by an infectious disease physician. a c c e p t e d m a n u s c r i p t this restriction, though, has limited effect as we found a number of repeat pui tests were not indicated but still done at the discretion of the provider (i.e. ordered without approval from infectious diseases). certainly, one way to improve diagnostic stewardship would be to institute prospective monitoring of pui orders, especially in the inpatient setting. as we demonstrated negative-to-positive conversions for pui testing in the outpatient setting, consistent with ongoing community spread of covid- , we believe it is advisable to continue to recommend and perform aggressive patient testing for pui in this setting. for asymptomatic screening we have also modified our procedures based on this data. we have recently extended the repeat asymptomatic screening to testing only once every days for asymptomatic inpatients undergoing certain procedures, which have also been revised to include mainly aerosol generating procedures rather than all procedures. as above with pui testing, though, we found numerous examples of providers ordering screening tests when not indicated. some of this is not unexpected because plans for a procedure are sometimes quite fluid, and thus there were instances where patients were screened ( ) in anticipation of a procedure that never occurred, ( ) for a procedure that was delayed, necessitating another screening test as it fell outside the testing window, or ( ) for a procedure that was later deemed not necessary. active prospective monitoring of the ordering could improve diagnostic stewardship practices in these situations as well. there are limitations to our study results and generalizability to other institutions as this was a single center, retrospective, observational study where the only type of specimen collected was an np swab. therefore, we were unable to examine the impact of sampling site on differences in congruency between first and subsequent sars-cov- rt-pcr testing results noted in our study versus those noted in other studies and sampling site may impact testing results . second, our results were noted in an area of the country with a prevalence of - per , population in dane county, wi (https://www.nytimes.com/interactive/ /us/wisconsin-coronavirus-cases.html#county). a c c e p t e d m a n u s c r i p t prevalence of covid- , testing procedures (e.g. sampling technique, type of testing platform), and infection control measures (e.g. ppe, hygiene measures, visitor policies, etc.) are different at each institution and could significantly affect the likelihood of discordant repeat testing results compared to initial results. the vast majority of medical centers in the us are utilizing commercially available platforms in which reagents, materials, and machines are all finite and may be further constrained by voluminous testing, making diagnostic stewardship critically important. thus, we believe our study may provide useful data for other institutions to use when considering diagnostic stewardship. in summary, we did not observe any inpatient negative-to-positive conversions for pui or asymptomatic screening purposes. this has led us to further refine our inpatient and ambulatory testing procedures to optimize sars-cov- rt-pcr testing resources. further diagnostic stewardship may be enhanced through prospective monitoring of tests ordered, particularly for inpatients. clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china detection of sars-cov- in different types of clinical specimens comparison of commercially available and laboratory developed assays for in vitro detection of sars-cov- in clinical laboratories challenges in laboratory diagnosis of the novel coronavirus sars-cov- . viruses strong social distancing measures in the united states reduced the covid- growth rate. health aff (millwood) presymptomatic sars-cov- infections and transmission in a skilled nursing facility characterization of an asymptomatic cohort of sars-cov- infected individuals outside of wuhan, china research letter -asymptomatic screening for sars-cov- in outpatients prior to procedures occurrence and timing of subsequent sars-cov- rt-pcr positivity among initially negative patients rt-pcr tests for sars-cov- processed at a large italian hospital and false negative results among covid- confirmed cases false-negative of rt-pcr and prolonged nucleic acid conversion in covid- : rather than recurrence variation in false-negative rate of reverse transcriptase polymerase chain reaction-based sars-cov- tests by time since exposure clinical performance of sars-cov- molecular tests swabs collected by patients or health care workers for sars-cov- testing a c c e p t e d m a n u s c r i p t funding "nasia safdar is supported by the national institute of allergy and infectious diseases of the national institutes of health under award number dp ai . the content is solely the responsibility of the authors and does not necessarily represent the official views of the national institutes of health." all authors report no conflicts of interest in relation to this study. the design of the work has been approved by local ethical committees or that it conforms to standards currently applied in the country of origin, and includes the name of the authorizing body which should be stated in the paper. as stated in manuscript above "the university of wisconsin institutional review board determined this study to be exempt." specifically, the irb determined the study met criteria for exempt human subjects research as it was secondary research for which patient consent is not required. the exemption is on file locally.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 key: cord- -fl lur h authors: may, larissa; tatro, grant; poltavskiy, eduard; mooso, benjamin; hon, simson; bang, heejung; polage, christopher title: rapid multiplex testing for upper respiratory pathogens in the emergency department: a randomized controlled trial date: - - journal: open forum infect dis doi: . /ofid/ofz sha: doc_id: cord_uid: fl lur h background: acute upper respiratory tract infections are a common cause of emergency department (ed) visits and often result in unnecessary antibiotic treatment. methods: we conducted a randomized clinical trial to evaluate the impact of a rapid, multipathogen respiratory panel (rp) test vs usual care (control). patients were eligible if they were ≥ months old, had symptoms of upper respiratory infection or influenza-like illness, and were not on antibiotics. the primary outcome was antibiotic prescription; secondary outcomes included antiviral prescription, disposition, and length of stay (clinicaltrials.gov# nct ). results: of patients enrolled, ( %) received rp testing; ( %) received usual care. fifty-three ( %) rp and ( %) control patients had a virus detected and reported during the ed visit (p = . ). twenty ( %) rp patients and ( %) usual care patients received antibiotics during the ed visit (– %; % confidence interval, – % to . %; p = . / . ); rp patients received antibiotics despite having a virus detected. the magnitude of antibiotic reduction was greater in children (– %) vs adults (– %, post hoc analysis). there was no difference in antiviral use, length of stay, or disposition. conclusions: rapid rp testing was associated with a trend toward decreased antibiotic use, suggesting a potential benefit from more rapid viral tests in the ed. future studies should determine if specific groups are more likely to benefit from testing and evaluate the relative cost and effectiveness of broad testing, focused testing, and a combined diagnostic and antimicrobial stewardship approach. acute respiratory tract infection (arti) is a common cause of emergency department (ed) visits, accounting for ~ . million cases annually from to [ ] . many of these cases are due to viral infection, and up to %- % are prescribed antibiotics inappropriately [ ] . this is worrisome, as overuse of antibiotics creates selective pressure for antibiotic-resistant pathogens that increases morbidity, mortality, and health care cost for affected patients [ ] . in addition, antibiotic use can lead to drug-related adverse reactions that could prompt patients to return to the ed [ , ] . factors contributing to antibiotic overprescribing include concerns regarding patient satisfaction scores, difference in patient expectation and understanding of antibiotic effectiveness for viral infections, medical liability, and diagnostic uncertainty [ , ] . the last point is especially applicable in the ed given the patient volume and current standard of care, where microbiologic testing results are often not available to inform diagnosis and treatment. therefore, the ed remains a highpriority target for rapid microbiologic testing and antimicrobial stewardship. recent improvements in molecular diagnostics and the development of rapid, multirespiratory pathogen molecular tests provide an opportunity to diagnose viral arti with high sensitivity and specificity during the ed visit and potentially improve patient management. hence, we sought to evaluate whether having a rapid, multipathogen test result available during the ed visit would have a significant impact on management and outcomes in patients with clinical signs and symptoms of arti. we conducted a prospective, patient-oriented, pilot randomized clinical trial of rapid multiplex respiratory pathogen testing (rp test group) vs usual care (usual care or control group) in a level emergency department with limited use of single-organism rapid point-of-care tests at a quaternary referral medical center. the study began in december and occurred over winter respiratory seasons and intervening nonrespiratory season. patients were eligible if they were age or older and being evaluated for influenza-like illness (ili; fever or cough and sore throat) or upper respiratory infection (uri; nonspecific upper respiratory symptoms without fever). patients were excluded if they were already on antibiotics at the time of ed presentation, not english-or spanish-speaking, cognitively impaired with no legally authorized representative, or expected to leave before multiplex test results were available. if a patient was deemed eligible for the study, the treating provider was approached by a research team member to confirm that uri or ili was suspected, and the patient was expected to be present for at least the next minutes. patients were recruited monday through friday between am and pm from rapid care and main adult and pediatric ed areas. screening was performed under a waiver of informed consent, and the study protocol was approved by the uc davis institutional review board. after informed consent, a patient questionnaire was administered by a trained research assistant to collect demographic information and medical history (supplementary data). information about the patient's medical history and current medications was reviewed in the electronic health record (ehr) and discussed with the patient. patients were specifically asked if they had chronic medical conditions, if they had medical conditions affecting their immune system (hiv, diabetes, cancer, liver disease, kidney disease, or dialysis, or if they were on immunosuppressive medications such as steroids), and if they were currently taking any medications. subjects were randomized to either rapid near point-of-care multirespiratory pathogen molecular testing (filmarray respiratory panel, biofire) plus clinician-directed usual care or usual care alone. this included but was not limited to no testing, targeted influenza and/or respiratory syncytial virus (rsv) point-of-care testing (quidel flu a/b or rsv before january , , then roche liat influenza a/b or rsv), rapid point-of-care testing for streptococcal pharyngitis (acceava strep a test before january , then roche liat), or multirespiratory pathogen panel testing (xtag respiratory viral panel, luminex before december , then genmark eplex) performed at an off-site laboratory - times weekly in scheduled daytime batches. simple randomization was used with a computer-generated randomized list to allocate subjects to the intervention or control arms of the study, and sealed, opaque envelopes were used to blind research staff to allocation up until written consent was completed. clinicians and patients were not blinded to the testing done, and usual care proceeded in both arms. after randomization, patients in the interventional arm had a nasopharyngeal swab specimen collected by a nurse or clinician. this specimen was transported via a tube system to an onsite clinical laboratory (upstairs), where the filmarray respiratory panel was performed in real time, with the goal of results reported in the ehr within hours. clinicians were informed that results of the patient's rapid molecular testing would be returned through the patient's ehr, and they received an automatic in-basket message through the ehr as well as a notification by the research coordinator or research assistant when results were back. follow-up treatment and outcome data were abstracted from each subject's ehr by a trained research staff member. abstracted data included medical history, clinical signs and symptoms, demographics, lab and radiology results, medications (including asthma, diabetes, chemotherapy, immunosuppressive, antibiotic, and antiviral medications), ed/hospital course, length of ed/hospital stay, clinician diagnoses from the index encounter, and limited review of subsequent encounters to identify deaths and -day revisits to the ed study site for similar complaints. up to return visits were recorded, and each was categorized as either "respiratory illness" or "nonrespiratory illness" according to the primary diagnoses of the encounter. in the case of patients who returned to the ed but left before being treated, their chief complaint was used instead of their diagnosis. chest x-ray results were reviewed by a clinical investigator (l.s.m.) to identify patients with imaging consistent with bacterial pneumonia or viral pattern illness. the primary outcome was antibiotic administration or prescription in the ed by an emergency medicine clinician. secondary outcomes included the proportion of patients with a respiratory pathogen identified by the filmarray respiratory panel test or any other upper respiratory pathogen diagnostic test ordered by the physician; the proportion of patients with a laboratory-confirmed influenza diagnosis; the proportion of patients receiving appropriate anti-influenza treatment or prescription in the ed by an emergency medicine clinician (composite rate of anti-influenza treatment in positive patients and nonuse of anti-influenza treatment in negative patients); the proportion of patients discharged home from the ed vs hospital admission; the proportion of patients with all-cause or respiratory illness-related repeat ed visit, hospital or icu admission, or death within days; clinician adherence to guidelines for the treatment of patients with influenza (recommendations for use of antivirals only); length of ed stay; length of hospital stay; time to influenza test results; and time to other respiratory pathogen test results. we summarized data by standard descriptive statistics: continuous variables by mean and standard deviation (sd) or median and range (= min-max), categorical variables by frequency and percentage. we analyzed the equality of the proportions for binary outcomes with the chi-square or fisher exact test, as appropriate (eg, cell count < ), and reported ( -sided) p values, unadjusted for multiple testing. we also computed the difference in event rates (ie, proportion) and the associated % confidence interval (ci). for continuous outcomes, the wilcoxon test was used for comparison. we also performed a post hoc stratified analysis for antibiotic use (primary outcome), antiviral use, and discharge status, based on the patient's age (eg, adult vs pediatric) for exploratory purposes. we analyzed the data based on the (modified) intent-to-treat principle; that is, we analyzed all patients as randomized, excluding early dropouts with outcomes data unavailable. we used sas, version . (sas institute, cary, nc, usa), for data analysis. the study was initiated in december with a target enrollment of participants over months, based on a power calculation that patients ( in each arm) would have % power to detect a % difference in antibiotic prescription between arms. the study was stopped in april ( months) due to budgetary constraints. our study enrolled patients, with ( . %) randomized to the interventional rp test group and ( . %) randomized to the usual care control group ( figure ). there was no statistically significant difference in age, race, or existence of a chronic medical condition between the groups. the complete baseline characteristics of the study participants are summarized in table . in the rp test group, ( %) patients had or more viruses detected and reported during the ed visit; ( %) additional rp patients had a positive virus result reported after the ed visit (table ). in the control group, ( %) patients had a virus detected and reported by existing single-organism tests during the ed visit, and an additional ( %) patients had a virus detected via the off-site laboratory multirespiratory pathogen panel after the ed visit. the results from the rapid rp tests were available in < hours on average ( table ) . the primary and secondary outcome results are shown in table (table ). there were no other outcome differences between groups in the post hoc stratified age analysis (table ) . large molecular panels capable of detecting - respiratory viruses simultaneously have been available for > years, but the utility of detecting noninfluenza, non-rsv viruses in outpatients is debated because results are delayed, and therapy does not exist [ ] . meanwhile, diagnostic advances have made it possible to get results within - hours, and reducing unnecessary antibiotic use has become a national priority [ ] . the filmarray respiratory panel provides results for different respiratory pathogens in approximately hour with %- % sensitivity and %- % specificity [ ] . however, ( ) ( ) diabetes mellitus ( ) ( ) other ( ) ( ) kidney disorders ( ) ( ) immunosuppressed ( ) ( ) abbreviations: bmi, body mass index; chf, congestive heart failure; copd, chronic obstructive pulmonary disease; rp, respiratory panel. a missing bmi measurements due to lack of height measurements for some patients. these large, multipathogen tests are more expensive than targeted point-of-care tests, and the clinical utility has not been rigorously evaluated, especially in the ed. as a result, some payers are currently moving to limit utilization and reimbursement of large multipathogen panels in favor of targeted influenza and/or rsv testing [ ] . this evidence gap in utility and reimbursement uncertainty create challenges for clinicians, laboratories, and hospitals in justifying the cost of instruments and tests, and there is a lack of guidance regarding optimal use. we hypothesized that rapid multirespiratory pathogen testing with results reported during the ed visit could alter treatment in the early phases of patient care and potentially impact patient and health care outcomes. thus, we conducted a randomized clinical trial of the filmarray rp vs usual care in ed patients with signs or symptoms of upper respiratory infection or influenza-like illness. the primary outcome was antibiotic prescription. the trial was stopped after months before reaching the prespecified sample size due to dwindling funds and slow enrollment. however, there was a trend toward decreased antibiotic use with rp testing (- % difference; p = . / . , chi-square/ fisher exact test) that was larger in pediatric patients (- % difference; p = . / . ) in an age-stratified post hoc analysis, suggesting a potential benefit of increased rapid rp testing in some ed patients. antiviral prescription (ie, oseltamivir) was not significantly affected despite a -fold increase in viral ( % vs %) and influenza detections ( % vs %), perhaps due to the lack of guidance regarding antiviral use in our study. other secondary outcomes, such as ed disposition, -day return visits, and -day deaths, did not differ between groups. thus, the main effects of rapid rp testing in this study were to increase the proportion of patients with a lab-confirmed viral detection for clinical decision-making by -fold and reduce antibiotic prescription by about one-third. it is unknown if similar benefits could be achieved with targeted testing for influenza and/or rsv or antimicrobial stewardship alone. however, it has been suggested that influenza testing alone may be sufficient and cost-effective when applied to outpatients, given that other viruses do not have any specific treatment at this time [ ] . other potential benefits of rapid rp testing, such as infection prevention and patient satisfaction, were not investigated. relatively few other studies have investigated the effect of large respiratory panels on outcomes, and no prior randomized controlled trials have been performed in us ed patients to our knowledge. a recent trial in an argentinian ed found reduced antibiotic and antiviral initiation in patients receiving the filmarray assay vs standard testing; this study was better powered ( patients) than our study but may not be generalizable to the united states as empiric treatment without testing is more common in this country [ , ] . in a retrospective analysis by rogers et al., the biofire filmarray was associated with decreased duration of antibiotic use, length of hospital stay, and length of isolation in children admitted to the hospital with arti [ ] . future investigations with more targeted use of rapid multiplex testing in the ed could yield more promising results, but additional research is needed to determine which patients would benefit most from testing. for example, xu et al. showed that the filmarray could be cost-effective when replacing off-site direct fluorescence antibody testing in pediatric ed patients [ ] . a recent randomized controlled trial from the united kingdom found an increase in patients with short courses of antibiotics and a -day reduction in length of stay in patients with rapid rp testing but did not see a difference in the overall proportion of antibiotic treatment compared with the control arm [ ] . however, this study was done outside the united states and included patients outside the ed, so the results may not be directly comparable to our study. our patients came from a heterogeneous ed patient population and included a wide range of individuals with arti anywhere on providers' differential diagnosis; in hindsight, this may not have been the ideal population, as clinicians would not necessarily have ordered rapid multiplex testing on these patients and may have been less likely to modify their behavior in response to the results. however, the high rate of chest x-ray testing in our study (~ %, both study arms) suggests that providers were at least considering a respiratory illness in most patients but may not have been in the habit of relying on viral testing for their clinical decision-making. another interpretation of our results is that while multiplex testing does well identifying influenza and other uri-causing viruses in the ed, implementation alone was not sufficient to significantly influence clinician decision-making and patient outcomes. for example, influenza testing alone may be enough for clinical decision-making during influenza season [ ] . it is likely that a thoughtful and comprehensive stewardship program around rapid diagnostics could be required to lead to meaningful changes in outcomes. it is also possible that deploying rapid diagnostic tools would lead to more significant changes if applied to an area that has higher baseline antibiotic prescription rates such as an urgent care setting. shortening the -minute turnaround time (tat) of the biofire filmarray respiratory panel might also be necessary for this test to be effective in the ed setting. although the current test was much faster than the off-site respiratory viral panel used at our facility, it is still not fast enough to match the fast-paced workflow of many eds. andrews et al. also encountered problems with tat in their point-of-care (poc) implementation of the filmarray [ ] . however, these problems were mainly attributed to staff availability to run the test after consenting subjects. the filmarray itself was reported by them to run in minutes in the poc setting. if the filmarray could be implemented into the ed as a poc test in a way that would fit seamlessly into ed workflow, the tat may have been minimized for this assay, and we may have seen more promising results. this was demonstrated in the post hoc analysis by brendish et al. on their randomized controlled trial in the uk. significant improvements to outcomes, including antibiotic treatment and duration of antibiotics, were seen in patients with virus-positive rp testing that achieved a tat of ≤ . hours vs those of > . hours [ ] . in this regard, it is encouraging to see newer poc nucleic acid amplification tests for influenza and rsv coming to market with shorter tats, on the order of - minutes [ ] . it is also possible that the pathogens detected do not provide sufficient information for clinicians to reduce antibiotics. the recently fda-cleared biofire filmarray pneumonia panel will identify a wider range of respiratory bacteria and viruses. depending on tat and ability to fit into ed workflow, a test such as this could help reduce diagnostic uncertainty when lower respiratory tract infections are also part of the differential diagnosis. however, detecting more pathogens may not be the answer. as a result of the recent palmetto gba decision, medicare will no longer provide coverage for large (≥ -target) multiplexed diagnostic viral panels such as the biofire filmarray for outpatients unless policy changes in the future [ ] . this decision to cover only - respiratory pathogen targets and limit their use to infectious disease clinicians except in the case of urgent care, ed, and inpatient settings highlights the importance of implementation and evaluation of diagnostic tests in the context of a value-based health care system. simply providing test results without consideration of the behavioral aspects of antimicrobial prescribing may result in lack of clinical utility, when these tests could be beneficial if paired with behavioral economics strategies or as part of a comprehensive stewardship program to reduce inappropriate antibiotic use. this study was limited by a small sample size, which most likely did not provide enough power to see a significant difference in outcomes, as suggested by the wide confidence intervals we observed. the subjects themselves were selected based on symptoms, rather than a clinical decision to order multiplex testing. this in turn led to a heterogeneous subject population, many of whom might not be expected to benefit from viral testing. locating a specific target population for rapid multiplex testing in the ed may be necessary for significant differences in outcomes. finally, during the - influenza season, activities were undertaken to reduce inappropriate prescribing for viral respiratory infections in otherwise healthy patients using patient and provider education, provider public commitment to reducing inappropriate antibiotic use, and peer comparison data. thus, our already low prescribing rate may have been reduced, and this may have compounded our loss of power from underenrollment by decreasing the difference between the rp and usual care groups that we anticipated when we powered the study. we also did not analyze cost-effectiveness, and more research is needed to determine if multiplex testing can be economically feasible in the ed. finally, it is likely that use of comprehensive stewardship strategies and guidelines could have improved effectiveness beyond simple introduction of rapid diagnostic tests. there were also several strengths to this study, including the rigorous experimental study design, relatively rapid tat given the current state of the art, and generation of preliminary data for future more rigorous multicenter clinical trials evaluating the implementation of rapid respiratory panels in eds and other acute care settings. in summary, this randomized controlled trial aimed to evaluate the impact of rapid multiplex respiratory panel testing in the ed for patients with concern for acute respiratory tract infection. although our study lacked the power to see significant differences in outcomes, we did observe a trend in decreased antibiotic use for those who received multiplex testing vs the standard of care. further evaluation of rapid multiplex testing in the ed could see changes in outcomes if the limitations of this study were addressed. this mainly includes identifying the right patient population where testing can alter patient care (vs targeted testing or no testing) and focusing on implementing comprehensive stewardship strategies alongside diagnostic tools to ensure that testing is utilized appropriately and effectively. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. antibiotic utilization for acute respiratory tract infections in u.s. emergency departments unnecessary antibiotics for acute respiratory tract infections: association with care setting and patient demographics a call to action for antimicrobial stewardship in the emergency department: approaches and strategies emergency department visits for antibiotic-associated adverse events antibiotic prescriptions are associated with increased patient satisfaction with emergency department visits for acute respiratory tract infections multiplex pcr point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use clinical impact of rapid molecular detection of respiratory pathogens in patients with acute respiratory infection an automated nested multiplex pcr system for multi-pathogen detection: development and application to respiratory tract infection clinical utility of on-demand multiplex respiratory pathogen testing among adult outpatients antibiotic use in acute upper respiratory tract infections clinical diagnosis of influenza in the ed impact of a rapid respiratory panel test on patient outcomes implementation of filmarray respiratory viral panel in a core laboratory improves testing turnaround time and patient care 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 imact of turnaround time on outcome with point-of-care testing for respiratory viruses: a post hoc analysis from a randomised controlled trial clinical utility of a near patient care microarray based diagnostic test for influenza and respiratory syncytial virus infections palmetto final lcd denies coverage to large respiratory panels the authors would like to thank nicolle ocampo, m. czarina ganzon, and fatemeh memar for helping with study management and data collection. potential conflicts of interest. l.s.m. and c.r.p. have received consulting fees from biofire diagnostics, inc. all other authors report no conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- -asem xjz authors: mallipattu, s k; jawa, r; moffit, r; hajagos, j; fries, b; nachman, s; gan, t j; saltz, m; saltz, j; kaushansky, k; skopicki, h; abell-hart, k; chaudhri, i; deng, j; garcia, v; gayen, s; kurc, t; bolotova, o; yoo, j; dhaliwal, s; nataraj, n; sun, s; tsai, c; wang, y; abbasi, s; abdullah, r; ahmad, s; bai, k; bennett-guerrero, e; chua, a; gomes, c; griffel, m; kalogeropoulos, a; kiamanesh, d; kim, n; koraishy, f; lingham, v; mansour, m; marcos, l; miller, j; poovathor, s; rubano, j; rutigliano, d; sands, m; santora, c; schwartz, j; shroyer, k; skopicki, h; spitzer, s; stopeck, a; talamini, m; tharakan, m; vosswinkel, j; wertheim, w title: geospatial distribution and predictors of mortality in hospitalized patients with covid- : a cohort study date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: asem xjz background: the global coronavirus disease (covid- ) pandemic offers the opportunity to assess how hospitals managed the care of hospitalized patients with varying demographics and clinical presentation. the goal of this study is to demonstrate the impact of densely populated residential areas on hospitalization and to identify predictors of length of stay and mortality in hospitalized patients with covid- in one of the hardest hit counties internationally. methods: this is a single-center cohort study of sequentially hospitalized patients with covid- in new york between march , to may , . geospatial distribution of study patients’ residence relative to population density in the region were mapped and data analysis included hospital length of stay, need and duration of invasive mechanical ventilation (imv), and mortality. logistic regression models were constructed to predict discharge dispositions in the remaining active study patients. results: the median age of the study cohort was years (iqr - - ), and more than half were male ( %) with history of hypertension ( %), obesity ( %), and diabetes ( %). geographic residence of the study patients was disproportionately associated with areas of higher population density (r(s)= . , p= . ), with noted “hot spots” in the region. study patients were predominantly hypertensive (map> mmhg ( , %)) on presentation with lymphopenia ( , %), hyponatremia ( , %), and kidney dysfunction (egfr& ml/min/ . m ( ) ( , %)). of the patients with a disposition ( / ), % ( / ) required imv and % ( / ) developed acute kidney injury. in patients on imv, median hospital length of stay in survivors ( days; . - . ) was significantly longer than non-survivors ( days; - . ), but this was not due to prolonged time on the ventilator. the overall mortality in all hospitalized patients was % and in patients receiving imv was %, which is predicted to minimally rise from % to % based on logistic regression models constructed to project the disposition in the remaining patients on the ventilator. acute kidney injury during hospitalization (or(e)= . ) was the strongest predictor of mortality in patients requiring imv. conclusions: this is the first study to collectively utilize the demographics, clinical characteristics and hospital course of covid- patients to identify predictors of poor outcomes that can be used for resource allocation in future waves of the pandemic. m a n u s c r i p t december in wuhan, china, the devastating morbidity and mortality coupled with disastrous economic and societal ramifications have characterized this global pandemic [ ] . as of may , , new york state far exceeds any other state for the number of individuals infected with severe acute respiratory syndrome coronavirus (sars-cov- ), with suffolk county in the top six counties in the entire united states at the time of this report [ ] . the global covid- pandemic offered the opportunity to assess how different geographies managed the care of patients with a predominantly devastating respiratory illness with significant inflammatory, thrombotic, kidney and cardiovascular morbidities. suffolk county lies directly east of nassau county and the greater new york city, and was chronologically later affected by sars-cov- after its appearance in the five boroughs of new york (manhattan, queens, brooklyn, staten island and the bronx) and nassau county. together nassau and suffolk counties constitute the long island region, and have approximately similar populations ( , , versus , , people, respectively), albeit with varying population demographics [ ] . recent case series of hospitalized patients in the new york metropolitan area have highlighted the presenting clinical characteristics, morbidity and mortality at medical centers in the region [ , ] . to allow for comparison of these factors with patient outcomes in one of the most highly affected regions in the world, we report our clinical endpoints based on patient demographics, population density and ethnicity, presenting clinical characteristics and therapeutic interventions for over , hospitalized patients with confirmed sars-cov- infection. a c c e p t e d m a n u s c r i p t the study was conducted at the renaissance school of medicine at stony brook university, the largest academic medical center in suffolk county, new york, which provided care for the greatest number of patients with covid- of the eleven hospitals in the county. patients hospitalized between march , , and may , with covid- as confirmed by at least one positive result for sars-cov- on pcr testing of nasopharyngeal samples were included in this study. data was extracted from hospitalized patients from the electronic health record (ehr; cerner millennium, kansas city, mo) and mapped to an observational health data sciences and informatics common data model (ohdsi cdm), version . [ ] . medications were mapped to ohdsi based rxnorm codes and to world health organization anatomical therapeutic chemical drug classifications. data collection included baseline patient demographic information, comorbidities based on icd codes mapped to clinical classification software (ccs) groups occurring days prior to admission beginning january , , admission vital signs, and initial laboratory tests. race and ethnicity were based on self-reporting at the time of registration and mapped to broader categories using relationships in the ohdsi controlled vocabulary. patient locations were geolocated to latitude and longitude using the most recent patient addresses in the ehr with easy geocoder [ ] . total population at the census tract level was based on the american community survey (acs) -year estimates [ ]. population density was calculated using the tiger shape file estimates for land area in a census tract. initial laboratory testing was defined as the first test results available within hours of admission. total patients with available laboratory values are described after exclusion of a c c e p t e d m a n u s c r i p t outlier values. for each of the laboratory values and vital signs provided, we reviewed histograms and defined a range of presumed "valid" measurements (for example, patients had recorded respiratory rates above breaths per minute (bpm) and had values below bpm) and values outside of these ranges were replaced as "missing" for all subsequent analysis. acute kidney injury during hospitalization was defined as an increase in serum creatinine of . mg/dl within hours [ ] . estimated glomerular filtration (egfr) was calculated using the chronic kidney disease epidemiology collaboration (ckd-epi) equation [ ] . kidney replacement therapy was defined as onset of hemodialysis (hd) and/or a c c e p t e d m a n u s c r i p t a student"s t test was used to compare continuous data between two groups. chi-square or fisher"s exact testing, as appropriate, was used to compare the significance between categorical variables. for continuous variables, data are expressed as interquartile range (iqr) ( th and th percentiles) and/or the number and percentage of patients for categorical variables. statistical significance was defined as p < . . all analyses were performed using the r programming language (r project for statistical computing; r foundation). logistic regression models were constructed to predict discharge dispositions in our patient population (excluding patients that remained actively hospitalized at the end of the study period)-one model used only variables available at the beginning of an encounter to predict overall outcomes and a second model included more variables in an attempt to find associations with outcomes in mechanically ventilated patients. for each model, we constructed a parsimonious logistic regression with a penalty on the sum of coefficients, i.e. lasso, using the glmnet package in r. models were cross-validated and trained on the set of cases with complete, non-missing, values for all variables considered. our models were tested on the remaining patient data, after missing values were replaced using multivariate imputation by chained equations, as implemented in the mice package in r. a total of sars-cov- infected patients were seen in our emergency department, with patients discharged to home quarantine for recovery and patients admitted for hospitalization. demographics of real-time pcr confirmed sars-cov- hospitalized patients ≥ years of age ( / ) are presented in table . among the patients with comorbidities identified during a prior visit, % had more than one a c c e p t e d m a n u s c r i p t comorbidity with a predominance of hypertension ( / , %), obesity ( / , %), and diabetes ( / , %). figure , demonstrating the geographic residence, the number of hospitalized covid- patient cases, and the population density per census tract (persons per km area). furthermore, the number of hospitalized covid- patient cases per , persons was associated with higher population density per kilometer area (r s = . , p= . ) when census tracts centroids were restricted to a km distance (catchment area) from the medical center. vital signs on presentation are shown in supplemental table and are noteworthy for diastolic hypertension as evidenced by a map > mmhg ( / , %) and sbp > mmhg ( / , %). laboratory data was available for > % of the laboratory investigations performed in the study cohort, exceptions noted in supplemental table . a significant proportion of the cohort were lymphopenic, as defined by absolute lymphocyte count < cells/ul, % ( / ) and hyponatremic, as defined by serum sodium < meq/l ( / , %). end-organ dysfunction was noted on admission with approximately % ( / ) of study cohort with evidence of kidney dysfunction (egfr ml/min/ . m ), myocardial injury as measured by elevation in troponin t ( / , %)), or hepatic injury with elevation in transaminases (ast ( / , %) and alt ( / , %)). a majority of the cohort also had procalcitonin levels . ( / , %) on presentation, suggesting the absence of concomitant superimposed bacterial infection at the start of the disease (supplemental table ). a c c e p t e d m a n u s c r i p t of the patients studied, patients were discharged alive, patients died, and patients remain hospitalized. discharge disposition, as well as length of stay for those who died or were discharged alive ( / ), are presented in figure and supplemental table . among these patients with a disposition, the overall mortality was significantly higher in males (p= . ). this was most prominent in age groups - and - years, and that difference confers an advantage to females in whom the death rate does not exceed % until age , whereas in males that threshold was crossed at age . overall, the median hospital length of stay (los) was significantly longer in patients who died ( days; iqr - ) as compared to patients discharged alive ( days; iqr - ; p= . ) ( figure a , supplemental table ). no such difference in hospital length of stay was noted for patients who did not receive imv (supplemental figure , figure b (bottom panel)). interestingly, the overall hospital los in patients on imv was significantly longer in those discharged alive ( days; iqr . - . ) as compared to those that died ( days; iqr - . ; p= . e- ) ( figure b, top panel) . however, length of time on the ventilator in patients discharged alive ( days; iqr - ) was slightly shorter from those that died ( days; iqr . - . ; p= . ) due to skewing of the interquartile range in the deceased population ( figure c) . these data suggest that the longer hospital length of stay in patients discharged alive after being on imv is attributable to a greater number of nonventilator hospital days. it is noteworthy that in the remaining active patients in the hospital by the end of the study period, the duration of invasive mechanical ventilatory support was significantly prolonged as compared to the patients with a disposition by the study end point ( figure c) . a c c e p t e d m a n u s c r i p t of patients with a disposition, ( %) patients required imv (supplemental table ), with a majority of these patients ( %) eventually discharged alive. acute kidney injury developed in % ( / ) of the patients with approximately % ( / ) of these patients requiring kidney replacement therapy (crrt or hd) (supplemental table ). fiftythree percent ( / ) of patients who received kidney replacement therapy were eventually discharged alive (supplemental table ). approximately . % ( / ) of our encounters represented readmissions, and the majority of these readmitted patients were eventually discharged alive ( / , %). furthermore, of individuals that were discharged alive, approximately % ( / ) were discharged home as compared to a rehabilitation or skilled nursing facility (supplemental table ). finally, the overall mortality was % ( / ) in all hospitalized patients and % ( / ) in patients on imv with a disposition. a univariate analysis performed with parameters assessed on admission demonstrated that age years and male gender as well as several comorbidities were associated with mortality (supplemental table ). clinical measures such as the need for imv and kidney replacement therapy were associated with mortality, with acute kidney injury during hospitalization as having the highest odds ratio (supplemental table a c c e p t e d m a n u s c r i p t predicted lower survival in these patients, if found on initial presentation (supplemental table ). in patients who received imv, only age years, male gender, comorbidities (hypertension, heart failure), need for kidney replacement therapy, and acute kidney injury during hospitalization were significantly associated with increased mortality in the univariate analysis (supplemental table ). subsequent multivariate modeling in these patients demonstrated that, of the variables individually associated with outcomes, only male gender, older age, history of heart failure, and acute kidney injury during hospitalization were predictive of mortality; with acute kidney injury remaining as the most important predictor in this analysis (table ) . despite multiple therapeutic interventions; hydroxychloroquine, azithromycin, therapeutic anticoagulation, tocilizumab, zinc, thiamine, and ascorbic acid, none were associated with improved survival in the patients on imv (supplemental table ). however, we observed a trend toward improved survival in patients on imv that received therapeutic enoxaparin as compared to intravenous unfractionated heparin. a logistic regression model was constructed to predict discharge disposition in the remaining active patients that received imv, with noted characteristics of the predictive performance (supplemental figure ) . the mortality in these patients is projected to rise from % to %, based on the prediction that patients are likely to expire as compared to patients that are likely to be discharged alive in the remaining patients on mechanical ventilation. the observation that the geographic residence of the hospitalized covid- patient cases was disproportionately associated with higher population density is not surprising, in light of the imperative to maintain physical distancing to reduce transmission and mitigate the peak intensity of this pandemic. while our medical center catchment area overlaps with several medical centers in the county, the identification of these "hot-spots" will be essential for future resource allocation planning. investigating the potential cofounders, including comorbidities, socioeconomic status, occupational exposure, education level and ethnicallybased differences contained within these geographic spaces are also critical for future responses. over % of hospitalized patients (with a documented previous visit to our system) had at least one comorbidity, with % of individuals reporting more than one comorbidity. while our findings support those of studies in the new york city area [ , ] , we observed much higher rates of these comorbidities than the original wuhan study , and a metaanalysis of approximately patients from china [ , , ] . this likely represents our older patient cohort, but may also represent underlying differences in the prevalence of these a c c e p t e d m a n u s c r i p t diseases in different countries as well as the detection and definition of disease during previous visits to our system. while, the history of cancer, pre-existing diabetes and heart failure were independent predictors of mortality on presentation, the presence of pre-existing heart failure alone predicted mortality in patients requiring imv. our model revealed that other strong predictors for mortality in mechanically ventilated covid patients were older age, male gender, and acute kidney injury during hospitalization. still, these features remain correlative, making it difficult to assign relative importance to any one factor. however, our model of mortality on presentation used only basic data available in the first hours of admission and achieved a % positive predictive value for survival (auroc %, sensitivity %, specificity %). additional studies are required to determine if these observations can be validated in cohorts with differing demographics. the lack of an overwhelming clinical response to the evolving treatment strategies not surprising, the overall hospital length of stay was longer in individuals who died as compared to those that survived. however, in patients that required imv, we observed the opposite; the overall hospital length of stay was significantly longer in those that survived as compared to those that died. interestingly, this prolonged hospital course was not driven by the duration of mechanical ventilation, but rather by hospitalization events pre-dating or post- m a n u s c r i p t covid- data analysis group covid- clinical coordinating group clinical characteristics of coronavirus disease in china coronavirus covid- global cases detailed tables; generated by janos hajagos outcomes among patients hospitalized with covid- in the new york city area hospitalizations and deaths across new york city boroughs feasibility and utility of applications of the common data model to multiple, disparate observational health databases effective scalable and integrative geocoding for massive address datasets kdigo clinical practice guidelines for acute kidney injury a new equation to estimate glomerular filtration rate characteristics and outcomes of critically ill patients with covid- in washington state prevalence of underlying diseases in hospitalized patients with covid- : a systematic review and meta-analysis national institutes of health association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid- in new york state a c c e p t e d m a n u s c r i p t funding none the authors declare that they have no competing interests 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 key: cord- - i zi authors: rawlings, stephen a; ignacio, caroline; porrachia, magali; du, pinyi; smith, davey m; chaillon, antoine title: no evidence of sars-cov- seminal shedding despite sars-cov- persistence in the upper respiratory tract date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: i zi rna viruses (eg, zika, ebola, hiv) are often shed in male genital secretions. we evaluated the presence and level of sars-cov- rna in semen, nasal secretion, and saliva collected after confirmed infection. sars-cov- rna was not detected in semen – days after the onset of symptoms despite concomitant shedding in oral secretions. while it is known that severe acute respiratory coronavirus (sars-cov- ) infection often starts with - days of asymptomatic shedding before a person gets sick, there are limited data about the biological source and duration of viral shedding after symptom resolution in recently infected individuals. besides respiratory droplets, sars-cov- rna has been isolated in other biological samples including urine, blood, feces, and saliva [ , ] . the expression of sars-cov- receptor angiotensin -converting enzyme (ace ) across multiple tissues also suggests that sars-cov- could be found in other tissues and body fluids [ ] , including in the testis and male genital tract [ , ] . very few studies exist on the presence of sars-cov- rna in semen, and these studies have been limited by considerable time between semen sampling and diagnosis of active infection. in particular, when semen has been examined ~ - weeks after sars-cov- infection, the virus was not detected, and a case report of a single male acutely infected revealed no sars-cov- in seminal fluid [ ] [ ] [ ] . whether sars-cov- can be detected in semen during the acute phase of sars-cov- infection when the virus is concomitantly present in nasal and/or oral secretions remains a concern. here, we evaluated the presence and level of sars-cov- in paired semen, nasal secretion, and saliva samples collected in the short and medium term after confirmed sars-cov- symptomatic infections. all participants provided informed, written consent. this study was conducted under a protocol for collecting samples from persons with known sars-cov- infection approved by the institutional review board of university of california san diego. men who had been diagnosed with sars-cov- based on a combination of medical history, symptoms, and the presence of sars-cov- rna in the upper respiratory tract were invited to enroll in this study. all participants were outpatients at the time of enrollment and sample collection. they were instructed to self-collect saliva (passive drool), nasal swab, and semen by masturbation without lubricant after hours of abstinence. samples were collected within - weeks after the onset of symptoms. semen was processed as in butler et al. [ ] . briefly, viral transport medium ( ml of rpmi with mmol/l of glutamine and % fetal bovine serum [fbs] , with the addition of u/ml of penicillin, μl/ml of streptomycin, and u/ml of nystatin) was added to seminal samples at collection. seminal plasma was separated from seminal cells by centrifugation at × g for minutes within hours of collection and stored at − °c and − °c, as previously described [ ] . rna was extracted from seminal plasma, saliva, and viral transport media that contained the nasopharyngeal (np) swab; µl of each type of sample was extracted for rna using qiagen's qiaamp viral rna mini kit (cat# ) according to the manufacturer's recommendation. cdna from sars-cov- rna was generated using the bio-rad one-step rt-ddpcr advanced kit for probes (cat# - ). qualitative tests for sars-cov- were performed on the first collected nasal/np specimen for diagnostic confirmation using the fluxergy platform (irvine, ca, usa), which is currently available as a research use only (ruo) or investigational use only (iuo) device for the development of new diagnostic products. quantitative measure of sars-cov- in saliva and semen was performed using digital droplet polymerase chain reaction (ddpcr; bio-rad qx droplet reader). copy numbers were calculated as the mean of replicates. briefly, we have adapted our validated protocol [ ] to quantify sars-cov- in various samples following the centers for disease control and prevention recommendations and the -ncov real-time rt-pcr diagnostic panel targeting the virus nucleocapsid (n) and the orf gene [ ] . based on testing and dilutions with known positive and negative clinical samples (data not shown), the current level of detection is . copies/µl. a total of participants aged - years were enrolled in this study (supplementary table ). all initially presented with clinical symptoms compatible with sars-cov- and/or recent history of close contact with a confirmed case. symptoms included cough, shortness of breath, fever, myalgia, fatigue, anosmia, headache, anorexia, and diarrhea. before enrollment, / participants tested positive for sars-cov- rna on np swab samples collected within - days following the onset of symptoms. id was not initially tested by his clinical team, but the diagnosis was supported by both clinical symptoms and recent close contact with a confirmed case. upon enrollment in the study, the diagnosis of active sars-cov- infection was confirmed by positive pcr on np swab on day post-symptom onset. the clinical conditions of all participants improved, with complete resolution of initial symptoms, within - weeks from the onset. paired saliva and semen samples were collected a mean of days ( - days) after the onset of symptoms, and ddpcr was performed to quantify the sars-cov- level in all samples. half of the participants also had research nasal swabs performed. all semen samples were negative for sars cov- (≤ . copies/µl), while sars-cov- was still detected in all saliva samples ( participants) and all research nasal swabs ( participants). saliva levels of virus were quantified and varied from . to copies/µl of input saliva (figure , table ). the temporal dynamic of viral shedding and transmissibility of sars-cov- remains a major concern to control the spread of the virus and directly impacts control measures such as isolation, contact tracing, and enhanced hygiene or use of face masks for symptomatic persons. recent studies have shown persistant viral detection in the upper respiratory tract up to days after the onset of symptoms [ ] . ace expression across tissues and body fluid-including seminal fluid-suggests possible extrarespiratory transmission routes [ ] . here, we investigated the presence of sars-cov- in the semen of men in whom virus was demonstrably present in the respiratory tract. we found no evidence of sars-cov- in semen collected - days after the onset of symptoms despite all men having concomitant shedding of virus in oral secretions up to copies/µl. though the study is small in number, it adds to available literature that the male genital tract does not appear to be a site where sars-cov- is shed in either the acute or late phase of infection. identifying whether sars-cov- can table for quantitative measures via digital droplet polymerase chain reaction. abbreviation: np, nasopharyngeal. be shed in semen has implications for public health, as all predominant modes of transmission (ie, droplet, sexual contact, airborne, fomite, etc.) need to be identified in order to help curb the spread of the virus. with the small number of participants in this study, it is difficult to quantify the absolute probably of spread in a large population, but the complete absence of virus using ultrasensitive methods suggests that shedding of the virus in semen is certainly not common. a larger study would be needed to demonstrate and quantify rare events of shedding. whether sars-cov- can be detected in the semen at the very early phase of infection or during the incubation period when it is present in the upper respiratory tract [ ] would require further investigation, but collective evidence [ ] [ ] [ ] and our study suggest that sars-cov- is not present in semen. supplementary materials are available at open forum infectious diseases online. consisting of data provided by the authors to benefit the reader, the posted materials are not copyedited and are the sole responsibility of the authors, so questions or comments should be addressed to the corresponding author. ( ) ≤ . ( ) abbreviation: pcr, polymerase chain reaction. persistence and clearance of viral rna in novel coronavirus disease rehabilitation patients comparison of different samples for novel coronavirus detection by nucleic acid amplification tests high expression of ace receptor of -ncov on the epithelial cells of oral mucosa scrna-seq profiling of human testes reveals the presence of the ace receptor, a target for sars-cov- infection in spermatogonia, leydig and sertoli cells ace expression in kidney and testis may cause kidney and testis damage after -ncov infection absence of novel coronavirus in semen and testes of covid- patients † study of sars-cov- in semen and urine samples of a volunteer with positive naso-pharyngeal swab no evidence of severe acute respiratory syndromecoronavirus in semen of males recovering from coronavirus disease the origins of sexually transmitted hiv among men who have sex with men highly precise measurement of hiv dna by droplet digital pcr -ncov) real-time rt-pcr diagnostic panel temporal dynamics in viral shedding and transmissibility of covid- structure analysis of the receptor binding of -ncov fluxergy, inc. the authors thank the participants and their families. author contributions. s.a.r. performed study procedures, analyzed data, and reviewed the manuscript. b.s., l.l., m.p., and c.i. performed study procedures and reviewed the manuscript. a.c. and d.s. analyzed data and wrote the manuscript.financial support. this work was supported by the john and mary tu foundation and the translational virology core of the san diego center for aids research (cfar) grant number ai , a national institutes of health-funded program. s.a.r. was supported by the national institutes of health (grant number t ai ). a.c. was supported by the national institutes of health (grant number ai ) and the university of california office of the president (ucop r rg ).potential conflicts of interest. a.c., s.a.r., b.s., l.l., m.p., and c.i. have no conflicts. d.s. is a consultant for fluxergy, bayer, aids healthcare foundation and arena pharmaceuticals. all other authors report no conflicts of interest. all authors have submitted the icmje form for disclosure of potential conflicts of interest. conflicts that the editors consider relevant to the content of the manuscript have been disclosed. key: cord- - kc hyzo authors: beh, darius l l; ng, dorothy h l; ong, sean w x; sutjipto, stephanie; lee, pei hua; oon, jolene; wong, chen seong; archuleta, sophia title: the pandemic academy: reflections of infectious diseases fellows during covid- date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: kc hyzo the covid- pandemic has taken over the world at an unprecedented scale. as infectious diseases fellows, this has come straight into the heart of our specialty and created a unique impact on our training progress and perspective. here, we reflect on our early experiences during the first three months of battling covid- in singapore and glean some lessons for this pandemic and beyond. as coronavirus disease continues to spread with an exponentially rising death toll, around the world infectious diseases (id) specialists remain in short supply [ ] . interest in our specialty has waned over the years [ ] , partly influenced by lower compensation compared to other specialties [ ] . yet, as id fellows, we chose this path. for some, it was the thrill of the "detective work" required to diagnose a medical mystery [ ] . for others, it was the opportunity to add value to the hospital and improve patient outcomes [ , ] while working with the entire spectrum of medical and surgical disciplines. there are also those who were inspired by the extraordinary advancements in history's other pandemics such as smallpox and human immunodeficiency virus. nevertheless, for many of us, facing an emerging infectious disease of this unprecedented magnitude head-on might not have been what we expected [ ] . on january rd , singapore confirmed its first case of covid- , and by february th we moved to a heightened disease outbreak response level emphasizing the urgency of pandemic readiness [ ] . this came with a complete and sudden overhaul of the usual hospital routine. our id attendings diverted their attention to driving both hospital and national pandemic preparations, while our residents were diverted to run clinical services. all inperson meetings and tutorials were suspended. in-training examinations, external hospital and laboratory rotations, and annual leave were postponed indefinitely. many of the aspects that made id our chosen speciality were rapidly replaced by a new version of id trainingone projected to last at least a few months or perhaps the remainder of the year. as we mark months of our fellowship in the covid- era, we reflect on our experiences and the unique impact of this pandemic on id fellows. we share the lessons learned (table) to guide current and future id fellows, especially if history is to repeat itself. c c e p t e d m a n u s c r i p t are barriers to overcome when attempting to achieve this as a short elective [ ] . hence, as daunting as it seems, we strongly encourage fellows to embrace this as the invaluable experiential learning opportunity that it is. though simulations [ ] can teach us about pandemic preparation, one can only truly appreciate the intricate interplay of all the components needed to manage an outbreak through experiencing one. the emergent need for new policies and workflows in the hospital has provided a unique opportunity for us to have a seat at the table and have a say in the development and implementation of infection control policies and clinical operational workflows. learn faster than the virus spreads and find your new place as an id fellow. with a wide spectrum of manifestations, varying degrees of severity and multiple routes of transmission, covid- has proven that it is more than just another respiratory infection. the unknown nature of an emerging infectious disease meant that both attendings and fellows were on similar learning curves, redefining the mentor-mentee dynamic. we read the same studies and learned at the same pace, sharing patient care tips and best practices in real time. strange as it may be for id fellows, our specific role during a pandemic of this scale is not well-defined. we lack the experience or seniority to participate in operational planning and yet are not junior enough to participate solely in clinical work. as cases increased, the limits of our workforce were continually tested. hierarchies have been flattened by necessity, as id fellows stepped up to greater autonomy and attendings stepped down to do calls. it has been a period of steep learning, of finding our own footing, avoiding missteps and discovering our own strength through struggle. self-reflection and debriefing with our attendings and program directors have been important learning tools during this time. don't forget your other patients. attending to the growing epidemic and juggling that with maintaining a pared down id consult service has been difficult but necessary. while manpower and resources have been diverted to manage covid- , we have continued to treat patients with infections other than covid- . our training and career progression may be delayed by this pandemic, but regardless, continuing to see a variety of cases has been important to combat burnout, continue to build our competency across id and fulfil our fellowship requirements. as attending physicians were increasingly stretched by outbreak operational demands, this gave us the opportunity to find answers ourselves and accelerate our progress to managing patients independently. a c c e p t e d m a n u s c r i p t another important learning point was the recognition of cognitive biases in the management of patients presenting with respiratory symptomsnot everyone with fever and cough had covid- . most patients isolated with concerns of covid- turned out to have other diagnoses, such as tuberculosis or even newly-diagnosed hiv presenting with pneumocystis pneumonia [ ] . it was important to balance the need to protect staff by excluding covid- with the needs of our patients by ensuring that isolation policies did not become barriers to accessing diagnostic facilities and definitive care. try to get involved in research and communicate it. singapore was one of the first countries outside china to be seriously affected by covid- , and at the time there were still many unknowns. some of us participated in research early on in the pandemic [ ] , assisting with patient recruitment for observational cohort studies or clinical trials and even writing papers. for studies that were widely quoted in the media, it is equal parts exciting and terrifying to realise how our research impacted how the disease was handled internationally. another challenge was dealing with the rapidly evolving information and trying to communicate this to patients and their families, while at the same time trying to provide reassurance and comfort to patients with covid- . outside of clinical trials, discussions regarding experimental treatments have been difficult conversations. in a world where we like to tell patients that everything we do is informed by evidence, having to manage this delicate balance was another new skill to learn. understand that it will take a mental, physical and emotional tollwhich may be especially unrelenting given that you are in id, and that this will be a day-to-day reality until this is over. during sars in , it was widely reported that healthcare workers experienced heightened levels of anxiety, burnout and post-traumatic stress disorder in its wake [ ] . thus it was not surprising that many of us felt this way in the midst of the covid- pandemic [ ] . social distancing has been actively practiced in the hospital, with team segregation and even isolation during meal-times. this sense of isolation has also extended to our families due to a fear of acquiring covid- and passing it to a loved one [ ] . many of us have developed elaborate decontamination rituals before entering our homes, and some have already moved a c c e p t e d m a n u s c r i p t out to protect our families. though we have yet to experience this, with disruptions in supply chains and increasing demands [ ] , we anticipate that we may face a shortage of personal protective equipment as well, and reflect with sorrow and dread at the difficult decisions being made in many parts of the world, where physicians have to manage the shortage of critical resources such as ventilators [ ] . in our hospitals and in the media, there have been obvious efforts to maintain a sense of social solidarity. this has been particularly important as reported incidents of discrimination against frontline or healthcare workers did occur in singapore early on during the pandemic [ ] . one touching effort was the clap for #sgunited [ ] , inspired by #clapfornhs in the united kingdom, where singaporeans applauded the efforts of doctors, nurses, emergency services, cleaners, supermarket staff and everyone working to keep the country safe. within the community of fellows and residents, novel social interactions, such as yoga classes over zoom © (conducted by no less than the fellowship program director), provided a good avenue for stress-relief, maintaining team camaraderie, and networking. it is these gestures and little moments of reprieve that have made all the difference. such as "sharing" ice-cream with your residents at the end of another long dayeven if this means sitting rooms apart. though many have called this the "new normal", we must remember there is nothing normal about this. we are training under exceptional circumstances, and are expected to act exceptionally in them. when there is so much to do, it is only natural to feel you are not doing your best. just as sars defined the experience and training of our seniors, covid- will define oursthis is our coming-of-age story. for us, it is unique to be in the middle of id training during a (hopefully) 'once-in-a-century' pandemic [ ] . the inevitable sacrifices will be momentous, but this experience will teach us invaluable lessons. if nothing else, it has put us in better stead to fight the next one. charting the future of infectious disease: anticipating and addressing the supply and demand mismatch factors influencing internal medicine resident choice of infectious diseases or other specialties: a national cross-sectional study critical care crisis and some recommendations during the covid- epidemic in china #whyid: crowdsourcing the top reasons to choose infectious diseases in the age of twitter. open forum infectious diseases impact of infectious disease consultation on quality of care, mortality, and length of stay in staphylococcus aureus bacteremia: results from a large multicenter cohort study early initiation of appropriate treatment is associated with increased survival in cancer patients with candida glabrata fungaemia: a potential benefit from infectious disease consultation the perpetual challenge of infectious diseases confirmed imported case of novel coronavirus in singapore; multi-ministry taskforce ramps up precautionary measures residency training at the front of the west african ebola outbreak: adapting for a rare opportunity pandemic preparedness: nationally-led simulation to test hospital systems it's not all about covid- : pneumocystis pneumonia in the era of a respiratory outbreak absence of contamination of personal protective equipment (ppe) by severe acute respiratory syndrome coronavirus (sars-cov- ) long-term psychological and occupational effects of providing hospital healthcare during sars outbreak. emerging infectious diseases psychological impact of the covid- pandemic on health care workers in singapore air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient critical supply shortages -the need for ventilators and personal protective equipment during the covid- pandemic fair allocation of scarce medical resources in the time of covid- discrimination of healthcare workers due to coronavirus 'disgraceful': amrin amin. channel news asia claps for front-line fighters from windows, balconies 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 .gates, b., responding to covid- -a once-in-a-century pandemic? new england journal of medicine, .a c c e p t e d m a n u s c r i p t table . advice for id fellows during the covid- pandemic outbreak response and management  get involved with your hospital's infection prevention and epidemiology departments  assist with training, e.g. becoming a trainer for powered air-purifying respirators, teaching proper donning and doffing of ppe  participate in operational meetings with health system executives and incident command centres  work on strategies and systems to track and optimize the consumption of essential supplies, e.g. ppe  contribute to the decision-and policy-making processes, e.g. summarizing evidence to support a modified testing criteria in special populations (plha, transplant, pregnancy) and safe de-isolation criteria  volunteer to observe behaviours and infection control practices to develop interventions for population-dense facilities where clusters have occurred, e.g. migrant worker dormitories, elder-care homes, prisons and detention facilities rapid learning and growth  regularly review publications and data on various aspects of covid- (epidemiology, diagnostics and therapeutics)  organize journal clubs to present and discuss updates, exercise caution and systematic approaches and "sieve the wheat from the chaff" in the high-volume of literature, e.g. preprints, poor quality studies  strive to become increasingly independent  reflect during this period of self-discovery  regularly debrief with your attending and program directorthey are learning too! core id training and patient care  seek out evidence to manage your patients independently (with appropriate supervision)  leverage on peer learning by discussing cases with other fellows or holding your own "id grand rounds"  keep up your general id skills and guard against cognitive biasnot all those who cough have covid-  find a balance to avoid a delay in diagnosis or treatment  practice telemedicine for your stable outpatients (in line with your hospital's policies)research involvement  help with ethics submissions, grant proposals, consent-taking and collection of samples  consider strategies to pivot and re-direct your pre-existing or on-going research projects (e.g. by bringing in a covid- related aspect) to avoid having research put on hold due to social-distancing requirements and lockdowns  fellows may have to hold down the fort and ensure the smooth running of a regular id service, so your research may be paused -don't feel too disappointed mental health and wellbeing  keep in contact with co-fellows (and those in other specialties) in a non-work setting with virtual meetings  reconnect with old friends, and keep in touch with the extended family  find time to pursue hobbies and exercise  continue meeting regularly with your fellowship mentor or program director  help fellows with additional struggles e.g. those with young children to care for following school and childcare closures  do not be afraid to ask for helpbe it mental health or psychosocial support key: cord- - y jhmu authors: schwartz, carmela; oster, yonatan; slama, carole; benenson, shmuel title: a dynamic response to exposures of healthcare workers to newly diagnosed covid- patients or hospital personnel, in order to minimize cross transmission and need for suspension from work during the outbreak date: - - journal: open forum infect dis doi: . /ofid/ofaa sha: doc_id: cord_uid: y jhmu background: during the corona virus disease (covid- ) epidemic, many healthcare workers (hcws) were exposed to infected persons, leading to suspension from work. we describe a dynamic response to exposures of hcws at the hadassah hospital, jerusalem, to minimize the need for suspension from work. methods: we performed an epidemiological investigation following each exposure to a newly diagnosed covid- patient or hcw; close contacts were suspended from work. during the course of the epidemic, we adjusted our isolation criteria according to the timing of exposure related to symptoms onset, use of personal protective equipment and duration of exposure. in parallel, we introduced universal masking and performed periodic sars-cov- screening for all hospital personnel. we analyzed the number of hcws suspended weekly from work and those who subsequently acquired infection. results: in the investigations conducted during march-may , we interviewed hcws and suspended ( %) from work, most of them, ( %), during the first two weeks of the outbreak. the median duration of exposure was minutes (iqr, - ). only / ( . %) developed infection, all in the first two weeks of the epidemic. after introduction of universal masking and despite loosening the isolation criteria, none of the exposed hcws developed covid- . conclusions: relatively short exposures of hcws, even if only either the worker or the patient wore a mask, probably poses a very low risk for infection. this allows us to perform strict follow-up of exposed hcws in these exposures, combined with repeated testing, instead of suspension from work. as of may , israel has experienced more than , cases of coronavirus disease (covid- ) ( cases/million) and more than deaths ( deaths/million) ( ) . jerusalem and its surroundings is the area with the highest prevalence of covid- patients in israel ( ) .health care workers (hcws) are at increased risk of exposure to infected persons ( ) , and concern aroused early in the course of the epidemic that a substantial number of hcws might need to be suspended from work. this could seriously affect the functioning work force available at the hospital ( ) ( ) . understanding of the mode of transmission of severe acute respiratory syndrome corona virus (sars-cov- ), and strict guidelines for personal protective equipment (ppe) during direct patient contact and any interactions between hcws in the hospital, are essential for ensuring staff protection and safety ( ) . furthermore, immediate epidemiological investigation and, if needed, early suspension from work of exposed hcws is needed in order to limit the spread of infection to and between hcws and patients ( ) ( ) . in this research, we describe the outcomes of our dynamic response to exposures of hcws to newly diagnosed positive patients or personnel, aimed at minimizing infection of hcws and cross transmission during the covid- outbreak. (supplementary table) . especially at the beginning of the epidemic, in the second week of march, many health care workers (hcws) were exposed to covid- patients, in the hospital or outside. immediate epidemiological investigations of exposed hcws were initiated, in order to break the chain of cross-transmission between hcws as well as avoiding transmission from hcws to patients, thus keeping maximal work force available. a c c e p t e d m a n u s c r i p t the ipc team got a notice of any positive covid- hcw or patient in the hospital, either from the ministry of health (in a few hours after positive test results) or automatically from the hospital laboratory through the computerized information system (immediately upon verification of a positive test). in order to identify every possibly exposed hcw, a thorough epidemiological investigation was initiated immediately, even during evening shifts and weekends. the ipc team interviewed every such hcw and recorded the exact circumstances and duration of the encounter. we defined close contact as exposure of at least minutes, in proximity of less than two meters, to a positive covid- person ( ) . in case of a contact of less than one meter, we considered even five minutes of exposure as a close contact. according to the centers for disease control (cdc) guidelines ( ), wearing of ppe by the index case and/or the exposed hcw should be taken into consideration when deciding upon the need for home isolation of the exposed hcw. if both the index case and the hcw wore a facemask (surgical mask or n respirator), there was no need for isolation. the same decision was applied if the index case did not wear a facemask but the hcw wore a facemask and a face shield (table ) . during the course of the epidemic and the evolving understanding of the infectivity and transmission of sars-cov- , we adjusted our criteria for home isolation of exposed hcws (supplementary table) . during the first two weeks of the epidemic in israel, all exposed hcws meeting the criteria for close contact were suspended from work for days. after two weeks (on march ), during which over hcws were sustained from work, the need a c c e p t e d m a n u s c r i p t for home isolation was redefined according to the following principles: ) if the index case was symptomatic at the time of exposure (e.g., fever or chills, respiratory symptoms, loss of smell or taste), all close contacts were sent to home isolation for days following exposure date. ) if the exposure occurred more than four days before the index case developed symptoms, since most patients are only infective within four days prior to symptoms ( ), isolation was not required. ) if the exposure occurred four days or less before the index case developed symptoms (if the index case never had symptoms, than within four days before the positive sars-cov- test), isolation was required for ten days since the last exposure and return to work was approved after a negative nasopharyngeal pcr test on day ten ( ) . these principles are summarized in table . we asked every exposed hcw to inform us immediately in case of any evolving symptoms. needless to say that every exposed employee who developed any suspicious symptoms was tested for the presence of sars-cov- , and suspended from work while the results were pending. after relieve of symptoms and a negative test result, the employee was allowed back to work. in the beginning of the epidemic in israel (march ), we recommended the use of ppe for direct contact with suspected or positive covid- patients, according to the cdc and israeli ministry of health guidelines at that time ( - ). covid- positive patients were isolated in the designated wards and all hcws entering the area wore full airborne isolation ppe, e.g. waterproof gown, gloves, n respirator, face shield and head cover. patients with suspected covid- , according to symptoms or because of exposure to a positive person, were put in isolation rooms and hcws entered the room while wearing surgical mask, face a c c e p t e d m a n u s c r i p t shield, disposable gown and gloves. in these patients, in case of severe respiratory symptoms or aerosol producing procedures, ppe was upgraded to full airborne protection as described above. in the light of many exposed hcws, during the last week of march , the ipc team required the use of surgical masks by hospital personnel during every patient contact. in addition, staff meetings were restricted to ten attendees and allowed only while adhering to rules of social distancing, and interaction between staff during shifts was kept to a minimum. in parallel, a routine periodic screening program for sars-cov- of all hcws was introduced at the hospital ( ) . this included summoning all employees for pcr testing for sars-cov- performed on nasopharyngeal swabs. the employees were asked to undergo a second test after five days. periodic screening of all hcws is continues at the hospital until these days. on april , we changed our policy to universal masking of hcws and visitors at all times and of patients during any contact with a hcw. we used descriptive statistics for all investigations performed on hcws who were exposed to a covid- patient or colleague and their outcomes. categorical variables are presented with percentages and continuous variables are presented with median and inter-quartile range (iqr). we describe the number of hcws suspended weekly from work and those subsequently acquiring infection over the course of the epidemic. additionally, we examined the input of the changing strategies of ppe and criteria for suspension from work on these outcomes. we used extended mantel-haenszel test to compare the rates of hcws that we sent to home isolation in each investigation, before and after the demand for a c c e p t e d m a n u s c r i p t masking of hcws (winpepi version . ). significance was two tailed and determined at p< . . between march and may ( weeks), we performed exposure investigations. in / ( %) the index case was a hcw and in / ( %) a patient (emergency department, ( %); delivery room, ( %); medical, ( %); surgical, ( %); outpatient clinics, ( %)). in five out of these exposure investigations ( %), the index case was asymptomatic throughout the course of his disease. altogether, we interviewed hcws (table ) . out of these, ( %) hcws had close contact as defined by the cdc ( ). most of these were relatively short exposures (median min, iqr, - ). in most of these exposures, either the hcw and/or the index case were not fully protected as defined by the cdc guidelines (both without a mask, ( %); only one with a mask, ( %); both masked but exposure greater than three hours, ( %)). these workers were suspended from work and sent to home isolation. the vast majority of hcws, / ( %) were sent to home isolation during the first two weeks of the outbreak. of all hcws sent to home isolation following these investigations, only / ( . %) developed infection with covid- during the period of isolation, all at the very beginning of the epidemic (graph). none of the hcws investigated because of potential exposure, but not sent to isolation, had developed covid- . since our hospital performed routine screening for sars-cov- on all hcws, we were able to check and ascertain that we did not miss any positive hcw whom we might not have march , no hcw who was exposed after this change was infected until the end of the study period (graph). healthcare workers are at increased risk of acquiring covid- from unrecognized patients or colleagues during work ( ) ( ) . at the very beginning of the epidemic in israel, the ipc team of our hospital started epidemiological investigations of every exposure to a newly diagnosed sars-cov- positive patient or hcw. the first investigations resulted in the need to suspend a large number of hcws from work, requiring home isolation. serious concern aroused that departments would need to be totally shut down, threatening the ability of the hospital to keep functioning over time. as soon as we learned in mid-march from the cdc guidelines at that time, that wearing ppe (facemask with or without face shield) could reduce the need for excluding exposed hcws from work ( ), we updated our rules of protection. we introduced universal masking for hospital personnel, patients and visitors and social distancing between hcws. later on, this approach was suggested also in the literature ( ) . since then, the number of hcws whom we needed to suspend from work decreased significantly. as shown in the graph, this decline happened while the epidemic in israel was still on the rise. a single report from minnesota department of health, usa, also showed a reduction in hcws infections in the hospital following the introduction of universal masking ( ) . in addition, and according to new accumulating knowledge, we redefined the criteria for suspension from work and duration of isolation required ( ) . we differentiated between exposures to symptomatic or asymptomatic index cases and reduced the duration of home isolation needed after exposure to an asymptomatic index case. since % of exposed people who become infected, do so within days from exposure, we performed sars-cov- nasopharyngeal test on day for isolated workers, prior to allowing them to return to work ( ) . by that, we further reduced the number of hcws excluded from work at a given time. during epidemiological investigations performed, out of potentially exposed hcws whom we thoroughly interviewed, we defined as close contacts, prompting suspension from work. out of these, only five developed clinical signs of infection with sars-cov- , all in the early phase of the covid- outbreak. although we narrowed the criteria for isolation, none of the hcws investigated, but not isolated, developed clinical signs of infection with covid- . owing to the periodic universal screening of all hcws performed at our hospital, we were assured that there were no eventual asymptomatic hcws among those investigated or isolated. additionally, the proactive screening allowed us to assume that we probably did not miss any close contact during our investigation process, who potentially could become positive. furthermore, the results of this study raises the question whether the criteria for isolation were still too rigorous, since, after the initial phase, none of the hcws excluded from work developed covid- . in the light of these findings, and in the presence of universal masking and social distancing, it might be worth to consider substitution of suspension from work of exposed hcws by rigorous follow-up of symptoms together with repeated testing on days a c c e p t e d m a n u s c r i p t five and ten after exposure. this approach was recently studied in a mathematical model performed by . there are some limitations to this study: due to the retrospective nature of epidemiological investigations, there is a recall bias and hence, in some cases it was not trivial to define each contact unequivocally. our criteria for home isolation after exposure may need further specification. accumulating knowledge on the infectivity of asymptomatic or presymptomatic patients might shed light on this issue ( ) . in addition, despite periodic screening of all hcws, since we did not test them every day, we still might have missed asymptomatic positive personnel; however, we assume that the chance for that is negligible. our experience might be valid in hospitals with dedicated covid- departments and universal masking, and we assume that this by now is the standard of care in most countries. in conclusion, after introducing universal masking for hcws, patients and visitors, and social distancing, none of the exposed hcws developed covid- . based on the results of our study, we assume that relative short exposures of hcws, even if only either the worker or the patient wore a mask, probably poses a very low risk for infection. this allows us to consider performing strict follow-up of exposed hcws for symptoms, together with repeated pcr testing, instead of suspending them from work. a c c e p t e d m a n u s c r i p t figure about: israeli government: ministry of health protecting chinese healthcare workers while combating the novel coronavirus saving the frontline health workforce amidst the covid- crisis: challenges and recommendations challenges for nhs hospitals during covid- epidemic universal masking in hospitals in the covid- era investigation of three clusters of covid- in singapore: implications for surveillance and response measures european centre for disease prevention and control contact tracing: public health management of persons, including healthcare workers, having had contact with covid- cases in the european union covid- guidelines, procedures and information for professionals guidance for risk assessment and work restrictions for healthcare personnel with potential exposure to covid- temporal dynamics in viral shedding and transmissibility of covid- the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application ministry of health, israel. covid- guidelines, procedures and information for professionals interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease (covid- ) in healthcare settings proactive screening approach for sars-cov- among healthcare workers. clinical microbiology and infection prevalence and clinical presentation of health care workers with symptoms of coronavirus disease in dutch hospitals during an early phase of the pandemic covid- ) infection among health care workers and implications for prevention measures in a tertiary hospital in wuhan, china minnesota department of health, responding to and monitoring covid- exposures in health care settings individual quarantine versus active monitoring of contacts for the mitigation of covid- : a modelling study all authors report no conflict of interest. our study does not include factors necessitating patient consent. 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