key: cord-0987645-bhm5u0st authors: Zobrist, S.; Oliveira-Silva, M.; Vieira, A. M.; Bansil, P.; Gerth-Guyette, E.; Leader, B. T.; Golden, A.; Slater, H.; Cruz, C. D. d. L.; Garbin, E.; Sagalovsky, M.; Pal, S.; Gupta, V.; Wolansky, L.; Dall Acqua, D. S. V.; Naveca, F. G.; Nascimento, V. A. d.; Villalobos Salcedo, J. M.; Drain, P. K.; Costa, A. D. T.; Domingo, G. J.; Pereira, D. title: Screening for SARS-CoV-2 in close contacts of individuals with confirmed infection: performance and operational considerations date: 2022-01-28 journal: nan DOI: 10.1101/2022.01.27.22269904 sha: f1e834f3ab95733104bb37576cbd5e952e6d7f36 doc_id: 987645 cord_uid: bhm5u0st Background. Point-of-care and decentralized testing for SARS-CoV-2 is critical to inform public health responses. Performance evaluations in priority use cases such as contact tracing can highlight trade-offs in test selection and testing strategies. Methods. A prospective diagnostic accuracy study was conducted among close contacts of COVID-19 cases in Brazil. Two anterior nares swabs (ANS), a nasopharyngeal swab (NPS), and saliva were collected at all visits. Vaccination history and symptoms were assessed. Household contacts were followed longitudinally. Three rapid antigen tests and one molecular method were evaluated for usability and performance against reference RT-PCR on NPS. Results. Fifty index cases and 214 contacts (64 household) were enrolled. Sixty-five contacts were RT-PCR positive during at least one visit. Vaccination did not influence viral load. Gamma variants were most prevalent; Delta emerged increasingly during implementation. Overall sensitivity of evaluated tests ranged from 33% to 76%. Performance was higher among symptomatic cases and cases with Ct<34 and lower among oligo/asymptomatic cases. Assuming a 24-hour time-to-result for RT-PCR, the cumulative sensitivity of an ANS rapid antigen test was >70% and almost 90% after four days. Conclusions. The near immediate time-to-result for antigen tests significantly offsets lower analytical sensitivity in settings where RT-PCR results are delayed or unavailable. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, which causes COVID-19, has 54 significantly burdened health systems globally, with over 22 million confirmed cases in Brazil alone as of 55 2021 [1] . A key challenge of the pandemic response is access to appropriate diagnostic testing, which is 56 critical to inform public health strategies [2] . 57 The reference standard for SARS-CoV-2 testing is RT-PCR. While accurate, this method has many 58 practical limitations, including cost, laboratory infrastructure requirements, and often invasive sampling. 59 RT-PCR testing is typically centralized, which can lead to delays in reporting results to patients. Such 60 delays have important public health implications, including increased risk for transmission during the 61 period before results are available [3, 4] . Expanded access to decentralized and point-of-care (POC) 62 testing is essential to identify cases early and limit community transmission, particularly where RT-PCR 63 is unavailable. analyze data from the EoU questionnaire, a matrix was used to rank aspects of the products' usability as 126 "satisfactory," "average," or "unsatisfactory" (Supplementary Material E) [21] . 127 The sample size targeted at least 50 contacts with a positive reference result, including at least 20 129 asymptomatic individuals, to meet US FDA Emergency Use Authorization requirements [31] . 130 Participants with no symptoms at the time of sampling were classified as asymptomatic. Participants were 131 considered symptomatic if they presented with cough, shortness of breath, difficulty breathing, or at least 132 two of the following symptoms at the time of sampling: fever, chills, rigor, myalgia, headache, sore 133 throat, new olfactory or taste disorder [32] . Participants who presented with one or more mild symptoms 134 but did not fit the symptomatic case definition and reported no care seeking or changes to behavior were 135 considered oligosymptomatic. 136 Sensitivity, specificity, and positive and negative predictive values were calculated using standard 137 formulas and presented with 95% CIs. Samples for which both RT-PCR and evaluated test results were 138 available were included in the analysis. Using the longitudinal dataset, trade-offs between performance 139 and utility of the evaluated tests in terms of cumulative sensitivity at specified time points were assessed 140 as a function of time-to-results. 141 Data were collected and managed using REDCap electronic data capture tools hosted at the Institute of 142 Translational Health Sciences [33] . Statistical analyses were conducted using Stata 15.0 (StataCorp, 143 College Station, Texas, USA) and R 4.0.3 (R Foundation for Statistical Computing, Vienna, Austria). 144 145 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (Table 1) . Sixty-four contacts shared a primary residence with an index case and were therefore 153 included in the longitudinal sample. Contacts ranged from ages 13 to 79. The majority of participants 154 across all groups were female. Sixty-five contacts (30%, 65/214) were SARS-CoV-2 positive by the 155 reference assay during at least one visit ( Figure 1 ). For household contacts, positivity rates and symptom 156 status varied by visit. In total, 42 paired samples were collected at unique visits with oligo/asymptomatic 157 positive contacts, from 32 participants. 158 Most participants were either partially (45%, 118/264) or fully (27%, 70/264) vaccinated at enrollment 160 (Table 1) The two POC ANS antigen tests demonstrated comparable performance, with overall sensitivity of 55.0% 168 for the STANDARD Q (95% CI 43.5%-66.2%) and 50.6% for LumiraDx (95% CI 39.1%-62.1%) (Table 169 2). Performance increased to >80% sensitivity for both tests among symptomatic cases but decreased to 170 <30% among oligo/asymptomatic cases. For specimens with Ct values less than 34, above which viral 171 viability is negligent and quantification is not as reliable [34, 35] , performance of both tests improved, 172 with sensitivities in the ranges of 90% and 60% for symptomatic and oligo/asymptomatic cases, 173 respectively. 174 The SalivaDirect PCR assay showed the highest overall performance at 75.9% sensitivity (95% CI 175 65.0%-84.9%), which increased to 90.0% (95% CI 78.2%-96.7%) among contacts with Ct<34. In all 176 scenarios, the rapid STANDARD Q Saliva Test had a sensitivity of <53%. 177 Figure 3 presents the viral load of positive specimens, stratified by results of the STANDARD Q Nasal 178 and Saliva tests. Overall, specimens with low viral loads were more likely to yield negative results; 179 however, misclassification of specimens with high viral loads was more common with the saliva test. hours, >70% of contacts would have been identified by a POC test. At 48 hours, cumulative sensitivity is 189 80%, increasing to nearly 90% at four days. 190 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In this study, performances of three POC antigen tests (two ANS and one saliva) and one molecular saliva 195 assay were assessed among close contacts of COVID-19-positive index cases. All tests demonstrated 196 strongest performance among symptomatic cases-and particularly those with Ct<34. Performance 197 decreased among oligo/asymptomatic cases, which is consistent with results of prior studies [11, 13] and 198 may indicate that the tests are best able to detect those most likely to be infectious [34, 35] . However, 199 there is no universal Ct value cut-off-point that corresponds to infectivity, and the relationship between Ct 200 values and viral load varies by laboratory [11] . 201 The SalivaDirect assay had the best performance, with sensitivity of up to 90% among contacts with 202 Ct<34. Although this assay uses a noninvasive sample type and a simplified procedure that minimizes 203 processing time and costs, infrastructure and training requirements still limit the feasibility of 204 implementing this test in many settings, with potential implications for time-to-results. 205 The saliva antigen test had the lowest overall performance, consistent with the findings of other 206 evaluations of POC saliva antigen tests [36, 37] . One recent evaluation of this test reported an overall 207 sensitivity of 66.1%; however, the reference assay was conducted on saliva [38] . In this study, the test 208 was run on passively collected saliva. This may have impacted performance, as the manufacturer 209 recommends use of actively collected saliva with snorted nasal mucus. 210 The two POC ANS antigen tests-STANDARD Q Nasal and LumiraDx-demonstrated comparable 211 performance which was best among cases with Ct<34. Among symptomatic cases and those with Ct<34, 212 both tests met WHO performance criteria (≥ 80% sensitivity and ≥ 97% specificity) [10] . Both tests were 213 also considered easy to use; however, the LumiraDx test requires use of an instrument. 214 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 28, 2022. Overall, the observed positivity rate among close contacts (65/214, 30%) highlights the importance of 215 contact tracing and testing as a public health strategy [39] . The longitudinal data demonstrate the value of 216 serial testing (particularly for individuals with known exposures) and the practical benefits of timely 217 results [40, 41] . In this study, we show that in settings where RT-PCR is unavailable or where time-to-218 results is >4 days, close to 90% of individuals with Ct<34 could benefit from an earlier result via a POC 219 test. Even in settings where RT-PCR results are available within 24 hours, cumulative sensitivity of a 220 POC test is >70%. With repeat serial testing over a period of 9 days, the cumulative sensitivity of a POC 221 ANS antigen test increases from 70% to near 90%. In many settings, limited RT-PCR testing capacity-222 especially during high demand-can lead to delays in results. Immediate results can impact behavior of 223 potentially infectious individuals, encouraging earlier isolation and signaling where additional testing is 224 warranted [4] . The emergence of antiviral therapies-which are more effective the sooner they are The authors would like to thank all study participants as well as the clinical and laboratory staff at 247 CEPEM involved with this study. We also thank SD Biosensor and LumiraDx for facilitating the 248 availability of their tests for this study. Finally, we also thank Amanda Tsang and Christine Waresak for 249 editorial support with the manuscript. 250 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 28, 2022. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 28, 2022. All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 28, 2022. b. An individual with no or mild symptoms whose reference positivity status fluctuated between visits, with high Ct values overall, and no positive point-of-care test results. 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