key: cord-0822021-kkbed30m authors: Smith, R. L.; Gibson, L. L.; Martinez, P. P.; Ke, R.; Mirza, A.; Conte, M.; Gallagher, N.; Conte, A.; Wang, L.; Fredrickson, R.; Edmonson, D. C.; Baughman, M. E.; Chiu, K. K.; Choi, H.; Jensen, T. W.; Scardina, K. R.; Bradley, S.; Gloss, S. L.; Reinhart, C.; Yedetore, J.; Owens, A. N.; Broach, J.; Barton, B.; Lazar, P.; Henness, D.; Young, T.; Dunnett, A.; Robinson, M. L.; Mostafa, H. H.; Pekosz, A.; Manabe, Y. C.; Heetderks, W. J.; McManus, D. D.; Brooke, C. B. title: Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection date: 2021-03-20 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2021.03.19.21253964 sha: d65da44a32b17683d1c3dbd3b9524dc5d2ff9171 doc_id: 822021 cord_uid: kkbed30m What is already known about this topic? Diagnostic tests and sample types for SARS-CoV-2 vary in sensitivity across the infection period. What is added by this report? We show that both RTqPCR (from nasal swab and saliva) and the Quidel SARS Sofia FIA rapid antigen tests peak in sensitivity during the period in which live virus can be detected in nasal swabs, but that the sensitivity of RTqPCR tests rises more rapidly in the pre-infectious period. We also use empirical data to estimate the sensitivities of RTqPCR and antigen tests as a function of testing frequency. What are the implications for public health practice? RTqPCR tests will be more effective than rapid antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (provided results reporting is timely). All modalities, including rapid antigen tests, showed >94% sensitivity to detect infection if used at least twice per week. Regular surveillance/screening using rapid antigen tests 2-3 times per week can be an effective strategy to achieve high sensitivity (>95%) for identifying infected individuals. Diagnostic tests and sample types for SARS-CoV-2 vary in sensitivity across the infection 48 period. What is added by this report? We show that both RTqPCR (from nasal swab and saliva) and the Quidel SARS Sofia FIA rapid 52 antigen tests peak in sensitivity during the period in which live virus can be detected in nasal 53 swabs, but that the sensitivity of RTqPCR tests rises more rapidly in the pre-infectious period. We also use empirical data to estimate the sensitivities of RTqPCR and antigen tests as a 55 function of testing frequency. What are the implications for public health practice? 58 RTqPCR tests will be more effective than rapid antigen tests at identifying infected individuals 59 prior to or early during the infectious period and thus for minimizing forward transmission 60 (provided results reporting is timely). All modalities, including rapid antigen tests, showed >94% Recently, there has been considerable interest in the potential of rapid antigen tests to expand 75 diagnostic testing capacity due to the ease of use, availability, cost, and rapid time-to-results 1 . However, data for their use in screening asymptomatic individuals is sparse. Enthusiasm for 77 their widespread deployment has been further tempered by well-publicized examples of false 78 positive results in people with low pre-test probability of infection, and by reports suggesting 79 they lack sensitivity compared with RTqPCR, potentially making them less effective at mitigating 80 community spread 2,3 . Here, we compare the sensitivities of nasal and saliva RTqPCR tests with the Quidel Sofia (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Individuals were recruited via either a link shared in an automated text message providing 101 isolation information sent within 30 minutes of a positive test result, a call from a study recruiter, 102 or a link shared by an enrolled study participant or included in information provided to all 103 quarantining close contacts. In addition, signs were used at each testing location and a website 104 was available to inform the community about the study. Participants were required to be at least 18 years of age, have a valid university ID, speak Participants who tested positive prior to enrollment or during quarantine were followed for up to 113 14 days. Quarantining participants who continued to test negative by saliva RTqPCR were 114 followed for up to 7 days after their last exposure. All participants' data and survey responses 115 were collected in the Eureka digital study platform. Sample collection 118 Each day, participants were remotely observed by study staff collecting: The order of nostrils (left vs. right) used for the two different swabs was randomized. For nasal 126 swabs, participants were instructed to insert the soft tip of the swab at least 1 cm into the 127 indicated nostril until they encountered mild resistance, rotate the swab around the nostril 5 128 times, leaving it in place for 10-15 seconds. After daily sample collection, participants completed 129 a symptom survey. A courier collected all participant samples within 1 hour of collection using a 130 no-contact pickup protocol designed to minimize courier exposure to infected participants. After collection, saliva samples were stored at room temperature and RTqPCR was run within 134 12 hours of initial collection. The protocol for direct saliva-to-RTqPCR assay used has been 135 detailed previously 4 . In brief, saliva samples were heated at 95°C for 30 minutes, followed by 136 the addition of 2X TBS at a 1:1 ratio (final concentration 1X TBE) and Tween-20 to a final 137 concentration of 0.5%. Samples were assayed using the Thermo Taqpath COVID-19 assay. Quidel assay 140 Foam-tipped nasal swabs were placed in collection tubes and stored at 4°C overnight based on 141 guidance from the manufacturer. The morning after collection, swabs were run through the Sofia 142 SARS antigen FIA on Sofia 2 devices according to the manufacturer's protocol. Nasal swab RTqPCR 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. were conducted based on a limited participant set. All confidence intervals around sensitivity 167 were calculated using binconf from the Hmisc package in R version 3.6.2. The sensitivity of each of the tests was analyzed in three different ways: First, the ability of each test (antigen, saliva RTqPCR, or nasal RTqPCR) to detect an infected 171 person on a particular day relative to the day of first positive viral culture ("daily sensitivity") was 172 calculated. Daily sensitivity was not calculated for timepoints with fewer than 5 observed 173 person-days. Second, the ability of each test to detect an infected person according to their viral culture status 176 ("status sensitivity") was calculated. Viral culture status was defined as "pre-positive" on days Finally, we calculated the ability of repeated testing over a 14-day period to detect an infected 183 person ("protocol sensitivity") using a value-of-information approach. Seven different testing All code used in analyses can be found here: https://github.com/rlsdvm/CovidDetectAnalysis 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. 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. 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 March 20, 2021. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. We next estimated the protocol sensitivities, or how the ability of each of test platform to detect 236 infected individuals was affected by differences in testing frequencies (Table 3, Figure 3 ). Protocol sensitivity was defined at the schedule level, where the numerator is the number of 238 testing schedules resulting in at least one positive test and the denominator is the number of 239 testing schedules examined, where a testing schedule is defined as a set of samples from one 240 participant taken at a given frequency. In Figure 3 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. RTqPCR tests were higher than that of the Quidel Sofia SARS Antigen FIA, suggesting that 264 RTqPCR tests will be more effective at identifying infected individuals before they transmit to 265 others. Both RTqPCR and antigen tests peak in daily and status sensitivities when infectious virus is 268 detectable in nasal swab samples, suggesting that all three modalities can be effective at 269 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. These dynamics are consistent with those described previously for RTqPCR 8, 9 . In contrast, the 272 daily sensitivity of the antigen test declined very quickly, suggesting that this test will be less 273 effective at identifying individuals during later stages of infection. This may limit diagnosis and 274 contact-tracing efforts in test-limited environments. Previous studies have suggested that frequent testing would maximize the ability of a given test 277 modality to detect infected individuals 10,11 . We found that all testing modalities showed almost 278 95% protocol sensitivity to detect infection if used at least twice per week. When applied weekly, 279 protocol sensitivity remained very high for nasal RTqPCR, declined slightly to 90% for saliva 280 RTqPCR, and dropped to only 76% for the antigen test. When we compared the abilities of different testing frequencies to identify individuals while 283 infectious virus was detectable in nasal samples, we observed a clear reduction in protocol 284 sensitivity for all testing modalities when testing frequencies decreased below daily. The 285 reduction in protocol sensitivity was most pronounced for the antigen test, which dropped to 286 0.72 with testing every fourth day, however, both RTqPCR tests were only slightly better at 0.74 287 (saliva) and 0.77 (nasal). Altogether, these data demonstrate the importance of frequent testing 288 regardless of test modality for identifying individuals while they are contagious. This is the first study to compare the longitudinal performance of rapid antigen and RTqPCR 291 tests with infectious virus shedding in a well-defined population early in SARS-CoV-2 infection. We found that all three diagnostic tests demonstrated a high degree of daily sensitivity during 293 the presumed infectious period, but that the RTqPCR tests exhibited superior daily sensitivities 294 prior to this period. Our data suggest that RTqPCR tests can be more effective than antigen 295 tests at mitigating community spread of SARS-CoV-2, but only if the turnaround time for RTqPCR results is short. Finally, these data also quantitatively demonstrate the importance of Denkinger CM, for the study team. Evaluation of the 327 accuracy, ease of use and limit of detection of novel, rapid, antigen-detecting point-of-care 328 diagnostics for SARS-CoV-2 Evaluation of three rapid lateral flow antigen detection tests for the 332 diagnosis of SARS-CoV-2 infection SARS-CoV-2 transmission in 336 intercollegiate athletics not fully mitigated with daily antigen testing Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing 346 cells Antigen-Based Testing but Not Real-Time Polymerase Chain 349 Reaction Correlates With Severe Acute Respiratory Syndrome Coronavirus 2 Viral Culture Triplex Real-Time RT-PCR for Severe Acute 353 Respiratory Syndrome Coronavirus 2. Emerg Infect Dis SARS-CoV-2 viral dynamics in acute infections 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 Inferred duration of infectious period of 361 SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic 362 and symptomatic COVID-19 cases Assessment of SARS-CoV-2 Screening Strategies to 364 Permit the Safe Reopening of College Campuses in the United States Test sensitivity is secondary to frequency and turnaround time for COVID-19 368 screening. Sci Adv 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.