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While detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by diagnostic reverse-transcription polymerase chain reaction (RT-PCR) is highly sensitive for viral RNA, the nucleic acid amplification of subgenomic RNAs (sgRNAs) that are the product of viral replication may more accurately identify replication. We characterized the diagnostic RNA and sgRNA detection by RT-PCR from nasal swab samples collected daily by participants in postexposure prophylaxis or treatment studies for SARS-CoV-2. Among 1932 RT-PCR-positive swab samples with sgRNA tests, 40% (767) had detectable sgRNA. Above a diagnostic RNA viral load (VL) threshold of 5.1 log10 copies/mL, 96% of samples had detectable sgRNA with VLs that followed a linear trend. The trajectories of diagnostic RNA and sgRNA VLs differed, with 80% peaking on the same day but duration of sgRNA detection being shorter (8 vs 14 days). With a large sample of daily swab samples we provide comparative sgRNA kinetics and a diagnostic RNA threshold that correlates with replicating virus independent of symptoms or duration of illness., Competing Interests: Potential conflicts of interest. M. E. D. is funded by the Infectious Diseases Clinical Research Consortium through the National Institute for Allergy and Infectious Diseases, National Institutes of Health (NIH; award UM1AI148684), outside the submitted work. M. L. W. H. and M. H. W. report funding from the BMGF, outside the submitted work. A. B. reports personal fees from Gates Ventures and grant funding from the NIH, the BMGF, and the New York City Department of Health and Mental Hygiene, outside the submitted work. H. Y. C. reports consulting with Ellume, Pfizer, the BMGF, GlaxoSmithKline, and Merck; she has also received research funding from Gates Ventures and Sanofi Pasteur and support and reagents from Ellume and Cepheid, outside the submitted work. H. C. S. K. is funded by the Research Supplement to Promote Diversity in Health-Related Research Program, the National Cancer Institute, NIH (grant R01 CA213130-S) and a Department of Medicine Diversity Academic Development Scholar Award from the University of Washington. C. M. J. reports consulting with AbbVie and Gilead, outside the submitted work. R. B. reports funding from BMGF and the NIH, outside the submitted work, and support for abstract and manuscript writing from Regeneron Pharmaceuticals, also outside the submitted work. All other authors report no potential 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., (© The Author(s) 2022. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

Background: Transmission rates after exposure to a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive individual within households and healthcare settings varies significantly between studies. Variability in the extent of exposure and community SARS-CoV-2 incidence may contribute to differences in observed rates., Methods: We examined risk factors for SARS-CoV-2 infection in a randomized controlled trial of hydroxychloroquine as postexposure prophylaxis. Study procedures included standardized questionnaires at enrollment and daily self-collection of midturbinate swabs for SARS-CoV-2 polymerase chain reaction testing. County-level incidence was modeled using federally sourced data. Relative risks and 95% confidence intervals were calculated using modified Poisson regression., Results: Eighty-six of 567 (15.2%) household/social contacts and 12 of 122 (9.8%) healthcare worker contacts acquired SARS-CoV-2 infection. Exposure to 2 suspected index cases (vs 1) significantly increased risk for both household/social contacts (relative risk [RR], 1.86) and healthcare workers (RR, 8.18). Increased contact time also increased risk for healthcare workers (3-12 hours: RR, 7.82, >12 hours: RR, 11.81, vs ≤2 hours), but not for household/social contacts. County incidence did not impact risk., Conclusions: In our study, increased exposure to SARS-CoV-2 within household or healthcare settings led to higher risk of infection, but elevated community incidence did not. This reinforces the importance of interventions to decrease transmission in close contact settings., (© The Author(s) 2022. Published by Oxford University Press for the Infectious Diseases Society of America.)