Quantitative SARS-CoV-2 Viral-Load Curves in Paired Saliva Samples and Nasal Swabs Inform Appropriate Respiratory Sampling Site and Analytical Test Sensitivity Required for Earliest Viral Detection
Abstract
Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and presymptomatic transmission, curb the spread of variants, and maximize treatment efficacy. Low-analytical-sensitivity nasal-swab testing is commonly used for surveillance and symptomatic testing, but the ability of these tests to detect the earliest stages of infection has not been established. In this study, conducted between September 2020 and June 2021 in the greater Los Angeles County, California, area, initially SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity reverse-transcription quantitative PCR (RT-qPCR) and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, testing saliva with a high-analytical-sensitivity assay detected infection up to 4.5 days before viral loads in nasal swabs reached concentrations detectable by low-analytical-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva but were undetectable or at lower loads during the first few days of infection. High-analytical-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to designing optimal testing strategies with emerging variants in the current pandemic and to respond to future viral pandemics.
Additional Information
© 2022 Savela et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Received 24 August 2021; Returned for modification 21 September 2021; Accepted 10 December 2021; Accepted manuscript posted online 15 December 2021; Published 16 February 2022. We thank Lauriane Quenee, Junie Hildebrandt, Grace Fisher-Adams, RuthAnne Bevier, Chantal D'Apuzzo, Ralph Adolphs, Victor Rivera, Steve Chapman, Gary Waters, Leonard Edwards, Gaylene Ursua, Cynthia Ramos, and Shannon Yamashita for their assistance and advice on study implementation and/or administration. We thank Jessica Leong, Jessica Slagle, Mika Walton, Angel Navarro, Daniel Brenner, and Ojas Pradhan for volunteering their time to help with this study, Si Hyung Jin for helping with a literature review, and Mary Arrastia for providing biosafety support. We thank Maira Phelps, Lienna Chan, Lucy Li, Dan Lu, and Amy Kistler at the Chan Zuckerberg Biohub for performing SARS-CoV-2 sequencing. We thank Angie Cheng, Susan Magdaleno, Christian Kis, Monica Herrera, and Zaina Lemeir for technical discussions regarding saliva extraction and ddPCR detection. We thank Jennifer Fulcher, Debika Bhattacharya, and Matthew Bidwell Goetz for their ideas on potential study populations and early study design. We thank Omai Garner and David Beenhouwer for providing materials for initial nasal-swab validation. We thank Martin Hill, Alma Sanchez, Scott Kim, Debbie Noble, Nina Paddock, Whitney Harrison, Emily Holman, Isaac Turner, Vivek Desai, Luke Wade, Tom Mayell, Stu Miller, and Jennifer Howes for their support with recruitment. We thank Allison Rhines, Karen Heichman, and Dan Wattendorf for valuable discussions. Finally, we thank all the case investigators and contact tracers at the Pasadena Public Health Department and the City of Long Beach Department of Health & Human Services for their efforts in study recruitment and their work in the pandemic response. R.F.I. is a cofounder, consultant, and a director and has stock ownership of Talis Biomedical Corp. In addition, R.F.I. is an inventor on a series of patents licensed by the University of Chicago to Bio-Rad Laboratories, Inc., in the context of ddPCR. This study is based on research funded in part by the Bill & Melinda Gates Foundation (INV-023124). The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation. This work was also funded by the Ronald and Maxine Linde Center for New Initiatives at the California Institute of Technology and the Jacobs Institute for Molecular Engineering for Medicine at the California Institute of Technology. A.V.W. is supported by a National Institutes of Health NIGMS predoctoral training grant (GM008042) and a UCLA DGSOM Geffen fellowship; M.M.C. is supported by a Caltech graduate student fellowship, and M.K.P. and J.T.B. are each partially supported by a National Institutes of Health Biotechnology Leadership Predoctoral Training Program (BLP) fellowship from Caltech's Donna and Benjamin M. Rosen Bioengineering Center (T32GM112592).Attached Files
Published - jcm.01785-21.pdf
Submitted - 2021.04.02.21254771v2.full.pdf
Supplemental Material - jcm.01785-21-s0001.pdf
Files
Additional details
- Alternative title
- SARS-CoV-2 is detectable using sensitive RNA saliva testing days before viral load reaches detection range of low-sensitivity nasal swab tests
- PMCID
- PMC8849374
- Eprint ID
- 108641
- Resolver ID
- CaltechAUTHORS:20210407-080559241
- INV-023124
- Bill and Melinda Gates Foundation
- Ronald and Maxine Linde Center for New Initiatives
- Jacobs Institute for Molecular Engineering for Medicine
- GM008042
- NIH Predoctoral Fellowship
- UCLA
- Caltech
- Donna and Benjamin M. Rosen Bioengineering Center
- T32GM112592
- NIH Predoctoral Fellowship
- Created
-
2021-04-08Created from EPrint's datestamp field
- Updated
-
2022-05-31Created from EPrint's last_modified field
- Caltech groups
- COVID-19, Rosen Bioengineering Center, Jacobs Institute for Molecular Engineering for Medicine, Division of Biology and Biological Engineering