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Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking

Winnett, Alexander Viloria and Porter, Michael K. and Romano, Anna E. and Savela, Emily S. and Akana, Reid and Shelby, Natasha and Reyes, Jessica A. and Schlenker, Noah W. and Cooper, Matthew M. and Carter, Alyssa M. and Ji, Jenny and Barlow, Jacob T. and Tognazzini, Colten and Feaster, Matthew and Goh, Ying-Ying and Ismagilov, Rustem F. (2022) Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking. . (Unpublished)

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Background. The analytical sensitivities of SARS-CoV-2 diagnostic tests span 6 orders of magnitude. Optimizing sample-collection methods to achieve the most reliable detection for a given sensitivity would increase the effectiveness of testing and minimize COVID-19 outbreaks. Methods. From September 2020 to April 2021 we performed a household-transmission study in which participants self-collected samples every morning and evening throughout acute SARS-CoV-2 infection. Seventy mildly symptomatic participants collected saliva and, of those, 29 also collected nasal-swab samples. Viral load was quantified in 1194 saliva and 661 nasal-swab samples using a high-analytical-sensitivity RT-qPCR assay (LOD, 1,000 SARS-CoV-2 RNA copies/mL). Findings. Viral loads in both saliva and nasal-swab samples were significantly higher in morning-collected samples than evening-collected samples after symptom onset. We used these quantitative measurements to infer which diagnostic tests would have detected infection (based on sample type and test analytical sensitivity). We find that morning collection would have resulted in significantly improved detection and that this advantage would be most pronounced for tests with low to moderate analytical sensitivity, which would likely have missed infections if sampling in the evening. Interpretation. Collecting samples for COVID-19 testing in the morning offers a simple and low-cost improvement to clinical diagnostic sensitivity of low- to moderate-analytical-sensitivity tests. The phenomenon of higher viral loads in the morning may also have implications related to when transmission is more likely to occur. Funding. Bill & Melinda Gates Foundation, Ronald and Maxine Linde Center for New Initiatives (Caltech), Jacobs Institute for Molecular Engineering for Medicine (Caltech) RESEARCH IN CONTEXT. Evidence before this studyReliable COVID-19 diagnostic testing is critical to reducing transmission of SARS-CoV-2 and reducing cases of severe or fatal disease, particularly in areas with limited vaccine access or uptake. Saliva and anterior-nares nasal swabs are common sample types; however, different diagnostic tests using these sample types have a range of analytical sensitivities spanning 6 orders of magnitude, with limits of detection (LODs) between 102 and 108 genomic copy equivalents of SARS-CoV-2 RNA (copies) per mL of sample. Due to limitations in clinical laboratory capacity, many low-resource settings rely on COVID-19 tests that fall on the moderate (LODs of 104 to 105 copies/mL) to lower (LODs of 105 to 108 copies/mL) end of this spectrum of analytical sensitivity. Alterations in sample collection methods, including time of sample collection, may improve the performance of these diagnostics.Added value of this studyThis study quantifies viral loads from saliva and nasal-swab samples that were longitudinally self-collected by symptomatic patients in the morning immediately after waking and in the evening just prior to sleeping throughout the course of acute SARS-CoV-2 infection. The study cohort was composed of mildly or moderately symptomatic individuals (outpatients). This analysis demonstrates significantly higher viral loads in samples collected in the morning, relative to those collected in the evening. When using moderate to lower analytical sensitivity test methods, these loads are inferred to result in significantly better detection of infected individuals in the morning. Implications of available evidence. These findings suggest that samples collected in the morning immediately after waking will better detect SARS-CoV-2 infection in symptomatic individuals tested by moderate to lower analytical sensitivity COVID-19 diagnostic tests (LODs at or above 104 viral copies per mL of sample), such as many rapid antigen tests currently available.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper ItemJournal Article
Winnett, Alexander Viloria0000-0002-7338-5605
Porter, Michael K.0000-0002-0777-7563
Romano, Anna E.0000-0003-1871-1727
Savela, Emily S.0000-0001-9614-4276
Akana, Reid0000-0003-4422-587X
Shelby, Natasha0000-0001-9097-3663
Reyes, Jessica A.0000-0002-5507-7633
Schlenker, Noah W.0000-0002-8581-4403
Cooper, Matthew M.0000-0002-5868-5159
Carter, Alyssa M.0000-0002-2776-9421
Ji, Jenny0000-0002-7901-5605
Barlow, Jacob T.0000-0002-1842-4835
Tognazzini, Colten0000-0002-2754-3588
Feaster, Matthew0000-0001-9966-2845
Goh, Ying-Ying0000-0001-5136-7214
Ismagilov, Rustem F.0000-0002-3680-4399
Additional Information:The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Paper in collection COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv. 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. AVW is supported by a National Institutes of Health NIGMS Predoctoral Training Grant (GM008042) and a UCLA DGSOM Geffen Fellowship; MMC is supported by a Caltech Graduate Student Fellowship; and MKP and JTB were each partially supported by National Institutes of Health Biotechnology Leadership Predoctoral Training Program (BLP) fellowships from Caltech's Donna and Benjamin M. Rosen Bioengineering Center (T32GM112592). DATA AVAILABILITY: Data are available on CaltechDATA at: COMPETING INTERESTS STATEMENT: RFI is a co‐founder, consultant, and a director and has stock ownership of Talis Biomedical Corp. Author Declarations: I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes. The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Institutional Review Board of the California Institute of Technology gave ethical approval for this work (IRB protocol #20-1026). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes. I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes. I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes.
Group:COVID-19, Jacobs Institute for Molecular Engineering for Medicine, Rosen Bioengineering Center
Funding AgencyGrant Number
Bill and Melinda Gates FoundationINV-023124
Ronald and Maxine Linde Center for New InitiativesUNSPECIFIED
Jacobs Institute for Molecular Engineering for MedicineUNSPECIFIED
NIH Predoctoral FellowshipGM008042
NIH Predoctoral FellowshipT32GM112592
Donna and Benjamin M. Rosen Bioengineering CenterUNSPECIFIED
Subject Keywords:COVID‐19, SARS‐CoV‐2, pandemic, diagnostic, testing, screening, sensitivity, saliva, nasal swab, outpatient, ambulatory, mild, circadian, rhythm, morning, evening, collection, sample, viral load
Record Number:CaltechAUTHORS:20220307-188444000
Persistent URL:
Official Citation:Morning SARS-CoV-2 testing yields better detection of infection due to higher viral loads in saliva and nasal swabs upon waking Alexander Viloria Winnett, Michael K. Porter, Anna E. Romano, Emily S. Savela, Reid Akana, Natasha Shelby, Jessica A. Reyes, Noah W. Schlenker, Matthew M. Cooper, Alyssa M. Carter, Jenny Ji, Jacob T. Barlow, Colten Tognazzini, Matthew Feaster, Ying-Ying Goh, Rustem F. Ismagilov medRxiv 2022.03.02.22271724; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:113768
Deposited By: George Porter
Deposited On:08 Mar 2022 16:29
Last Modified:28 Feb 2023 21:40

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