Viral Dynamics of Omicron and Delta Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants With Implications for Timing of Release from Isolation: A Longitudinal Cohort Study

  1. Tara C Bouton
  2. Joseph Atarere
  3. Jacquelyn Turcinovic
  4. Scott Seitz
  5. Cole Sher-Jan
  6. Madison Gilbert
  7. Laura White
  8. Zhenwei Zhou
  9. Mohammad M Hossain
  10. Victoria Overbeck
  11. Lynn Doucette-Stamm
  12. Judy Platt
  13. Hannah E Landsberg
  14. Davidson H Hamer
  15. Catherine Klapperich
  16. Karen R Jacobson
  17. John H Connor

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Abstract

Background

In January 2022, US guidelines shifted to recommend isolation for 5 days from symptom onset, followed by 5 days of mask-wearing. However, viral dynamics and variant and vaccination impact on culture conversion are largely unknown.

Methods

We conducted a longitudinal study on a university campus, collecting daily anterior nasal swabs for at least 10 days for reverse-transcription polymerase chain reaction (RT-PCR) testing and culture, with antigen rapid diagnostic testing (RDT) on a subset. We compared culture positivity beyond day 5, time to culture conversion, and cycle threshold trend when calculated from diagnostic test, from symptom onset, by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, and by vaccination status. We evaluated sensitivity and specificity of RDT on days 4–6 compared with culture.

Results

Among 92 SARS-CoV-2 RT-PCR–positive participants, all completed the initial vaccine series; 17 (18.5%) were infected with Delta and 75 (81.5%) with Omicron. Seventeen percent of participants had positive cultures beyond day 5 from symptom onset, with the latest on day 12. There was no difference in time to culture conversion by variant or vaccination status. For 14 substudy participants, sensitivity and specificity of day 4–6 RDT were 100% and 86%, respectively.

Conclusions

The majority of our Delta- and Omicron-infected cohort culture-converted by day 6, with no further impact of booster vaccination on sterilization or cycle threshold decay. We found that rapid antigen testing may provide reassurance of lack of infectiousness, though guidance to mask for days 6–10 is supported by our finding that 17% of participants remained culture-positive after isolation.

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  1. Version published to 10.1093/cid/ciac510
  2. ScreenIT

    SciScore for 10.1101/2022.04.04.22273429: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsField Sample Permit: 11 Study isolates are collected in viral transport media and frozen following collection.
    IRB: The study was approved by both the BU Charles River Campus Institutional Review Board and the BU Medical Campus Institutional Review Board.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    First, the presence of SARS-CoV-2 viral nucleic acid in the sample is determined by SARS-CoV-2 CDC N1 RT-PCR and second, 200 microliters of sample are incubated with Caco2 cells for 4 days.
    Caco2
    suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025)
    Software and Algorithms
    SentencesResources
    Participants are asked to upload a photograph of the test strip at the time it is read into our REDCap database (version 12.1.1, Vanderbilt University), where study staff then interpret the results.
    REDCap
    suggested: (REDCap, RRID:SCR_003445)
    Finally, for the antigen RDT sub-study, we calculated the sensitivity and specificity of the Abbott BinaxNow compared to culture positivity at days 4 through 6 from diagnosis and plotted Ct values by day from diagnosis and RDT result.
    Abbott
    suggested: (Abbott, RRID:SCR_010477)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2022.04.04.22273429 on medRxiv