Where is Omicron? Comparison of SARS-CoV-2 RT-PCR and Antigen Test Sensitivity at Commonly Sampled Anatomic Sites Over the Course of Disease

  1. Jessica Lin
  2. Jennifer K Frediani
  3. Gregory L Damhorst
  4. Julie A Sullivan
  5. Adrianna Westbrook
  6. Kaleb McLendon
  7. Tyler J Baugh
  8. William H O’Sick
  9. John D Roback
  10. Anne L Piantadosi
  11. Jesse J Waggoner
  12. Leda Bassit
  13. Anuradha Rao
  14. Morgan Greenleaf
  15. Jared W O’Neal
  16. Seegar Swanson
  17. Nira R Pollock
  18. Greg S Martin
  19. Wilbur A Lam
  20. Joshua M Levy

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

Upper respiratory samples for SARS-CoV-2 detection include the gold standard nasopharyngeal (NP) swab, and mid-turbinate (MT) nasal swabs, oropharyngeal (OP) swabs, and saliva. Following the emergence of the omicron (B.1.1.529) variant, limited preliminary data suggest that OP swabs or saliva samples may be more sensitive than nasal swabs, highlighting the need to understand differences in viral load across different sites.

Methods

MT, OP, and saliva samples were collected from symptomatic individuals presenting for evaluation in Atlanta, GA, in January 2022. Longitudinal samples were collected from a family cohort following COVID-19 exposure to describe detection of viral targets over the course of infection.

Results

SARS-CoV-2 RNA and nucleocapsid antigen measurements demonstrated a nares-predominant phenotype in a familial cohort. A consistent dominant location for SARS-CoV-2 was not found among 54 individuals. Positive percent agreement for virus detection in MT, OP and saliva specimens were 66.7 [54.1–79.2], 82.2 [71.1–93.4], and 72.5 [60.3–84.8] by RT-PCR, respectively, and 46.2 [32.6–59.7], 51.2 [36.2–66.1], and 72.0 [59.6–84.4] by ultrasensitive antigen assay. The composite of positive MT or OP assay was not significantly different than either alone for both RT-PCR and antigen assay (PPA 86.7 [76.7–96.6] and 59.5 [44.7–74.4], respectively).

Conclusions

Our data suggest that SARS-CoV-2 nucleocapsid and RNA exhibited similar kinetics and diagnostic yield in three upper respiratory sample types across the duration of symptomatic disease. Collection of OP or combined nasal and OP samples does not appear to increase sensitivity versus validated nasal sampling for rapid detection of viral antigen.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2022.02.08.22270685: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: This study was approved by the Emory University Institutional Review Board under STUDY00001082.
    Consent: Exclusion criteria included asymptomatic patients, those with symptoms associated with COVID-19 for greater than 7 days, and those unable to provide informed consent.
    Field Sample Permit: Saliva specimens were collected using the SalivaDirect unsupervised collection kit (New Haven, CT) under the supervision of a healthcare provider, including a short straw (Salimetrics Saliva Collection Aid (Carlsbad, CA), catalog #5016.02) and a sterile 2 mL plastic tube containing 3 ceramic beads.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Clinical and demographic variables were collected in a centralized, web-based database (REDcap, Nashville, TN).
    REDcap
    suggested: (REDCap, RRID:SCR_003445)
    Absolute agreement of Ct values and antigen concentrations across sample types were calculated via an intraclass correlation coefficient (ICC) using a two-way mixed effects model in IBM SPSS Statistics for Windows, version 28 (IBM Corp.,
    SPSS
    suggested: (SPSS, RRID:SCR_002865)

    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: We detected the following sentences addressing limitations in the study:
    Limitations of our data include the use of self-collected swabs in the familial cohort, which may not have been collected as reliably as those collected by a healthcare provider in the cross-sectional cohort. RT-PCR assays were performed with a common assay (Cepheid GeneXpert) for MT and OP samples while saliva was assayed based on the SalivaDirect protocol. Neither assay has EUA approval as a quantitative test and this may limit conclusions, particularly from comparison of Ct values between saliva and the other specimens. Additionally, the quantity of cellular material and mucous may be inherently different between sample types with different collection methodologies, particularly with saliva collected as a pooled drool specimen compared to MT and OP samples obtained with collection swabs eluted in buffer. Despite this, the pragmatic question of viral yield for diagnostic samples can be investigated in this manner particularly because a consistent sample volume and a common assay was used for nucleocapsid measurements across all sample types. Thus, our data appear to suggest that higher antigen levels may be found in saliva specimens, but calculation of PPA failed to show benefit in diagnostic yield. Conclusions as to the utility of saliva for antigen testing may be limited by missing specimens from some participants and a small sample size. The observation of OP- and MT-predominant phenotypes is a key finding in our data in addition to the absence of an effect of days of sy...

    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.

  2. Version published to 10.1101/2022.02.08.22270685 on medRxiv