A SARS-CoV-2 Negative Antigen Rapid Diagnostic in RT-qPCR Positive Samples Correlates With a Low Likelihood of Infectious Viruses in the Nasopharynx

  1. Isadora Alonso Corrêa
  2. Débora Souza Faffe
  3. Rafael Mello Galliez
  4. Cássia Cristina Alves Gonçalves
  5. Richard Araújo Maia
  6. Gustavo Peixoto da Silva
  7. Filipe Romero Rebello Moreira
  8. Diana Mariani
  9. Mariana Freire Campos
  10. Isabela de Carvalho Leitão
  11. Marcos Romário de Souza
  12. Marcela Sabino Cunha
  13. Érica Ramos dos Santos Nascimento
  14. Liane de Jesus Ribeiro
  15. Thais Felix Cordeiro da Cruz
  16. Cintia Policarpo
  17. Luis Gonzales
  18. Mary A. Rodgers
  19. Michael Berg
  20. Roy Vijesurier
  21. Gavin A. Cloherty
  22. John Hackett
  23. Orlando da Costa Ferreira
  24. Terezinha Marta Pereira Pinto Castiñeiras
  25. Amilcar Tanuri
  26. Luciana Jesus da Costa

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) transmission occurs even among fully vaccinated individuals; thus, prompt identification of infected patients is central to control viral circulation. Antigen rapid diagnostic tests (Ag-RDTs) are highly specific, but sensitivity is variable. Discordant RT-qPCR vs. Ag-RDT results are reported, raising the question of whether negative Ag-RDT in positive RT-qPCR samples could imply the absence of infectious viruses. To study the relationship between negative Ag-RDT results with virological, molecular, and serological parameters, we selected a cross-sectional and a follow-up dataset and analyzed virus culture, subgenomic RNA quantification, and sequencing to determine infectious viruses and mutations. We demonstrated that RT-qPCR positive while SARS-CoV-2 Ag-RDT negative discordant results correlate with the absence of infectious virus in nasopharyngeal samples. A decrease in sgRNA detection together with an expected increase in detectable anti-S and anti-N IgGs was also verified in these samples. The data clearly demonstrate that a negative Ag-RDT sample is less likely to harbor infectious SARS-CoV-2 and, consequently, has a lower transmissible potential.

Article activity feed

  1. Version published to 10.3389/fmicb.2022.912138
  2. ScreenIT

    SciScore for 10.1101/2022.03.17.22272008: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Membranes were probed with primary antibodies anti-Nucleocapsid (cat n°: 26369, Cell Signaling) and Anti-Spike (cat n°: 56996, Cell Signaling).
    anti-Nucleocapsid
    suggested: None
    Anti-Spike
    suggested: None
    The secondary antibodies used were the horseradish peroxidase HRP-conjugated Anti-Rabbit (KPL).
    Anti-Rabbit
    suggested: None
    The plates were washed five times with PBST, and polyclonal anti-human IgG antibody conjugated to HRP (Promega) added for one hour at room temperature.
    anti-human IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    For viral titration, 10-fold dilutions of each sample from passage #2 were used to infect Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    Afterwards, to further contextualize the novel genome sequences, a maximum likelihood phylogenetic inference was performed with IQ-Tree v2.0.3 (28), under the GTR+F+I+G4 model.
    IQ-Tree
    suggested: (IQ-TREE, RRID:SCR_017254)
    GraphPad Prism version 9.2.0 (GraphPad Software, San Diego, California USA)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 10.1101/2022.03.17.22272008v1 on medRxiv