Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2

  1. Olha Puhach
  2. Kenneth Adea
  3. Nicolas Hulo
  4. Pascale Sattonnet
  5. Camille Genecand
  6. Anne Iten
  7. Frédérique Jacquérioz
  8. Laurent Kaiser
  9. Pauline Vetter
  10. Isabella Eckerle
  11. Benjamin Meyer

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Abstract

No abstract available

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  1. Version published to 10.1038/s41591-022-01816-0
  2. Version published to 10.21203/rs.3.rs-1293087/v1 on Research Square
  3. Version published to 10.1101/2022.01.10.22269010v2 on medRxiv
  4. ScreenIT

    SciScore for 10.1101/2022.01.10.22269010: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethical approval: The study was approved by the Cantonal ethics committee (CCER Nr. 2021-01488).
    Consent: All study participants and/or their legal guardians provided informed consent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Plates were incubated with an anti-SARS-CoV monoclonal nucleocapsid protein primary antibody targeting SARS-CoV-2 nucleocapsid protein (Geneva Antibody facility; JS02) for 1 hour at room temperature and then with peroxidase-conjugated secondary antibody (Jackson ImmunoResearch, #109-036-09) for 30 minutes at room temperature.
    anti-SARS-CoV
    suggested: None
    SARS-CoV-2 nucleocapsid protein
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Nasopharyngeal swab samples were serially diluted and applied on a monolayer of VeroE6 cells in duplicates.
    VeroE6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Focus-forming assay for comparison of infectious viral loads in Delta vs Omicron was performed in Vero E6-TMPRSS cells.
    Vero E6-TMPRSS
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Software and Algorithms
    SentencesResources
    Statistical analysis: All statistical analyses were performed using R Statistical Software version 4.1.1 (Foundation for Statistical 185 Computing, Austria) and Prism version 8.0.1 (GraphPad, San Diego, CA, USA).
    R Statistical Software
    suggested: None
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    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: We detected the following sentences addressing limitations in the study:
    Our study has several limitations. We included only samples with Ct values below 27, collected during the first 5 dpos but not afterwards. Therefore, absolute numbers on RNA copies are biased towards higher viral loads as patients with low viral load were not included here. However, patients with low viral load have likely little relevance in terms of transmission and other factors, such as poor swab quality can be a confounding factor leading to low viral loads. Furthermore, our focus was on infectious virus shedding and it has been shown that SARS-CoV-2 culture is unlikely to be successfully from samples with higher Ct values (35) and that the vast majority of secondary transmission occurs before 5 dpos although this needs to be formally assessed in Omicron cases (5). Due to its recent emergence, we did not yet have access to samples from Omicron infected unvaccinated individuals. Last, we also would like to emphasize that almost all patients in this study were vaccinated with mRNA vaccines that induce high titres of neutralizing antibodies in the blood but relatively low mucosal antibodies. Therefore, our results cannot be generalized to other vaccines, i.e. those that are used mainly in low- and middle-income countries. In conclusion, this study provides strong evidence for higher infectiousness of the Delta VOC as well as a significantly lower infectiousness and a faster clearance of infectious virus in vaccinated individuals. In addition, we could show that Omicron has ...

    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.

  5. Version published to 10.1101/2022.01.10.22269010v1 on medRxiv