Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals

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Abstract

The BNT162b2 mRNA vaccine is highly effective against SARS-CoV-2. However, apprehension exists that variants of concern (VOCs) may evade vaccine protection, due to evidence of reduced neutralization of the VOCs B.1.1.7 and B.1.351 by vaccine sera in laboratory assays. We performed a matched cohort study to examine the distribution of VOCs in infections of BNT162b2 mRNA vaccinees from Clalit Health Services (Israel) using viral genomic sequencing, and hypothesized that if vaccine effectiveness against a VOC is reduced, its proportion among breakthrough cases would be higher than in unvaccinated controls. Analyzing 813 viral genome sequences from nasopharyngeal swabs, we showed that vaccinees who tested positive at least 7 days after the second dose were disproportionally infected with B.1.351, compared with controls. Those who tested positive between 2 weeks after the first dose and 6 days after the second dose were disproportionally infected by B.1.1.7. These findings suggest reduced vaccine effectiveness against both VOCs within particular time windows. Our results emphasize the importance of rigorously tracking viral variants, and of increasing vaccination to prevent the spread of VOCs.

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  1. Our take

    In a matched pair case-control study, available as a preprint and thus not yet peer-reviewed, comparing breakthrough cases in 247 partially and 149 fully immunized adults with BNT162b2 vaccine to unvaccinated controls in Israel, the odds of COVID-19 infection by the B.1.1.7 variant versus the wild-type were twice as high among partially immunized adults compared to unvaccinated controls but there was no difference between fully vaccinated cases and unvaccinated controls. All 8 B.1.351 variant infections in the fully immunized group were detected prior to the 14-day threshold for optimal immune protection by BNT162b2 vaccination. Observed associations are not measures of vaccine effectiveness, as study inclusion was restricted to individuals with confirmed COVID-19 infections.

    Study design

    case-control

  2. Shivakumar Narayanan, Shyam Kottilil, Joel V. Chua

    Review 3: "Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals"

    This preprint investigates SARS-CoV-2 variant breakthrough rates and finds VOCs more prevalent in COVID19+ vaccinees relative to the unvaccinated. Reviewers deem claims compelling, but warn findings do not concern disease severity and larger follow-up studies are needed.

  3. Konstantin Chumakov

    Review 2: "Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals"

    This preprint investigates SARS-CoV-2 variant breakthrough rates and finds VOCs more prevalent in COVID19+ vaccinees relative to the unvaccinated. Reviewers deem claims compelling, but warn findings do not concern disease severity and larger follow-up studies are needed.

  4. Art Reingold

    Review 1: "Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals"

    This preprint investigates SARS-CoV-2 variant breakthrough rates and finds VOCs more prevalent in COVID19+ vaccinees relative to the unvaccinated. Reviewers deem claims compelling, but warn findings do not concern disease severity and larger follow-up studies are needed.

  5. Strength of evidence

    Reviewers: Art Reingold (UC Berkeley) | 📗📗📗📗◻️
    Konstantin Chumakov (U.S. Food and Drug Administration) | 📒📒📒◻️◻️
    Shivakumar Narayanan, Shyam Kottilil, Joel V. Chua (University of Maryland School of Medicine) | 📒📒📒◻️◻️

  6. SciScore for 10.1101/2021.04.06.21254882: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics statement: The study was approved by the CHS institutional review board (IRB #0016-21-COM2) and was exempt from the requirement for informed consent.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.


    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:
    Additionally, sequencing limitations prevented us from sequencing very low …