The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission

  1. David W Eyre
  2. Donald Taylor
  3. Mark Purver
  4. David Chapman
  5. Tom Fowler
  6. Koen Pouwels
  7. Ann Sarah Walker
  8. Tim EA Peto

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Abstract

Background Pre-Delta, vaccination reduced SARS-CoV-2 transmission from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents transmission. Methods We performed a retrospective observational cohort study of adult contacts of SARS-CoV-2-infected adult index cases using English contact testing data. We used multivariable Poisson regression to investigate associations between transmission and index case and contact vaccination, and how these vary with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination. Results 54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination. Conclusions Vaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.

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  1. Version published to 10.1101/2021.09.28.21264260v2 on medRxiv
  2. ScreenIT

    SciScore for 10.1101/2021.09.28.21264260: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: PHE’s Research Ethics and Governance Group (PHE’s Research Ethics Committee) reviewed the study protocol and confirmed compliance with all regulatory requirements.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    15 Only index cases with PCR tests performed by three national “lighthouse” laboratories (Milton Keynes, Alderley Park, Glasgow) were included, as these tests used the same standardised workflow and PCR assay (Thermo Fisher TaqPath, assessing for S gene, N gene and ORF1ab targets).
    Thermo Fisher TaqPath
    suggested: None

    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:
    This study has several limitations. We considered only contacts who underwent PCR testing, to minimise bias introduced by differences in testing behaviour that may occur for multiple reasons including vaccination of contacts. This means we cannot estimate secondary attack rates by case and contact vaccination status, and that absolute protective effects of vaccination on transmission may be under-estimated as vaccine-protected uninfected contacts may not have sought testing. Our approach is also not likely to eliminate bias, particularly if test-seeking behaviour is related to perceived vaccine efficacy, given non-specificity of many symptoms.24 We did not have sufficient data to consider the impact of previous infection status, which is also imperfectly ascertained in national testing programs. It is likely that part of the explanation for the declines over time in the adjusted probability of contacts testing positive (Figure S4), is increasing prevalence of prior infection in the unvaccinated group, along with changes in test seeking behaviour and the incidence of other infections causing similar symptoms.25 We also had to use SGTF and time as a proxy for Alpha vs. Delta infection rather than sequencing, which means some low viral load Delta infections with SGTF may have been misclassified as Alpha, however we restricted the time period of our dataset to minimise this. As we considered all PCR results in contacts, not just those tested with assays including an S-gene target...

    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

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  3. Version published to 10.1101/2021.09.28.21264260v1 on medRxiv