SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron’s impact in South African population cohorts

  1. Kaiyuan Sun
  2. Stefano Tempia
  3. Jackie Kleynhans
  4. Anne von Gottberg
  5. Meredith L. McMorrow
  6. Nicole Wolter
  7. Jinal N. Bhiman
  8. Jocelyn Moyes
  9. Mignon du Plessis
  10. Maimuna Carrim
  11. Amelia Buys
  12. Neil A. Martinson
  13. Kathleen Kahn
  14. Stephen Tollman
  15. Limakatso Lebina
  16. Floidy Wafawanaka
  17. Jacques D. du Toit
  18. Francesc Xavier Gómez-Olivé
  19. Thulisa Mkhencele
  20. Cécile Viboud
  21. Cheryl Cohen

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Abstract

Understanding the build-up of immunity with successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the epidemiological conditions that favor rapidly expanding epidemics will help facilitate future pandemic control. We analyzed high-resolution infection and serology data from two longitudinal household cohorts in South Africa to reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the history of past exposures to different SARS-CoV-2 variants and vaccination in the cohort most representative of South Africa’s high urbanization rate, we used mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modeling suggests that the Omicron wave likely infected a large fraction (44 to 81%) of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. We project that future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.

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  1. Version published to 10.1126/scitranslmed.abo7081
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    SciScore for 10.1101/2022.02.11.22270854: (What is this?)

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

    Table 1: Rigor

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    Table 2: Resources

    Antibodies
    SentencesResources
    Aliquots of prespecified volume according to manufacturer instructions were tested for the presence of SARS-CoV-2 antibodies by the Roche Elecsys Anti-SARS-CoV-2 assay against nucleocapsid (N) antigen (56).
    Anti-SARS-CoV-2 assay against nucleocapsid ( N ) antigen ( 56
    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:
    A few caveats are worth noting. First, our findings about the persistence of infection-induced immunity are based on a 13-month study. The duration and quality of protective immunity over longer timescales remain open questions. Recent studies have found that antibody responses improve over time through affinity maturation (47, 48) and that long-lived plasma cells can be identified in the bone marrow at least one year after infection, suggesting that immunity conferred by infection or vaccination could be potent and durable against non-immune evasive variants (49). Persistent germinal center responses and durable T cell memory have also been observed among vaccine recipients (50–52). However, how the protection holds up against immune-evasive variant such as Omicron remains an outstanding question. Unfortunately, the PHIRST-C cohorts did not cover the Omicron wave, thus we could not directly measure immune protection at the individual level and relied on modelling of population-level dynamics. Post-Omicron serologic surveys following up the cohort population could provide deeper insight into the full impact of the Omicron wave. In our projections of SARS-CoV-2 resurgences, we did not consider waning explicitly since our cohort data did not support pronounced waning of infection-induced immunity. Accordingly, our projections are most relevant to short time scales, in the order of a few months. Interestingly, we find that resurgences are likely even over short time horizons. A ...

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT02519803Unknown statusA Prospective Household Observational Cohort Study of Influe…

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2022.02.11.22270854 on medRxiv