SARS-CoV-2 seroprevalence in three Kenyan health and demographic surveillance sites, December 2020-May 2021

  1. Anthony O. Etyang
  2. Ifedayo Adetifa
  3. Richard Omore
  4. Thomas Misore
  5. Abdhalah K. Ziraba
  6. Maurine A. Ng’oda
  7. Evelyn Gitau
  8. John Gitonga
  9. Daisy Mugo
  10. Bernadette Kutima
  11. Henry Karanja
  12. Monica Toroitich
  13. James Nyagwange
  14. James Tuju
  15. Perpetual Wanjiku
  16. Rashid Aman
  17. Patrick Amoth
  18. Mercy Mwangangi
  19. Kadondi Kasera
  20. Wangari Ng’ang’a
  21. Donald Akech
  22. Antipa Sigilai
  23. Boniface Karia
  24. Angela Karani
  25. Shirine Voller
  26. Charles N. Agoti
  27. Lynette I. Ochola-Oyier
  28. Mark Otiende
  29. Christian Bottomley
  30. Amek Nyaguara
  31. Sophie Uyoga
  32. Katherine Gallagher
  33. Eunice W. Kagucia
  34. Dickens Onyango
  35. Benjamin Tsofa
  36. Joseph Mwangangi
  37. Eric Maitha
  38. Edwine Barasa
  39. Philip Bejon
  40. George M. Warimwe
  41. J. Anthony G. Scott
  42. Ambrose Agweyu

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Abstract

Most of the studies that have informed the public health response to the COVID-19 pandemic in Kenya have relied on samples that are not representative of the general population. We conducted population-based serosurveys at three Health and Demographic Surveillance Systems (HDSSs) to determine the cumulative incidence of infection with SARS-CoV-2.

Methods

We selected random age-stratified population-based samples at HDSSs in Kisumu, Nairobi and Kilifi, in Kenya. Blood samples were collected from participants between 01 Dec 2020 and 27 May 2021. No participant had received a COVID-19 vaccine. We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Locally-validated assay sensitivity and specificity were 93% (95% CI 88–96%) and 99% (95% CI 98–99.5%), respectively. We adjusted prevalence estimates using classical methods and Bayesian modelling to account for the sampling scheme and assay performance.

Results

We recruited 2,559 individuals from the three HDSS sites, median age (IQR) 27 (10–78) years and 52% were female. Seroprevalence at all three sites rose steadily during the study period. In Kisumu, Nairobi and Kilifi, seroprevalences (95% CI) at the beginning of the study were 36.0% (28.2–44.4%), 32.4% (23.1–42.4%), and 14.5% (9.1–21%), and respectively; at the end they were 42.0% (34.7–50.0%), 50.2% (39.7–61.1%), and 24.7% (17.5–32.6%), respectively. Seroprevalence was substantially lower among children (<16 years) than among adults at all three sites (p≤0.001).

Conclusion

By May 2021 in three broadly representative populations of unvaccinated individuals in Kenya, seroprevalence of anti-SARS-CoV-2 IgG was 25–50%. There was wide variation in cumulative incidence by location and age.

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  1. Version published to 10.1371/journal.pgph.0000883
  2. ScreenIT

    SciScore for 10.1101/2022.02.07.22270012: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Written informed consent (and assent where applicable) was obtained from all participants, or their guardians before their participation in the study.
    Sex as a biological variablenot detected.
    RandomizationAt each of the three sites, we randomly selected an age-stratified sample of 50 individuals in each 5-year age band from 15-65+ years and above, and 100 in each 5-year age band from 0-14 years.
    Blindingnot detected.
    Power Analysisnot 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:
    A key limitation of the study is that we were unable to fully account for waning of antibodies, which could have led to an underestimation of seroprevalence. In a previous study, we undertook mixture modelling,24 which does not rely on thresholds, but instead assumes that the population sampled consists of two groups with different distributions of antibody levels; this suggested that the threshold-based method was significantly underestimating the true seroprevalence. We were however unable to conduct similar analysis for this dataset, as the mixture modelling requires control data from the respective sites which we did not have. An additional limitation was the fact that nearly half of those who were targeted through the random sampling were not present at home. These were in most cases individuals who had gone to their workplaces. Given that these individuals would have had more interactions with others both at the workplace and during commuting, it is likely that the seroprevalence figures presented here are an underestimate of the true value. In conclusion, in this population-based study at three health and demographic surveillance sites, broadly representative of the population in Kenya, we found that between a quarter and a half of the population had evidence of previous infection by May 2021, though with marked variation in infection risk by age and geographical region.

    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 10.1101/2022.02.07.22270012 on medRxiv