Revealing the extent of the first wave of the COVID-19 pandemic in Kenya based on serological and PCR-test data

  1. John Ojal
  2. Samuel P. C. Brand
  3. Vincent Were
  4. Emelda A. Okiro
  5. Ivy K. Kombe
  6. Caroline Mburu
  7. Rabia Aziza
  8. Morris Ogero
  9. Ambrose Agweyu
  10. George M. Warimwe
  11. Sophie Uyoga
  12. Ifedayo M. O. Adetifa
  13. J. Anthony G. Scott
  14. Edward Otieno
  15. Lynette I. Ochola-Oyier
  16. Charles N. Agoti
  17. Kadondi Kasera
  18. Patrick Amoth
  19. Mercy Mwangangi
  20. Rashid Aman
  21. Wangari Ng’ang’a
  22. Benjamin Tsofa
  23. Philip Bejon
  24. Edwine Barasa
  25. Matt J. Keeling
  26. D. James Nokes

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Abstract

Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.

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  1. Version published to 10.12688/wellcomeopenres.16748.2
  2. ScreenIT

    SciScore for 10.1101/2020.09.02.20186817: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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.

    About SciScore

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  3. Version published to 10.1101/2020.09.02.20186817 on medRxiv