Impact of the COVID-19 epidemic on mortality in rural coastal Kenya

  1. M Otiende
  2. A Nyaguara
  3. C Bottomley
  4. D Walumbe
  5. G Mochamah
  6. D Amadi
  7. C Nyundo
  8. EW Kagucia
  9. AO Etyang
  10. IMO Adetifa
  11. E Maitha
  12. E Chondo
  13. E Nzomo
  14. R Aman
  15. M Mwangangi
  16. P Amoth
  17. K Kasera
  18. W Ng’ang’a
  19. E Barasa
  20. B Tsofa
  21. J Mwangangi
  22. P Bejon
  23. A Agweyu
  24. TN Williams
  25. JAG Scott

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Abstract

Background

The impact of COVID-19 on all-cause mortality in sub-Saharan Africa remains unknown.

Methods

We monitored mortality among 306,000 residents of Kilifi Health and Demographic Surveillance System, Kenya, through four COVID-19 waves from April 2020-September 2021. We calculated expected deaths using negative binomial regression fitted to baseline mortality data (2010-2019) and calculated excess mortality as observed-minus-expected deaths. We excluded deaths in infancy because of under-ascertainment of births during lockdown. In February 2021, after two waves of wild-type COVID-19, adult seroprevalence of anti-SARS-CoV-2 was 25.1%. We predicted COVID-19-attributable deaths as the product of age-specific seroprevalence, population size and global infection fatality ratios (IFR). We examined changes in cause of death by Verbal Autopsy (VA).

Results

Between April 2020 and February 2021, we observed 1,000 deaths against 1,012 expected deaths (excess mortality -1.2%, 95% PI -6.6%, 5.8%). Based on SARS-CoV-2 seroprevalence, we predicted 306 COVID-19-attributable deaths (a predicted excess mortality of 30.6%) within this period. Monthly mortality analyses showed a significant excess among adults aged ≥45 years in only two months, July-August 2021, coinciding with the fourth (Delta) wave of COVID-19. By September 2021, overall excess mortality was 3.2% (95% PI -0.6%, 8.1%) and cumulative excess mortality risk was 18.7/100,000. By VA, there was a transient reduction in deaths attributable to acute respiratory infections in 2020.

Conclusions

Normal mortality rates during extensive transmission of wild-type SARS-CoV-2 through February 2021 suggests that the IFR for this variant is lower in Kenya than elsewhere. We found excess mortality associated with the Delta variant but the cumulative excess mortality risk remains low in coastal Kenya compared to global estimates.

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  1. ScreenIT

    SciScore for 10.1101/2022.04.06.22273516: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    RandomizationThe cumulative incidence of SARS-CoV-2 was derived from a serosurvey of a random sample of 850 KHDSS residents between 1st December 2020 and 28th April 2021 (median sample date 17th Feb 2021).
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your 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.

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

    About SciScore

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  2. Version published to 10.1101/2022.04.06.22273516v1 on medRxiv