Imported SARS-CoV-2 Variants of Concern Drove Spread of Infections across Kenya during the Second Year of the Pandemic

  1. Carolyne Nasimiyu
  2. Damaris Matoke-Muhia
  3. Gilbert K. Rono
  4. Eric Osoro
  5. Daniel O. Ouso
  6. J. Milkah Mwangi
  7. Nicholas Mwikwabe
  8. Kelvin Thiong’o
  9. Jeanette Dawa
  10. Isaac Ngere
  11. John Gachohi
  12. Samuel Kariuki
  13. Evans Amukoye
  14. Marianne Mureithi
  15. Philip Ngere
  16. Patrick Amoth
  17. Ian Were
  18. Lyndah Makayotto
  19. Vishvanath Nene
  20. Edward O. Abworo
  21. M. Kariuki Njenga
  22. Stephanie N. Seifert
  23. Samuel O. Oyola

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Abstract

Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Over the pandemic duration (March 2020–January 2022), Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. In conclusion, the emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.

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  1. Version published to 10.3390/covid2050044
  2. ScreenIT

    SciScore for 10.1101/2022.02.28.22271467: (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.
    Randomizationnot detected.
    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 limitation of the study is that reported COVID-19 cases and deaths and samples used for genomic surveillance were based on the KMOH surveillance, and which likely underestimated the extent of the pandemic at any one time. Nonetheless, surveillance plays a critical role in monitoring trends and control of global pandemics. In conclusion, the emergence of Alpha, Delta, and Omicron VoCs was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country, with varying fatality rates. Enhanced genomic and molecular surveillance for SARS-CoV-2 in developing countries can support early detection of VoCs and guide public health control measures such application of mitigation measures.

    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.
    • Thank you for including a protocol registration statement.

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

    About SciScore

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  3. Version published to 10.1101/2022.02.28.22271467 on medRxiv