Abstract

Background: Detailed understanding on SARS-CoV-2 regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic.

Methods: Here, we analysed 1,139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction and virus dispersal between counties were estimated using discrete phylogeographic analysis.

Results: During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; nine of which occurred in both waves, and four seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1 and N.8). Most of the sequenced infections belonged to lineage B.1 (n=723, 63%) which predominated in both Wave 1 (73%, followed by lineages N.8 (6%) and B.1.1 (6%)) and Wave 2 (56%, followed by lineages B.1.549 (21%) and B.1.530 (5%). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many COVID-19 government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity.

Conclusions: Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission.

Funding: This work was funded by The Wellcome (grant numbers; 220985, 203077/Z/16/Z, and 222574/Z/21/Z) and the National Institute for Health Research (NIHR), project references: 17/63/and 16/136/33 using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office.

Data availability

1) Sequence data have been deposited in GISAID database under accession numbers provided in Supplement File 22) Source Data files have been provided for Figures 1-2 and 4-10.3) Source Code associated with the figures has been uploaded (Source Code File 1) and also been made available through Harvard Dataverse

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Charles N Agoti

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    For correspondence
    cnyaigoti@kemri-wellcome.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2160-567X
  2. Lynette Isabella Ochola-Oyier

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  3. Simon Dellicour

    Department of Microbiology, Immunology and Transplantation, University of Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  4. Khadija Said Mohammed

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  5. Arnold W Lambisia

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  6. Zaydah R de Laurent

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  7. John M Morobe

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2398-6717
  8. Maureen W Mburu

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  9. Donwilliams O Omuoyo

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3900-5354
  10. Edidah M Ongera

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  11. Leonard Ndwiga

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  12. Eric Maitha

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  13. Benson Kitole

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  14. Thani Suleiman

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  15. Mohamed Mwakinangu

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  16. John K Nyambu

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  17. John Otieno

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  18. Barke Salim

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  19. Jennifer Musyoki

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  20. Nickson Murunga

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  21. Edward Otieno

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8014-7306
  22. John N Kiiru

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  23. Kadondi Kasera

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  24. Patrick Amoth

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  25. Mercy Mwangangi

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  26. Rashid Aman

    Ministry of Health, Nairobi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  27. Samson Kinyanjui

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  28. George Warimwe

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  29. My Phan

    Medical Research Centre, Uganda Virus Research Institute, Entebbe, Uganda
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6905-8513
  30. Ambrose Agweyu

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  31. Matthew Cotten

    Medical Research Centre, Uganda Virus Research Institute, Entebbe, Uganda
    Competing interests
    The authors declare that no competing interests exist.
  32. Edwine Barasa

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  33. Benjamin Tsofa

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1000-1771
  34. D James Nokes

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  35. Philip Bejon

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
  36. George Githinji

    Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9640-7371

Funding

National Institute for Health Research (17/63/82)

  • D James Nokes

National Institute for Health Research (16/136/33)

  • Charles N Agoti
  • Samson Kinyanjui
  • George Warimwe
  • D James Nokes
  • George Githinji

Wellcome Trust (220985)

  • D James Nokes
  • George Githinji

Wellcome Trust (203077/Z/16/Z)

  • Edwine Barasa
  • Benjamin Tsofa
  • Philip Bejon

Wellcome Trust (220977/Z/20/Z)

  • My Phan
  • Matthew Cotten

Medical Research Council (NC_PC_19060)

  • My Phan
  • Matthew Cotten

H2020 European Research Council (n{degree sign}874850)

  • Simon Dellicour

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Mary Kate Grabowski, Johns Hopkins University, United States

Ethics

Human subjects: Samples analysed here were collected under the Ministry of Health protocols as part of the national COVID-19 public health response. The whole genome sequencing study protocol was reviewed and approved by the Scientific and Ethics Review Committee (SERU) at Kenya Medical Research Institute (KEMRI), Nairobi, Kenya (SERU protocol #4035). Individual patient consent was not required by the committee for the use of these samples for studies of genomic epidemiology to inform public health response.

Version history

  1. Received: June 27, 2021
  2. Preprint posted: July 7, 2021 (view preprint)
  3. Accepted: June 10, 2022
  4. Accepted Manuscript published: June 14, 2022 (version 1)
  5. Version of Record published: July 14, 2022 (version 2)

Copyright

© 2022, Agoti et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Charles N Agoti
  2. Lynette Isabella Ochola-Oyier
  3. Simon Dellicour
  4. Khadija Said Mohammed
  5. Arnold W Lambisia
  6. Zaydah R de Laurent
  7. John M Morobe
  8. Maureen W Mburu
  9. Donwilliams O Omuoyo
  10. Edidah M Ongera
  11. Leonard Ndwiga
  12. Eric Maitha
  13. Benson Kitole
  14. Thani Suleiman
  15. Mohamed Mwakinangu
  16. John K Nyambu
  17. John Otieno
  18. Barke Salim
  19. Jennifer Musyoki
  20. Nickson Murunga
  21. Edward Otieno
  22. John N Kiiru
  23. Kadondi Kasera
  24. Patrick Amoth
  25. Mercy Mwangangi
  26. Rashid Aman
  27. Samson Kinyanjui
  28. George Warimwe
  29. My Phan
  30. Ambrose Agweyu
  31. Matthew Cotten
  32. Edwine Barasa
  33. Benjamin Tsofa
  34. D James Nokes
  35. Philip Bejon
  36. George Githinji
(2022)
Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: a retrospective genomic study
eLife 11:e71703.
https://doi.org/10.7554/eLife.71703

Share this article

https://doi.org/10.7554/eLife.71703

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