eLife (Jun 2022)

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

  • Charles N Agoti,
  • Lynette Isabella Ochola-Oyier,
  • Simon Dellicour,
  • Khadija Said Mohammed,
  • Arnold W Lambisia,
  • Zaydah R de Laurent,
  • John M Morobe,
  • Maureen W Mburu,
  • Donwilliams O Omuoyo,
  • Edidah M Ongera,
  • Leonard Ndwiga,
  • Eric Maitha,
  • Benson Kitole,
  • Thani Suleiman,
  • Mohamed Mwakinangu,
  • John K Nyambu,
  • John Otieno,
  • Barke Salim,
  • Jennifer Musyoki,
  • Nickson Murunga,
  • Edward Otieno,
  • John N Kiiru,
  • Kadondi Kasera,
  • Patrick Amoth,
  • Mercy Mwangangi,
  • Rashid Aman,
  • Samson Kinyanjui,
  • George Warimwe,
  • My Phan,
  • Ambrose Agweyu,
  • Matthew Cotten,
  • Edwine Barasa,
  • Benjamin Tsofa,
  • D James Nokes,
  • Philip Bejon,
  • George Githinji

DOI
https://doi.org/10.7554/eLife.71703
Journal volume & issue
Vol. 11

Abstract

Read online

Background: Detailed understanding of severe acute respiratory syndrome coronavirus 2 (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 1139 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 was 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; 9 of which occurred in both waves and 4 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 Coronavirus Disease 2019 (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, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care 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. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.

Keywords