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06 14, 2022;11

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
Author Information
  1. Charles N Agoti: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. ORCID
  2. Lynette Isabella Ochola-Oyier: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  3. Simon Dellicour: Spatial Epidemiology Lab (SpELL), Universit�� Libre de Bruxelles, Bruxelles, Belgium. ORCID
  4. Khadija Said Mohammed: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  5. Arnold W Lambisia: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  6. Zaydah R de Laurent: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  7. John M Morobe: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. ORCID
  8. Maureen W Mburu: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  9. Donwilliams O Omuoyo: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. ORCID
  10. Edidah M Ongera: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  11. Leonard Ndwiga: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  12. Eric Maitha: Ministry of Health, Nairobi, Kenya.
  13. Benson Kitole: Ministry of Health, Nairobi, Kenya.
  14. Thani Suleiman: Ministry of Health, Nairobi, Kenya.
  15. Mohamed Mwakinangu: Ministry of Health, Nairobi, Kenya.
  16. John K Nyambu: Ministry of Health, Nairobi, Kenya.
  17. John Otieno: Ministry of Health, Nairobi, Kenya.
  18. Barke Salim: Ministry of Health, Nairobi, Kenya.
  19. Jennifer Musyoki: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  20. Nickson Murunga: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  21. Edward Otieno: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. ORCID
  22. John N Kiiru: Ministry of Health, Nairobi, Kenya.
  23. Kadondi Kasera: Ministry of Health, Nairobi, Kenya.
  24. Patrick Amoth: Ministry of Health, Nairobi, Kenya.
  25. Mercy Mwangangi: Ministry of Health, Nairobi, Kenya.
  26. Rashid Aman: Ministry of Health, Nairobi, Kenya.
  27. Samson Kinyanjui: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  28. George Warimwe: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  29. My Phan: Medical Research Centre (MRC)/ Uganda Virus Research Institute, Entebbe, Uganda. ORCID
  30. Ambrose Agweyu: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  31. Matthew Cotten: Medical Research Centre (MRC)/ Uganda Virus Research Institute, Entebbe, Uganda. ORCID
  32. Edwine Barasa: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  33. Benjamin Tsofa: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. ORCID
  34. D James Nokes: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. ORCID
  35. Philip Bejon: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
  36. George Githinji: Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya. ORCID
PMID: 35699426 DOI: 10.7554/eLife.71703

Abstract

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

Africa SARS-CoV-2 epidemiology genomics global health infectious disease microbiology spread transmission viruses

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Grants

  1. NC_PC_19060/Medical Research Council
  2. MC_UU_12014/12/Medical Research Council
  3. MC_PC_19026/Medical Research Council
  4. 220977/Z/20/Z/Wellcome Trust
  5. 203077/Z/16/Z/Wellcome Trust
  6. /Wellcome Trust
  7. MC_PC_20010/Medical Research Council
  8. 220985/Wellcome Trust

MeSH Term

COVID-19
Genomics
Humans
Kenya
Phylogeny
Retrospective Studies
SARS-CoV-2
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 17

Word Cloud

Created with Highcharts 10.0.01BtransmissionWaveSARS-CoV-22localKenyaviruslineageshealthcountiesCoastalusingUKnetworksAfricaacrosssixMombasafirsttwowavesinfectionsimportationsestimatedanalysisdetectedoccurred530549N8predominatedfollowed[6%]studyregionCOVID-19governmentstrategiesglobalBackground:Detailedunderstandingsevereacuterespiratorysyndromecoronavirusregionalwithinsub-SaharankeyguidingpublicinterventionspandemicMethods:analysed1139genomespositivesamplescollectedMarch2020February2021KilifiTaitaTavetaKwaleTanaRiverLamuinferintroductionspatternsVirusinferredancestralstatereconstructiondispersaldiscretephylogeographicResults:23distinctPango2994seemedspecific596sequencedbelongedlineagen=72363%73%56%[21%][5%]period280CityvitaltouristcommercialcentremajorrouteimportsmanyCoronavirusDisease2019restrictionsstillforceinter-countyresultingemergencechainsdiversityConclusions:supportsmovingcontrolfocusinternationaltravelwillreduceFunding:workfundedWellcomegrantnumbers:220985203077/Z/16/Z220977/Z/20/Z222574/Z/21/ZNationalInstituteHealthCareResearchNIHRprojectreferences:17/63/and16/136/33AidsupportresearchForeignCommonwealthDevelopmentOfficeviewsexpressedpublicationauthorsnecessarilyfundingagenciesTransmissionwaves:retrospectivegenomicepidemiologygenomicsinfectiousdiseasemicrobiologyspreadviruses

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