Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study
Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study
ABSTRACT BackgroundThe transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood. MethodsWe undertook phylogenetic analysis of 747 SARS-CoV-2 positive samples collected across six counties in coastal Kenya during the first two waves (March 2020 - February 2021). Viral imports and exports from the region were inferred using ancestral state reconstruction (ASR) approach. ResultsThe genomes were classified into 35 Pango lineages, six of which accounted for 79% of the sequenced infections: B.1 (49%), B.1.535 (11%), B.1.530 (6%), B.1.549 (4%), B.1.333 (4%) and B.1.1 (4%). Four identified lineages were Kenya specific. In a contemporaneous global subsample, 990 lineages were documented, 261 for Africa and 97 for Eastern Africa. ASR analysis identified >300 virus location transition events during the period, these comprising: 69 viral imports into Coastal Kenya; 93 viral exports from coastal Kenya; and 191 inter-county import/export events. Most international viral imports (58%) and exports (92%) occurred through Mombasa City, a key touristic and commercial Coastal Kenya center; and many occurred prior to June 2020, when stringent local COVID-19 restriction measures were enforced. After this period, local virus transmission dominated, and distinct local phylogenies were seen. ConclusionsOur analysis supports moving control strategies from a focus on international travel to local transmission. FundingThis work was funded by Wellcome (grant#: 220985) 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.
Suleiman Thani、Nokes D. James、Agoti Charles N.、Ochola-Oyier Lynette Isabella、Lambisia Arnold W.、Morobe John M.、Omuoyo Donwilliams O.、Ongera Edidah M.、Maitha Eric、Kitole Benson、Mwakinangu Mohamed、Githinji George、Salim Barke、Musyoki Jennifer、Otieno Edward、Kiiru John、Kasera Kadondi、Aman Rashid、Phan My、Cotten Matthew、Mburu Maureen W.、Nyambu John、de Laurent Zaydah R.、Mohammed Khadija Said、Otieno John、Barasa Edwine、Mwangangi Mercy、Murunga Nickson、Bejon Philip、Agweyu Ambrose、Ndwiga Leonard、Tsofa Benjamin、Amoth Patrick、Warimwe George、Kinyanjui Samson
Ministry of HealthKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)||University of WarwickKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)||Pwani UniversityKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Ministry of HealthMinistry of HealthMinistry of HealthKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Ministry of HealthKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Ministry of HealthMinistry of HealthMinistry of HealthMedical Research Centre (MRC)/ Uganda Virus Research InstituteMedical Research Centre (MRC)/ Uganda Virus Research Institute||MRC-University of Glasgow Centre for Virus ResearchKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Ministry of HealthKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Ministry of HealthKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Ministry of HealthKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)||Nuffield Department of Medicine, University of OxfordKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)Ministry of HealthKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)||Nuffield Department of Medicine, University of OxfordKenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme (KWTRP)||Pwani University||Nuffield Department of Medicine, University of Oxford
医学研究方法基础医学微生物学
Suleiman Thani,Nokes D. James,Agoti Charles N.,Ochola-Oyier Lynette Isabella,Lambisia Arnold W.,Morobe John M.,Omuoyo Donwilliams O.,Ongera Edidah M.,Maitha Eric,Kitole Benson,Mwakinangu Mohamed,Githinji George,Salim Barke,Musyoki Jennifer,Otieno Edward,Kiiru John,Kasera Kadondi,Aman Rashid,Phan My,Cotten Matthew,Mburu Maureen W.,Nyambu John,de Laurent Zaydah R.,Mohammed Khadija Said,Otieno John,Barasa Edwine,Mwangangi Mercy,Murunga Nickson,Bejon Philip,Agweyu Ambrose,Ndwiga Leonard,Tsofa Benjamin,Amoth Patrick,Warimwe George,Kinyanjui Samson.Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study[EB/OL].(2025-03-28)[2025-06-12].https://www.medrxiv.org/content/10.1101/2021.07.01.21259583.点此复制
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