Publication
Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study
Publisher:
Cold Spring Harbor Laboratory
Date:
07-07-2021
DOI:
10.1101/2021.07.01.21259583
Abstract: The transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood. We undertook phylogenetic analysis of 747 SARS-CoV-2 positive s les 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. The 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 subs le, 990 lineages were documented, 261 for Africa and 97 for Eastern Africa. ASR analysis identified 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. Our analysis supports moving control strategies from a focus on international travel to local transmission. This 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.