Results from the first major genomic epidemiology of SARS-CoV-2 infections in Kenya were published today in the esteemed Nature Communications (DOI:10.1038/s41467-021-25137-x) peer-reviewed journal. The work carried by a team of scientist at the KEMRI-Wellcome Trust Research Programme and the Ministry of Health, examined cases during the early phase of the epidemic (March – July 2020). Out of […]

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17(th) March and 31(st) July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.