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

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 a

SUBMITTER: Agoti CN 

PROVIDER: S-EPMC9282859 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature