Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves
Agoti C., Ochola-Oyier LI., Mohammed KS., Lambisia A., de Laurent Z., Morobe J., Mburu M., Omuoyo D., Ongera E., Ndwiga L., Maitha E., Kitole B., Suleiman T., Mwakinangu M., Nyambu J., Otieno J., Salim B., Musyoki J., Murunga N., Otieno E., Kiiru J., Kasera K., Amoth P., Mwangangi M., Aman R., Kinyanjui S., Warimwe G., Phan M., Agweyu A., Cotten M., Barasa E., Tsofa B., Nokes J., Bejon P., Githinji G.
ABSTRACT The transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood. We analyzed 684 genomes from samples collected across six counties in coastal Kenya during the first two waves (March 2020 -February 2021). Up to 32 Pango lineages were detected in the local sample with six accounting for 88.0% of the sequenced infections: B.1 (60.4%), B.1.1 (8.9%), B.1.549 (7.9%), B.1.530 (6.4%), N.8 (4.4%) and A (3.1%). In a contemporaneous global sample, 571 lineages were identified, 247 for Africa and 88 for East Africa. We detected 262 location transition events comprising: 64 viral imports into Coastal Kenya; 26 viral exports from coastal Kenya; and 172 inter-county import/export events. Most international viral imports (61%) and exports (88%) occurred through Mombasa, a key coastal touristic and commercial center; and many occurred prior to June 2020, when stringent local COVID-19 restriction measures were enforced. After this period, local transmission dominated, and distinct local phylogenies were seen. Our analysis supports moving control strategies from a focus on international travel to local transmission.