Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves

Agoti, C. N.; Ochola-Oyier, L. I.; Mohammed, K. S.; Lambisia, A. W.; de Laurent, Z. R.; Morobe, J. M.; Mburu, M. W.; Omuoyo, D. O.; Ongera, E. M.; 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, D. J.; Bejon, P.; Githinji, G.

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.