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 across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity.

Conclusions:

Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission.

Cite as

Agoti, C., Ochola-Oyier, L., Dellicour, S., Mohammed, K., Lambisia, A., de Laurent, Z., Morobe, J., Mburu, M., Omuoyo, D., Ong'era, 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, D., Bejon, P. & Githinji, G. 2022, 'Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: a retrospective genomic study', eLife. https://doi.org/10.7554/eLife.71703

Downloadable citations

Download HTML citationHTML Download BIB citationBIB Download RIS citationRIS
Last updated: 01 November 2022
Was this page helpful?