Genomic surveillance and identification of SARS-CoV-2 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SAR-CoV-2. Genomic surveillance provides insights into circulating infections, and insights into the robustness and design of vaccines and other infection control approaches. We sequenced 56 SARS-CoV-2 isolates from a Kenyan clinical population, of which 52 passed the Ultrafast sample Placement on the existing tRE for the phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County). B.1.1.7 (Alpha; n = 32, 61.5%) and B.1 (n = 9, 17.3%) lineages were the most predominant variant with a wide-range of Ct values (5–31) and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across the sampling sites within the target population. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), USA (B.1.405, B.1.596), South Africa (B.1.617.2), and United Kingdom (B.1.1.7), indicating multiple introduction events. There were, however, no genetic isolates associated with the omicron (B.1.1.529) variant of concern that is less severe than the previous variants.

Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5–31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control.