A genomics dissection of Kenya’s COVID-19 waves: temporal lineage replacements and dominance of imported variants of concern

Abstract

Abstract Kenya’s COVID-19 epidemic was slow to peak. It was seeded early in March 2020, and did not peak until late-July 2020 (wave 1), mid-November 2020 (wave 2) and late-March 2021 (wave 3). Here we present SARS-CoV-2 lineages associated with the three COVID-19 waves through analysis of 483 genomes, which included 167 Alpha (B.1.1.7), 57 Delta (B.1.617.2) and 12 Beta (B.1.351) variants of concerns (VOC) that dominated the third wave. In total, 35 lineages were identified. The early European lineages B.1 and B.1.1 were the first to be seeded in Kenya. The B.1 lineage continued to expand and remained the most dominant lineage accounting for 55.8% and 56.3% in waves 1 and 2 respectively. The alpha (B.1.1.7), delta (B.1.167.2) and beta (B.1.351) VOCs dominated in wave 3 at 59.0%, 20.1% and 4.2% respectively. Eventually, the delta variant took over at the tail end of wave 3 and at the time of going to press, it had become the major lineage in the whole country. Phylogenetic analysis suggested multiple introductions of variants from outside Kenya especially during the first and third wave. Phylogeny also highlighted local lineage diversification as local transmission events supervened. The data highlights the importance of genome surveillance in determining circulating variants to aid in public health interventions.