ABSTRACT
Introduction/ Background: By end of October 2021, the Ministry of Health had confirmed over 250 thousand SARS-CoV-2 cases in Kenya following identification of the initial cases in March 2020. We setup a genome surveillance platform in Kenya to track introductions, local evolution and transmission of SARS-CoV-2 within the country and the region. Methods: Samples were collected from designated diagnostic centres across 47 Kenyan counties. Viral RNA was extracted from the Nasal and oropharyngeal swabs from RT-PCR confirmed cases followed by viral amplification of recovered cDNA using the ARTIC nCoV-2019 primer set and thereafter library preparation and sequencing using the Oxford Nanopore MinION platform. The raw signal files were base-called and processed to obtain consensus sequences followed by SARSCoV- 2 lineage assignment and phylogenetics analysis. Results: Phylogenetics and epidemiological analysis of 4,200 sequences provided insight on introduction of SARSCoV- 2 in Kenya. The first (March-September 2020), second (October 2020-February 2021) waves of infections were dominated by B-like lineages. The third wave (March-June 2021) coincided with introduction of Alpha and Beta variants (December 2020), merging into the fourth wave (June-October 2021), the Delta variant in April 2021. Ancestral reconstruction identified multiple introductions of the basal lineages (37<n<69) and Variants of Concern (Beta (n=14), Alpha (n=83), Delta (n=92)). We observed rapid replacement of ancestral lineages leading to dominance of the Delta variant that comprised the fourth wave of infections. Impact: Our genomic surveillance platform has improved monitoring of the diversity of circulating variants of concern (VOCs) and revealed transitions across the country in the dominance VOCs detected between late 2020 to October 2021. This output had fed into national decision-making through regular policy briefs. Conclusion: The Delta variant is the dominant variant of concern across the country. Genomic surveillance of SARSCoV- 2 should focus on identifying the emergence of local mutations with the potential to confer additional transmissibility and antigenic drift, particularly in the background of inadequate vaccine coverage and waning natural immunity.