The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya (preprint)

The emergence and establishment of SARS CoV 2 variants of concern presented a major global public health crisis across the world. There were six waves of SARS CoV 2 cases in Kenya that corresponded with the introduction and eventual dominance of the major SARS-COV-2 variants of concern, excepting the first 2 waves that were both wildtype virus. We estimate that more than 1000 SARS CoV 2 introductions occurred in the two-year epidemic period (March 2020 to September 2022) and a total of 930 introductions were associated with variants of concern namely Beta (n=78), Alpha(n=108), Delta(n=239) and Omicron (n=505). A total of 29 introductions were associated with A.23.1 variant that circulated in high frequencies in Uganda and Rwanda. The actual number of introductions is likely to be higher than these conservative estimates due to limited genomic sequencing. Our data suggested that cryptic transmission was usually underway prior to the first real-time identification of a new variant, and that multiple introductions were responsible. Following emergence of each VOC and subsequent introduction, transmission patterns were associated with hotspots of transmission in Coast, Nairobi and Western Kenya and follows established land and air transport corridors. Understanding the introduction and dispersal of major circulating variants and identifying the sources of new introductions is important to inform public health control strategies within Kenya and the larger East-African region. Border control and case finding reactive to new variants is unlikely to be a successful control strategy.

Genomic Surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu County, Kenya (preprint)

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.

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

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.