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

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.

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

“…Of the >2,800 SARS-CoV-2 genomes reported from Kenya in the current and other recent studies [37,38], there has been no VoC emerging from the country, with only B. 1.525 (Eta) that was detected in February 2021 in the Nairobi classified as variant of interest.…”

“…Of the >2,800 SARS-CoV-2 genomes reported from Kenya in the current and other recent studies [37,38], there has been no VoC emerging from the country, with only B.1.525 ( Eta ) that was detected in February 2021 in the Nairobi classified as variant of interest. Studies point at increased transmissibility and capacity to evade the immune response as the key factors associated with dominance of the VoCs [39,40].…”

Temporal distribution and clinical characteristics of the Alpha, Delta and Omicron SARS-CoV-2 variants of concern in Laikipia, Kenya: institutional and community-based genomic surveillance

“…In this study, the Alpha VOC was detected in Laikipia samples collected in May and June 2021 samples and contributed 8.2% of the sequences we recovered. However, an earlier analysis by another team in Kenya reported detection of the Alpha VOC in Laikipia in February 2021 5 . We detected the Delta VOC in samples collected between May and September 2021.…”

“…During the first two waves of infection, the dominant lineages were mainly B.1 and B.1.1 3 . However, in early 2021 the VOCs replaced the ancestral strain lineages to drive the three subsequent major waves of infection, observed between March and December 2021 4,5 .…”

Diagnostic accuracy of the Panbio™ COVID-19 Antigen rapid test device for SARS-CoV-2 detection in Kenya, 2021: A field evaluation

“…A recent study demonstrated increasing viral load with increasing age (14); higher sensitivities have been observed among individuals with higher viral loads compared to lower ones. The alpha variant and delta variants predominated our evaluation in Kenya (15,16). While some literature indicates that variants of concern (17,18) do not reduce the sensitivity and specificity of Ag RDTs, a recent study revealed that sensitivity of the Panbio™ Ag RDT declined significantly in individuals infected with the alpha variant (53.0%) compared to those with non-alpha variants (89.0%) even after adjusting for viral load (p <0.002) (19).…”