Temporal lineage replacements and dominance of imported variants of concern during the COVID-19 pandemic in Kenya

Abstract

Background

Kenya’s COVID-19 epidemic was seeded early in March 2020 and did not peak until early August 2020 (wave 1), late-November 2020 (wave 2), mid-April 2021 (wave 3), late August 2021 (wave 4), and mid-January 2022 (wave 5).

Methods

Here, we present SARS-CoV-2 lineages associated with the five waves through analysis of 1034 genomes, which included 237 non-variants of concern and 797 variants of concern (VOC) that had increased transmissibility, disease severity or vaccine resistance.

Results

In total 40 lineages were identified. The early European lineages (B.1 and B.1.1) were the first to be seeded. The B.1 lineage continued to expand and remained dominant, accounting for 60% (72/120) and 57% (45/79) in waves 1 and 2 respectively. Waves three, four and five respectively were dominated by VOCs that were distributed as follows: Alpha 58.5% (166/285), Delta 92.4% (327/354), Omicron 95.4% (188/197) and Beta at 4.2% (12/284) during wave 3 and 0.3% (1/354) during wave 4. Phylogenetic analysis suggests multiple introductions of variants from outside Kenya, more so during the first, third, fourth and fifth waves, as well as subsequent lineage diversification.

Conclusions

The data highlights the importance of genome surveillance in determining circulating variants to aid interpretation of phenotypes such as transmissibility, virulence and/or resistance to therapeutics/vaccines.

Plain language summary

The SARS-CoV-2 virus that causes COVID-19 has been changing over time. We investigated the changes in the virus present in Kenya from March 2020 to January 2022. During this period there were five successive waves of infection, during which time more people were infected with the virus. The virus arrived in Kenya from other countries many different times. Identifying the changes in the virus helps us to understand how the virus changes over time and the effect this has on its ability to infect people and make them ill.

Abstract

Kimita et al. detail the SARS-CoV-2 lineages present in Kenya during 5 waves of the COVID-19 pandemic between March 2020 and January 2022. Analysis of 1034 genomes identified 40 lineages, with phylogenetic analysis suggesting multiple introductions of variants from outside Kenya.