Imported SARS-CoV-2 variants of concern drove spread of infections across Kenya during the second year of the pandemic

Using classical and genomic epidemiology, this study tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities.

Whole SARS-CoV-2 genome sequencing was carried out on 1241 specimens. Over the pandemic duration (March 2020–January 2022), Kenya experienced five waves characterized by attack rates of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios averaging 3.5%, two-fold higher than the national average COVID-19 associated case-fatality ratio.

The first two waves that occurred before emergence of global variants of concerns had lower attack rates (65.4 and 118.2 per 100,000). Waves 3, 4 and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%) and Omicron (87.8%) variants of concern, respectively.

During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country.

In conclusion, the emergence of Alpha, Delta and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.