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

Abstract

Background. Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. Methods. 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 were carried out on 1241 specimens. Results. Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (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%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. Conclusions. 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.

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

“…We document multiple introductions of each VOC and subsequent local community transmission in the county. Sequential replacement of the VOCs was observed; from Alpha to Delta, to Omicron over the seven month period, as also observed in other regions within the country and globally 4,5,11 .…”

“…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 .…”

Genomic epidemiology of SARS-CoV-2 within households in coastal Kenya: a case ascertained cohort study

“…Until September 2022, Kenya had experienced six major waves of SARS-CoV-2 infections 23 . The current study coincided with national waves three, four, and five, a period during which Alpha (B.1.1.7) , Delta (B.1.617.2) and Omicron (B.1.1.529) variants of concern (VOC) predominated, respectively 24 . We undertook detailed genomic analysis to identify independent SARS-CoV-2 introductions into households during clustered infections, and understand frequency of infection spread within households in coastal Kenya.…”

Informing healthcare operations with integrated pathology, clinical, and epidemiology data: Lessons from a single institution in Kenya during COVID-19 waves

“…The characteristics of this trend matched very well with the national tracking which contained a larger sample size, giving external validity to the data set. Genomic epidemiology studies in the country revealed that the first two waves were predominantly caused by the original SARS-CoV-2 strain, while the third, fourth, and fifth were caused by the Alpha, Delta , and Omicron variants, respectively ( 20 ). The trend of the percentage of patients in ICU generally followed the positivity rate with less accentuated peaks.…”