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

<ns3:p> <ns3:bold>Background</ns3:bold> : Understanding the molecular epidemiology and clinical presentation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) in rural-urban populations in Kenya is important for informing future public health responses and clinical care. </ns3:p> <ns3:p> <ns3:bold>Methods</ns3:bold> : We undertook a retrospective analysis of the clinical presentation and phylogenetic relatedness of specimens from 97 SARS-CoV-2 cases collected between 24 <ns3:sup>th</ns3:sup> April and 31 <ns3:sup>st</ns3:sup> December 2021 in Laikipia county, Kenya. VOC were related to observed symptoms. Phylogenetic analyses included contemporaneous sequences from across Kenya and the globe, to contextualise local transmission dynamics. </ns3:p> <ns3:p> <ns3:bold>Results</ns3:bold> : These sequences fell into three VOC; Alpha (n=8), Delta (n=52) and Omicron (n=37). We estimated 75 independent SARS-CoV-2 introductions into the county. The Alpha and Delta VOC were commonly detected in persons aged 31 to 45 years, 50.0% and 30.8%, respectively. The Omicron VOC was mostly detected in 16 to 30-year-olds (51.4%). Whereas relative to the other VOCs, Omicron was associated with mild upper-respiratory tract symptoms (cough, OR 3.78; 95% CI 1.1 – 16.74, p= 0.026) and sore throat, OR 22.42; 95% CI 7.11 – 81.40, p&lt;0.001), Delta was associated with moderate to severe lower-respiratory tract symptoms (shortness of breath, OR 26.8; 95% CI 3.89 – 1158.14, p&lt;0.001) and fever (OR 6.11; 95% CI 1.57 – 35.35, p= 0.004). Post-acute phase neurological complications were suspected in four Delta infected cases (neuralgia, neuritis, peripheral neuropathy, numbness of hand and tinnitus). </ns3:p> <ns3:p> <ns3:bold>Conclusion</ns3:bold> : We highlight the distinctive clinical characteristics of SARS-CoV-2 VOCs, as observed in Laikipia, Kenya, to support evidence-based clinical decisions. Multiple introductions of the VOCs were recorded despite the public health measures that were in place questioning their effectiveness during the study period. </ns3:p>