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

• Published in: Wellcome open research 2022, Vol.7, p.235
• Main Authors: W. Lambisia, Arnold, H. Mudhune, Godfrey, M. Morobe, John, Said Mohammed, Khadija, O. Makori, Timothy, Ndwiga, Leonard, W. Mburu, Maureen, O. Moraa, Edidah, Musyoki, Jeniffer, Murunga, Nickson, N. Waliaula, Isaac, K. Mumelo, Arthur, Bejon, Philip, Isabella Ochola-Oyier, Lynette, Githinji, George, Nokes, James, Agoti, Charles
• Format: Article
• Language: English
• ISSN: 2398-502X; 2398-502X
• DOI: 10.12688/wellcomeopenres.18306.2

Background : 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. Methods : We undertook a retrospective analysis of the clinical presentation and phylogenetic relatedness of specimens from 97 SARS-CoV-2 cases collected between 24 th April and 31 st 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. Results : 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