Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study

• DOI: 10.7554/elife.71703
• Publication Date: 2022-06-14T12:01:19Z
• Authors: Charles N Agoti; Lynette Isabella ...; Simon Dellicour; Khadija Said Moha...; Arnold W Lambisia; Zaydah R de Laurent; John M Morobe; Maureen W Mburu; Donwilliams O Omuoyo; Edidah M Ongera; Leonard Ndwiga; Eric Maitha; Benson Kitole; Thani Suleiman; Mohamed Mwakinangu; John K Nyambu; John Otieno; Barke Salim; Jennifer Musyoki; Nickson Murunga; Edward Otieno; John N Kiiru; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Samson Kinyanjui; George Warimwe; My Phan; Ambrose Agweyu; Matthew Cotten; Edwine Barasa; Benjamin Tsofa; D James Nokes; Philip Bejon; George Githinji
• Keywords: 2019-20 coronavirus outbreak; Sars virus; Pandemic

Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, Lamu) to infer virus introductions patterns during first two waves infections. Virus importations were inferred using ancestral state reconstruction, dispersal was estimated discrete phylogeographic analysis. During Wave 1, 23 distinct Pango lineages detected counties, while 2, 29 detected; 9 which occurred in both 4 seemed be specific (B.1.530, B.1.549, B.1.596.1, N.8). Most sequenced infections belonged lineage B.1 (n = 723, 63%), predominated 1 (73%, followed by N.8 [6%] B.1.1 [6%]) (56%, B.1.549 [21%] B.1.530 [5%]). Over study period, 280 into Kenya. Mombasa City, a vital tourist commercial centre region, major route imports, most when many Coronavirus Disease 2019 (COVID-19) government restrictions still force. In inter-county predominated, resulting emergence chains diversity. Our analysis supports moving COVID-19 control strategies region focus on international travel that will reduce transmission. This work funded The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, 222574/Z/21/Z) National Institute Health Care Research (NIHR), project references: 17/63/and 16/136/33 UK Aid support global research, Foreign, Commonwealth Development Office. views expressed this publication are those author(s) not necessarily funding agencies.