The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya

The emergence and establishment of SARS-CoV-2 variants of concern presented a major global public health crisis across the world. There were six waves of SARS-CoV-2 cases in Kenya that corresponded with the introduction and eventual dominance of the major SARS-COV-2 variants of concern, excepting the first 2 waves that were both wild-type virus. We estimate that more than 1000 SARS-CoV-2 introductions occurred in the two-year epidemic period (March 2020 – September 2022) and a total of 930 introductions were associated with variants of concern namely Beta (n=78), Alpha(n=108), Delta(n=239) and Omicron (n=505). A total of 29 introductions were associated with A.23.1 variant that circulated in high frequencies in Uganda and Rwanda. The actual number of introductions is likely to be higher than these conservative estimates due to limited genomic sequencing. Our data suggested that cryptic transmission was usually underway prior to the first real-time identification of a new variant, and that multiple introductions were responsible. Following emergence of each VOC and subsequent introduction, transmission patterns were associated with hotspots of transmission in Coast, Nairobi and Western Kenya and follows established land and air transport corridors. Understanding the introduction and dispersal of major circulating variants and identifying the sources of new introductions is important to inform public health control strategies within Kenya and the larger East-African region. Border control and case finding reactive to new variants is unlikely to be a successful control strategy. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the National Institute for Health Research (NIHR) (project references 17/63/82 (PI Prof. James Nokes) and 16/136/33 (PI Prof. Mark Wooolhouse) using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office and Wellcome Trust (grant# 220985). The views expressed in this publication are those of the author (s) and not necessarily those of NIHR, the Department of Health and Social Care, Foreign Commonwealth and Development Office, Wellcome Trust or the UK government. Some members of COVID-19 Testing Team at KWTRP were supported by funding received by Dr Marta Maia (BOHEMIA study funded UNITAID), Dr Francis Ndungu (Senior Fellowship and Research and Innovation Action (RIA) grants from EDCTP), Dr Eunice Nduati (USAID grant to IAVI: AID-OAA-A-16-00032) and Prof. Anthony Scott (PCIVS grant from GAVI). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All the analyzed samples were collected under the Ministry of Health (MoH) protocols as part of the national response to the COVID-19 pandemic. The whole genome sequencing study protocol was reviewed and approved by the Scientific and Ethics Review Committee (SERU),Kenya Medical Research Institute (KEMRI), Nairobi, Kenya (SERU #4035). Individual patient consent was not required by the committee for the use of these samples for genomic surveillance to inform public health response I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced are available online at