Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya
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Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5–31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control.
Originalsprog | Engelsk |
---|---|
Artikelnummer | 627 |
Tidsskrift | BMC Genomics |
Vol/bind | 23 |
Udgave nummer | 1 |
Antal sider | 8 |
ISSN | 1471-2164 |
DOI | |
Status | Udgivet - 2022 |
Bibliografisk note
Funding Information:
This work was funded in part by The African Academy of Sciences grant number SARSCoV2–4–20-010 to JG. TGC is funded by a UKRI Global Effort on COVID-19 (GECO) Health Research grant (Ref. GEC2211; MR/V036890/1). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Funding Information:
We acknowledge the Mount Kenya University Rapid Response Team for sample collection and SARS-CoV-2 diagnosis, we also acknowledge United States Army Medical Research Unit, Kenya for sample sequencing. We thank Isabel Pötzsch for her insightful comments and suggestions on the manuscript.
Publisher Copyright:
© 2022, The Author(s).
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