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Open Access 01-12-2022 | SARS-CoV-2 | Short report

Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

Authors: Samoel Ashimosi Khamadi, Silvanos Opanda, Samwel Lifumo Symekher, Samson Konongoi Limbaso, Solomon Langat, Josyline Kaburi Cirindi, Milkah Mwangi, Nicholas Mwikwabe, Seth Okeyo, Edith Koskei, James Mutisya, Samwel Owaka, Albert Nyunja, Hellen Koka, Meshack Wadegu, Esther Chitechi, Rachel Achilla, Janet Masitsa Majanja, Lucy Kanyara, Evans Amukoye, Wallace Bulimo

Published in: Virology Journal | Issue 1/2022

Abstract

The emergence and rapid spread of SARS-CoV-2 variants of concern (VOC) have been linked to new waves of COVID-19 epidemics occurring in different regions of the world. The VOC have acquired adaptive mutations that have enhanced virus transmissibility, increased virulence, and reduced response to neutralizing antibodies. Kenya has experienced six waves of COVID-19 epidemics. In this study, we analyzed 64 genome sequences of SARS-CoV-2 strains that circulated in Nairobi and neighboring counties, Kenya between March 2021 and July 2021. Viral RNA was extracted from RT-PCR confirmed COVID-19 cases, followed by sequencing using the ARTIC network protocol and Oxford Nanopore Technologies. Analysis of the sequence data was performed using different bioinformatics methods. Our analyses revealed that during the study period, three SARS-CoV-2 variants of concern (VOC) circulated in Nairobi and nearby counties in Kenya. The Alpha (B.1.1.7) lineage predominated (62.7%), followed by Delta (B.1.617.2, 35.8%) and Beta (B.1.351, 1.5%). Notably, the Alpha (B.1.1.7) VOC were most frequent from March 2021 to May 2021, while the Delta (B.1.617.2) dominated beginning June 2021 through July 2021. Sequence comparisons revealed that all the Kenyan viruses were genetically similar to those that circulated in other regions. Although the majority of Kenyan viruses clustered together in their respective phylogenetic lineages/clades, a significant number were interspersed among foreign strains. Between March and July 2021, our study's findings indicate the prevalence of multiple lineages of SAR-CoV-2 VOC in Nairobi and nearby counties in Kenya. The data suggest that the recent increase in SARS-CoV-2 infection, particularly in Nairobi and Kenya as a whole, is attributable to the introduction and community transmission of SARS-CoV-2 VOC among the populace. In conclusion, the findings provide a snapshot of the SARS-CoV-2 variants that circulated in Kenya during the study period.

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Title: Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021
Authors: Samoel Ashimosi Khamadi
Silvanos Opanda
Samwel Lifumo Symekher
Samson Konongoi Limbaso
Solomon Langat
Josyline Kaburi Cirindi
Milkah Mwangi
Nicholas Mwikwabe
Seth Okeyo
Edith Koskei
James Mutisya
Samwel Owaka
Albert Nyunja
Hellen Koka
Meshack Wadegu
Esther Chitechi
Rachel Achilla
Janet Masitsa Majanja
Lucy Kanyara
Evans Amukoye
Wallace Bulimo
Publication date: 01-12-2022
Publisher: BioMed Central
Keywords: SARS-CoV-2
COVID-19
Coronavirus
Published in: Virology Journal / Issue 1/2022
Electronic ISSN: 1743-422X
DOI: https://doi.org/10.1186/s12985-022-01895-y

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