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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

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 neu...

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Autores principales: Khamadi, Samoel Ashimosi, Opanda, Silvanos, Symekher, Samwel Lifumo, Limbaso, Samson Konongoi, Langat, Solomon, Cirindi, Josyline Kaburi, Mwangi, Milkah, Mwikwabe, Nicholas, Okeyo, Seth, Koskei, Edith, Mutisya, James, Owaka, Samwel, Nyunja, Albert, Koka, Hellen, Wadegu, Meshack, Chitechi, Esther, Achilla, Rachel, Majanja, Janet Masitsa, Kanyara, Lucy, Amukoye, Evans, Bulimo, Wallace
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9640859/
https://www.ncbi.nlm.nih.gov/pubmed/36348341
http://dx.doi.org/10.1186/s12985-022-01895-y
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author Khamadi, Samoel Ashimosi
Opanda, Silvanos
Symekher, Samwel Lifumo
Limbaso, Samson Konongoi
Langat, Solomon
Cirindi, Josyline Kaburi
Mwangi, Milkah
Mwikwabe, Nicholas
Okeyo, Seth
Koskei, Edith
Mutisya, James
Owaka, Samwel
Nyunja, Albert
Koka, Hellen
Wadegu, Meshack
Chitechi, Esther
Achilla, Rachel
Majanja, Janet Masitsa
Kanyara, Lucy
Amukoye, Evans
Bulimo, Wallace
author_facet Khamadi, Samoel Ashimosi
Opanda, Silvanos
Symekher, Samwel Lifumo
Limbaso, Samson Konongoi
Langat, Solomon
Cirindi, Josyline Kaburi
Mwangi, Milkah
Mwikwabe, Nicholas
Okeyo, Seth
Koskei, Edith
Mutisya, James
Owaka, Samwel
Nyunja, Albert
Koka, Hellen
Wadegu, Meshack
Chitechi, Esther
Achilla, Rachel
Majanja, Janet Masitsa
Kanyara, Lucy
Amukoye, Evans
Bulimo, Wallace
author_sort Khamadi, Samoel Ashimosi
collection PubMed
description 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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spelling pubmed-96408592022-11-14 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 Khamadi, Samoel Ashimosi Opanda, Silvanos Symekher, Samwel Lifumo Limbaso, Samson Konongoi Langat, Solomon Cirindi, Josyline Kaburi Mwangi, Milkah Mwikwabe, Nicholas Okeyo, Seth Koskei, Edith Mutisya, James Owaka, Samwel Nyunja, Albert Koka, Hellen Wadegu, Meshack Chitechi, Esther Achilla, Rachel Majanja, Janet Masitsa Kanyara, Lucy Amukoye, Evans Bulimo, Wallace Virol J Short Report 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. BioMed Central 2022-11-08 /pmc/articles/PMC9640859/ /pubmed/36348341 http://dx.doi.org/10.1186/s12985-022-01895-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Short Report
Khamadi, Samoel Ashimosi
Opanda, Silvanos
Symekher, Samwel Lifumo
Limbaso, Samson Konongoi
Langat, Solomon
Cirindi, Josyline Kaburi
Mwangi, Milkah
Mwikwabe, Nicholas
Okeyo, Seth
Koskei, Edith
Mutisya, James
Owaka, Samwel
Nyunja, Albert
Koka, Hellen
Wadegu, Meshack
Chitechi, Esther
Achilla, Rachel
Majanja, Janet Masitsa
Kanyara, Lucy
Amukoye, Evans
Bulimo, Wallace
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
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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_short 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
title_sort 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
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9640859/
https://www.ncbi.nlm.nih.gov/pubmed/36348341
http://dx.doi.org/10.1186/s12985-022-01895-y
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