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Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares inte...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9504048/ https://www.ncbi.nlm.nih.gov/pubmed/36146671 http://dx.doi.org/10.3390/v14091865 |
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author | Katowa, Ben Kalonda, Annie Mubemba, Benjamin Matoba, Japhet Shempela, Doreen Mainza Sikalima, Jay Kabungo, Boniface Changula, Katendi Chitanga, Simbarashe Kasonde, Mpanga Kapona, Otridah Kapata, Nathan Musonda, Kunda Monze, Mwaka Tembo, John Bates, Matthew Zumla, Alimuddin Sutcliffe, Catherine G. Kajihara, Masahiro Yamagishi, Junya Takada, Ayato Sawa, Hirofumi Chilengi, Roma Mukonka, Victor Muleya, Walter Simulundu, Edgar |
author_facet | Katowa, Ben Kalonda, Annie Mubemba, Benjamin Matoba, Japhet Shempela, Doreen Mainza Sikalima, Jay Kabungo, Boniface Changula, Katendi Chitanga, Simbarashe Kasonde, Mpanga Kapona, Otridah Kapata, Nathan Musonda, Kunda Monze, Mwaka Tembo, John Bates, Matthew Zumla, Alimuddin Sutcliffe, Catherine G. Kajihara, Masahiro Yamagishi, Junya Takada, Ayato Sawa, Hirofumi Chilengi, Roma Mukonka, Victor Muleya, Walter Simulundu, Edgar |
author_sort | Katowa, Ben |
collection | PubMed |
description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs. |
format | Online Article Text |
id | pubmed-9504048 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-95040482022-09-24 Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern Katowa, Ben Kalonda, Annie Mubemba, Benjamin Matoba, Japhet Shempela, Doreen Mainza Sikalima, Jay Kabungo, Boniface Changula, Katendi Chitanga, Simbarashe Kasonde, Mpanga Kapona, Otridah Kapata, Nathan Musonda, Kunda Monze, Mwaka Tembo, John Bates, Matthew Zumla, Alimuddin Sutcliffe, Catherine G. Kajihara, Masahiro Yamagishi, Junya Takada, Ayato Sawa, Hirofumi Chilengi, Roma Mukonka, Victor Muleya, Walter Simulundu, Edgar Viruses Article Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs. MDPI 2022-08-24 /pmc/articles/PMC9504048/ /pubmed/36146671 http://dx.doi.org/10.3390/v14091865 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Katowa, Ben Kalonda, Annie Mubemba, Benjamin Matoba, Japhet Shempela, Doreen Mainza Sikalima, Jay Kabungo, Boniface Changula, Katendi Chitanga, Simbarashe Kasonde, Mpanga Kapona, Otridah Kapata, Nathan Musonda, Kunda Monze, Mwaka Tembo, John Bates, Matthew Zumla, Alimuddin Sutcliffe, Catherine G. Kajihara, Masahiro Yamagishi, Junya Takada, Ayato Sawa, Hirofumi Chilengi, Roma Mukonka, Victor Muleya, Walter Simulundu, Edgar Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern |
title | Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern |
title_full | Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern |
title_fullStr | Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern |
title_full_unstemmed | Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern |
title_short | Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern |
title_sort | genomic surveillance of sars-cov-2 in the southern province of zambia: detection and characterization of alpha, beta, delta, and omicron variants of concern |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9504048/ https://www.ncbi.nlm.nih.gov/pubmed/36146671 http://dx.doi.org/10.3390/v14091865 |
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