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Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to give rise to a highly transmissive and immune-escaping variant of concern, known as Omicron. Many aspects of the evolution of SARS-CoV-2 and the driving forces behind the ongoing Omicron outbreaks remain unclear. Substitutio...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10446972/ https://www.ncbi.nlm.nih.gov/pubmed/37621704 http://dx.doi.org/10.3389/fgene.2023.1220906 |
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author | Habib, Mohammad Tanbir Rahman, Saikt Afrad, Mokibul Hassan Howlader, Arif Mahmud Khan, Manjur Hossain Khanam, Farhana Alam, Ahmed Nawsher Chowdhury, Emran Kabir Rahman, Ziaur Rahman, Mustafizur Shirin, Tahmina Qadri, Firdausi |
author_facet | Habib, Mohammad Tanbir Rahman, Saikt Afrad, Mokibul Hassan Howlader, Arif Mahmud Khan, Manjur Hossain Khanam, Farhana Alam, Ahmed Nawsher Chowdhury, Emran Kabir Rahman, Ziaur Rahman, Mustafizur Shirin, Tahmina Qadri, Firdausi |
author_sort | Habib, Mohammad Tanbir |
collection | PubMed |
description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to give rise to a highly transmissive and immune-escaping variant of concern, known as Omicron. Many aspects of the evolution of SARS-CoV-2 and the driving forces behind the ongoing Omicron outbreaks remain unclear. Substitution at the receptor-binding domain (RBD) in the spike protein is one of the primary strategies of SARS-CoV-2 Omicron to hinder recognition by the host angiotensin-converting enzyme 2 (ACE2) receptor and avoid antibody-dependent defense activation. Here, we scanned for adaptive evolution within the SARS-CoV-2 Omicron genomes reported from Bangladesh in the public database GISAID (www.gisaid.org; dated 2 April 2023). The ratio of the non-synonymous (Ka) to synonymous (Ks) nucleotide substitution rate, denoted as ω, is an indicator of the selection pressure acting on protein-coding genes. A higher proportion of non-synonymous to synonymous substitutions (Ka/Ks or ω > 1) indicates positive selection, while Ka/Ks or ω near zero indicates purifying selection. An equal amount of non-synonymous and synonymous substitutions (Ka/Ks or ω = 1) refers to neutrally evolving sites. We found evidence of adaptive evolution within the spike (S) gene of SARS-CoV-2 Omicron isolated from Bangladesh. In total, 22 codon sites of the S gene displayed a signature of positive selection. The data also highlighted that the receptor-binding motif within the RBD of the spike glycoprotein is a hotspot of adaptive evolution, where many of the codons had ω > 1. Some of these adaptive sites at the RBD of the spike protein are known to be associated with increased viral fitness. The M gene and ORF6 have also experienced positive selection. These results suggest that although purifying selection is the dominant evolutionary force, positive Darwinian selection also plays a vital role in shaping the evolution of SARS-CoV-2 Omicron in Bangladesh. |
format | Online Article Text |
id | pubmed-10446972 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-104469722023-08-24 Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh Habib, Mohammad Tanbir Rahman, Saikt Afrad, Mokibul Hassan Howlader, Arif Mahmud Khan, Manjur Hossain Khanam, Farhana Alam, Ahmed Nawsher Chowdhury, Emran Kabir Rahman, Ziaur Rahman, Mustafizur Shirin, Tahmina Qadri, Firdausi Front Genet Genetics Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to give rise to a highly transmissive and immune-escaping variant of concern, known as Omicron. Many aspects of the evolution of SARS-CoV-2 and the driving forces behind the ongoing Omicron outbreaks remain unclear. Substitution at the receptor-binding domain (RBD) in the spike protein is one of the primary strategies of SARS-CoV-2 Omicron to hinder recognition by the host angiotensin-converting enzyme 2 (ACE2) receptor and avoid antibody-dependent defense activation. Here, we scanned for adaptive evolution within the SARS-CoV-2 Omicron genomes reported from Bangladesh in the public database GISAID (www.gisaid.org; dated 2 April 2023). The ratio of the non-synonymous (Ka) to synonymous (Ks) nucleotide substitution rate, denoted as ω, is an indicator of the selection pressure acting on protein-coding genes. A higher proportion of non-synonymous to synonymous substitutions (Ka/Ks or ω > 1) indicates positive selection, while Ka/Ks or ω near zero indicates purifying selection. An equal amount of non-synonymous and synonymous substitutions (Ka/Ks or ω = 1) refers to neutrally evolving sites. We found evidence of adaptive evolution within the spike (S) gene of SARS-CoV-2 Omicron isolated from Bangladesh. In total, 22 codon sites of the S gene displayed a signature of positive selection. The data also highlighted that the receptor-binding motif within the RBD of the spike glycoprotein is a hotspot of adaptive evolution, where many of the codons had ω > 1. Some of these adaptive sites at the RBD of the spike protein are known to be associated with increased viral fitness. The M gene and ORF6 have also experienced positive selection. These results suggest that although purifying selection is the dominant evolutionary force, positive Darwinian selection also plays a vital role in shaping the evolution of SARS-CoV-2 Omicron in Bangladesh. Frontiers Media S.A. 2023-08-09 /pmc/articles/PMC10446972/ /pubmed/37621704 http://dx.doi.org/10.3389/fgene.2023.1220906 Text en Copyright © 2023 Habib, Rahman, Afrad, Howlader, Khan, Khanam, Alam, Chowdhury, Rahman, Rahman, Shirin and Qadri. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Habib, Mohammad Tanbir Rahman, Saikt Afrad, Mokibul Hassan Howlader, Arif Mahmud Khan, Manjur Hossain Khanam, Farhana Alam, Ahmed Nawsher Chowdhury, Emran Kabir Rahman, Ziaur Rahman, Mustafizur Shirin, Tahmina Qadri, Firdausi Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh |
title | Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh |
title_full | Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh |
title_fullStr | Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh |
title_full_unstemmed | Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh |
title_short | Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh |
title_sort | natural selection shapes the evolution of sars-cov-2 omicron in bangladesh |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10446972/ https://www.ncbi.nlm.nih.gov/pubmed/37621704 http://dx.doi.org/10.3389/fgene.2023.1220906 |
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