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Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm
Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites und...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Sociedade Brasileira de Genética
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8908351/ https://www.ncbi.nlm.nih.gov/pubmed/35266951 http://dx.doi.org/10.1590/1678-4685-GMB-2021-0309 |
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author | Yépez, Yuri Marcano-Ruiz, Mariana Bezerra, Rafael S Fam, Bibiana Ximenez, João PB Silva, Wilson A Bortolini, Maria Cátira |
author_facet | Yépez, Yuri Marcano-Ruiz, Mariana Bezerra, Rafael S Fam, Bibiana Ximenez, João PB Silva, Wilson A Bortolini, Maria Cátira |
author_sort | Yépez, Yuri |
collection | PubMed |
description | Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses. |
format | Online Article Text |
id | pubmed-8908351 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Sociedade Brasileira de Genética |
record_format | MEDLINE/PubMed |
spelling | pubmed-89083512022-03-17 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm Yépez, Yuri Marcano-Ruiz, Mariana Bezerra, Rafael S Fam, Bibiana Ximenez, João PB Silva, Wilson A Bortolini, Maria Cátira Genet Mol Biol Human and Medical Genetics Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses. Sociedade Brasileira de Genética 2022-03-09 /pmc/articles/PMC8908351/ /pubmed/35266951 http://dx.doi.org/10.1590/1678-4685-GMB-2021-0309 Text en https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License |
spellingShingle | Human and Medical Genetics Yépez, Yuri Marcano-Ruiz, Mariana Bezerra, Rafael S Fam, Bibiana Ximenez, João PB Silva, Wilson A Bortolini, Maria Cátira Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm |
title | Evolutionary history of the SARS-CoV-2 Gamma variant of concern
(P.1): a perfect storm |
title_full | Evolutionary history of the SARS-CoV-2 Gamma variant of concern
(P.1): a perfect storm |
title_fullStr | Evolutionary history of the SARS-CoV-2 Gamma variant of concern
(P.1): a perfect storm |
title_full_unstemmed | Evolutionary history of the SARS-CoV-2 Gamma variant of concern
(P.1): a perfect storm |
title_short | Evolutionary history of the SARS-CoV-2 Gamma variant of concern
(P.1): a perfect storm |
title_sort | evolutionary history of the sars-cov-2 gamma variant of concern
(p.1): a perfect storm |
topic | Human and Medical Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8908351/ https://www.ncbi.nlm.nih.gov/pubmed/35266951 http://dx.doi.org/10.1590/1678-4685-GMB-2021-0309 |
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