Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/263006 |
Resumo: | 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. |
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Mora, Yuri Belisario YépezRuiz, Mariana Daniela Del Carmen MarcanoBezerra, Rafael dos SantosFam, Bibiana Sampaio de OliveiraXimenez, João Paulo BianchiSilva-Junior, Wilson AraujoBortolini, Maria Cátira2023-08-02T03:32:15Z20221415-4757http://hdl.handle.net/10183/263006001152508Our 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.application/pdfengGenetics and Molecular Biology. Ribeirão Preto. Vol. 45, n. 1 (2022), e20210309, 13 p.GammaCOVID-19Evolutionary history of GammaEvolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storminfo:eu-repo/semantics/articleinfo:eu-repo/semantics/otherinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSTEXT001152508.pdf.txt001152508.pdf.txtExtracted Texttext/plain70916http://www.lume.ufrgs.br/bitstream/10183/263006/2/001152508.pdf.txte49e3daa4c2d7c9cca65c8d269c62b22MD52ORIGINAL001152508.pdfTexto completo (inglês)application/pdf336225http://www.lume.ufrgs.br/bitstream/10183/263006/1/001152508.pdfb45f0316870f775135071569ff25ffcbMD5110183/2630062023-08-23 03:29:34.779362oai:www.lume.ufrgs.br:10183/263006Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2023-08-23T06:29:34Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
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 |
spellingShingle |
Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm Mora, Yuri Belisario Yépez Gamma COVID-19 Evolutionary history of Gamma |
title_short |
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_sort |
Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm |
author |
Mora, Yuri Belisario Yépez |
author_facet |
Mora, Yuri Belisario Yépez Ruiz, Mariana Daniela Del Carmen Marcano Bezerra, Rafael dos Santos Fam, Bibiana Sampaio de Oliveira Ximenez, João Paulo Bianchi Silva-Junior, Wilson Araujo Bortolini, Maria Cátira |
author_role |
author |
author2 |
Ruiz, Mariana Daniela Del Carmen Marcano Bezerra, Rafael dos Santos Fam, Bibiana Sampaio de Oliveira Ximenez, João Paulo Bianchi Silva-Junior, Wilson Araujo Bortolini, Maria Cátira |
author2_role |
author author author author author author |
dc.contributor.author.fl_str_mv |
Mora, Yuri Belisario Yépez Ruiz, Mariana Daniela Del Carmen Marcano Bezerra, Rafael dos Santos Fam, Bibiana Sampaio de Oliveira Ximenez, João Paulo Bianchi Silva-Junior, Wilson Araujo Bortolini, Maria Cátira |
dc.subject.por.fl_str_mv |
Gamma COVID-19 |
topic |
Gamma COVID-19 Evolutionary history of Gamma |
dc.subject.eng.fl_str_mv |
Evolutionary history of Gamma |
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. |
publishDate |
2022 |
dc.date.issued.fl_str_mv |
2022 |
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2023-08-02T03:32:15Z |
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http://hdl.handle.net/10183/263006 |
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001152508 |
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dc.language.iso.fl_str_mv |
eng |
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dc.relation.ispartof.pt_BR.fl_str_mv |
Genetics and Molecular Biology. Ribeirão Preto. Vol. 45, n. 1 (2022), e20210309, 13 p. |
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info:eu-repo/semantics/openAccess |
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openAccess |
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