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: | Genetics and Molecular Biology |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572022000100108 |
Resumo: | Abstract 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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Genetics and Molecular Biology |
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Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect stormGammaP.1evolutionCOVID-19Abstract 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 Genética2022-01-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572022000100108Genetics and Molecular Biology v.45 n.1 2022reponame:Genetics and Molecular Biologyinstname:Sociedade Brasileira de Genética (SBG)instacron:SBG10.1590/1678-4685-gmb-2021-0309info:eu-repo/semantics/openAccessYépez,YuriMarcano-Ruiz,MarianaBezerra,Rafael SFam,BibianaXimenez,João PBSilva Jr,Wilson ABortolini,Maria Cátiraeng2022-03-07T00:00:00Zoai:scielo:S1415-47572022000100108Revistahttp://www.gmb.org.br/ONGhttps://old.scielo.br/oai/scielo-oai.php||editor@gmb.org.br1678-46851415-4757opendoar:2022-03-07T00:00Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG)false |
dc.title.none.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 Yépez,Yuri Gamma P.1 evolution COVID-19 |
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 |
Yépez,Yuri |
author_facet |
Yépez,Yuri Marcano-Ruiz,Mariana Bezerra,Rafael S Fam,Bibiana Ximenez,João PB Silva Jr,Wilson A Bortolini,Maria Cátira |
author_role |
author |
author2 |
Marcano-Ruiz,Mariana Bezerra,Rafael S Fam,Bibiana Ximenez,João PB Silva Jr,Wilson A Bortolini,Maria Cátira |
author2_role |
author author author author author author |
dc.contributor.author.fl_str_mv |
Yépez,Yuri Marcano-Ruiz,Mariana Bezerra,Rafael S Fam,Bibiana Ximenez,João PB Silva Jr,Wilson A Bortolini,Maria Cátira |
dc.subject.por.fl_str_mv |
Gamma P.1 evolution COVID-19 |
topic |
Gamma P.1 evolution COVID-19 |
description |
Abstract 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.none.fl_str_mv |
2022-01-01 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572022000100108 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572022000100108 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/1678-4685-gmb-2021-0309 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
text/html |
dc.publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
dc.source.none.fl_str_mv |
Genetics and Molecular Biology v.45 n.1 2022 reponame:Genetics and Molecular Biology instname:Sociedade Brasileira de Genética (SBG) instacron:SBG |
instname_str |
Sociedade Brasileira de Genética (SBG) |
instacron_str |
SBG |
institution |
SBG |
reponame_str |
Genetics and Molecular Biology |
collection |
Genetics and Molecular Biology |
repository.name.fl_str_mv |
Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG) |
repository.mail.fl_str_mv |
||editor@gmb.org.br |
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1752122390566928384 |