Identification of a novel SARS-CoV-2 P.1 sub-lineage in Brazil provides new insights about the mechanisms of emergence of variants of concern

Abstract One of the most remarkable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) features is the significant number of mutations they acquired. However, the specific factors that drove the emergence of such variants since the second half of 2020 are not full...

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Published in:Virus evolution 2021-12, Vol.7 (2), p.veab091-veab091
Main Authors: Gräf, Tiago, Bello, Gonzalo, Venas, Taina Moreira Martins, Pereira, Elisa Cavalcante, Paixão, Anna Carolina Dias, Appolinario, Luciana Reis, Lopes, Renata Serrano, Mendonça, Ana Carolina Da Fonseca, da Rocha, Alice Sampaio Barreto, Motta, Fernando Couto, Gregianini, Tatiana Schäffer, Salvato, Richard Steiner, Fernandes, Sandra Bianchini, Rovaris, Darcita Buerger, Cavalcanti, Andrea Cony, Leite, Anderson Brandão, Riediger, Irina, Debur, Maria do Carmo, Bernardes, André Felipe Leal, Ribeiro-Rodrigues, Rodrigo, Grinsztejn, Beatriz, Alves do Nascimento, Valdinete, de Souza, Victor Costa, Gonçalves, Luciana, da Costa, Cristiano Fernandes, Mattos, Tirza, Dezordi, Filipe Zimmer, Wallau, Gabriel Luz, Naveca, Felipe Gomes, Delatorre, Edson, Siqueira, Marilda Mendonça, Resende, Paola Cristina
Format: Article
Language:English
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Summary:Abstract One of the most remarkable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) features is the significant number of mutations they acquired. However, the specific factors that drove the emergence of such variants since the second half of 2020 are not fully resolved. In this study, we describe a new SARS-CoV-2 P.1 sub-lineage circulating in Brazil, denoted here as Gamma-like-II, that as well as the previously described lineage Gamma-like-I shares several lineage-defining mutations with the VOC Gamma. Reconstructions of ancestor sequences support that most lineage-defining mutations of the Spike (S) protein, including those at the receptor-binding domain (RBD), accumulated at the first P.1 ancestor. In contrast, mutations outside the S protein were mostly fixed at subsequent steps. Our evolutionary analyses estimate that P.1-ancestral strains carrying RBD mutations of concern probably circulated cryptically in the Amazonas for several months before the emergence of the VOC Gamma. Unlike the VOC Gamma, the other P.1 sub-lineages displayed a much more restricted dissemination and accounted for a low fraction (
ISSN:2057-1577
2057-1577
DOI:10.1093/ve/veab091