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

• Autor(a) principal: Gräf, Tiago
• Data de Publicação: 2021
• Outros Autores: Bello, Gonzalo, Venas, Taina Moreira Martins, Pereira, Elisa Cavalcante, Paixão, Anna Carolina Dias, Appolinario, Luciana Reis, Lopes, Renata Serrano, Mendonça, Ana Carolina da Fonseca, Rocha, Alice Sampaio Barreto da, 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, Rodrigues, Rodrigo Ribeiro, Grinsztejn, Beatriz, Nascimento, Valdinete Alves do, Souza, Victor Costa de, Gonçalves, Luciana, Costa, Cristiano Fernandes da, Mattos, Tirza, Dezordi, Filipe Zimmer, Resende, Paola Cristina, Fiocruz COVID-19 Genomic Surveillance Network
• Tipo de documento: Artigo
• Idioma: eng
• Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
• Texto Completo: https://www.arca.fiocruz.br/handle/icict/50917
• topic: SARS-CoV-2; Vigilância genômica; Variante de preocupação Gama; Linhagem P.1; Brasil; SARS-CoV-2; Genomic surveillance; Variant of concern Gamma; Brazil; Lineage P.1

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 (<2 per cent) of SARS-CoV-2 infections in Brazil in 2021. The stepwise diversification of lineage P.1 through multiple inter-host transmissions is consistent with the hypothesis that partial immunity acquired from natural SARS-CoV-2 infections in heavily affected regions might have been a major driving force behind the natural selection of some VOCs. The lag time between the emergence of the P.1 ancestor and the expansion of the VOC Gamma and the divergent epidemic trajectories of P.1 sub-lineages support a complex interplay between the emergence of mutations of concern and viral spread in Brazil.