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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

2021; University of Oxford; Volume: 7; Issue: 2 Linguagem: Inglês

10.1093/ve/veab091

2057-1577

Tiago Gräf, Gonzalo Bello, Tainá Moreira Martins Venas, Elisa Cavalcante Pereira, Anna Carolina Dias Paixão, Luciana Appolinario, Renata Serrano Lopes, Ana Carolina da Fonseca Mendonça, Alice Sampaio Barreto da Rocha, Fernando Couto Motta, Tatiana Schäffer Gregianini, Richard Steiner Salvato, Sandra Bianchini Fernandes, Darcita Büerger Rovaris, Andréa Cony Cavalcanti, Anderson Brandão Leite, Irina Nastassja Riediger, Maria do Carmo Debur, André Felipe Leal Bernardes, Rodrigo Ribeiro‐Rodrigues, Beatriz Grinsztejn, Valdinete Alves do Nascimento, Victor Costa de Souza, Luciana Gonçalves, Cristiano Fernandes da Costa, Tirza Mattos, Filipe Zimmer Dezordi, Gabriel Luz Wallau, Felipe Gomes Naveca, Edson Delatorre, Marilda Mendonça Siqueira, Paola Cristina Resende,

Viral Infections and Outbreaks Research

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 (<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.