Article
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
Fecha
2021Registro en:
GRÄF, Tiago et al. 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. Virus Evolution, v. 7, n. 2, p. 1-10, 2021.
2057-1577
10.1093/ve/veab091
Autor
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
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
Institución
Resumen
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.