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.

Details

Title
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
Author
Gräf, Tiago 1 ; Bello, Gonzalo 2 ; Taina Moreira Martins Venas 3 ; Elisa Cavalcante Pereira 3 ; Anna Carolina Dias Paixão 3 ; Luciana Reis Appolinario 3 ; Renata Serrano Lopes 3 ; Ana Carolina Da Fonseca Mendonça 3 ; Alice Sampaio Barreto da Rocha 3 ; Fernando Couto Motta 3 ; Tatiana Schäffer Gregianini 4 ; Richard Steiner Salvato 4 ; Sandra Bianchini Fernandes 5 ; Darcita Buerger Rovaris 5 ; Cavalcanti, Andrea Cony 6 ; Anderson Brandão Leite 7 ; Riediger, Irina 8 ; Maria do Carmo Debur 8 ; André Felipe Leal Bernardes 9 ; Ribeiro-Rodrigues, Rodrigo 10 ; Grinsztejn, Beatriz 11 ; Valdinete Alves do Nascimento 12 ; Costa de Souza, Victor 12 ; Gonçalves, Luciana 12 ; Cristiano Fernandes da Costa 13 ; Mattos, Tirza 14 ; Filipe Zimmer Dezordi 15 ; Gabriel Luz Wallau 15 ; Felipe Gomes Naveca 12 ; Delatorre, Edson 16 ; Marilda Mendonça Siqueira 3 ; Resende, Paola Cristina 3 

 Plataforma de Vigilância Molecular, Instituto Gonçalo Moniz, Fiocruz , Salvador, Bahia 40296-710, Brazil 
 Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz , Rio de Janeiro 21040-900, Brazil 
 Laboratório de Vírus Respiratórios e do Sarampo (LVRS), Instituto Oswaldo Cruz, Fiocruz , Rio de Janeiro 21040-900, Brazil 
 Laboratório Central de Saúde Pública do Estado do Rio Grande do Sul (LACEN-RS) , Porto Alegre 90610-000, Brazil 
 Laboratório Central de Saúde Pública do Estado de Santa Catarina (LACEN-SC) , Florianópolis 88010-001, Brazil 
 Laboratório Central de Saúde Pública do Estado do Rio de Janeiro (LACEN-RJ) , Rio de Janeiro 20231-000, Brazil 
 Laboratório Central de Saúde Pública do Estado de Alagoas (LACEN-AL) , Maceió 57036-000, Brazil 
 Laboratório Central de Saúde Pública do Estado do Paraná (LACEN-PR) , Curitiba 80045-150, Brazil 
 Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG) , Belo Horizonte 30510-010, Brazil 
10  Laboratório Central de Saúde Pública do Estado do Espírito Santo (LACEN-ES) , Vitória 29052-121, Brazil 
11  Instituto Nacional de Infectologia (INI), Fiocruz , Rio de Janeiro 21040-900, Brazil 
12  Laboratório de Ecologia de Doenças Transmissíveis na Amazônia (EDTA), Instituto Leônidas e Maria Deane, FIOCRUZ , Manaus, Amazonas 69027-070, Brazil 
13  Fundação de Vigilância em Saúde do Amazonas , Manaus 69093-018, Brazil 
14  Laboratório Central de Saúde Pública do Amazonas , Manaus 69020-040, Brazil 
15  Departamento de Entomologia, Instituto Aggeu Magalhães, Fiocruz , Recife, Pernambuco 50670-420, Brazil 
16  Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo , Alegre 29500-000, Brazil 
Publication year
2021
Publication date
Sep 2021
Publisher
Oxford University Press
e-ISSN
20571577
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
3171770407
Copyright
© The Author(s) 2021. Published by Oxford University Press. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.