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Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 variant of concern Gamma and lineage P.2 in Brazil
Tiago Graf; Gonzalo Bello; Felipe Gomes Naveca; Marcelo Gomes; Vanessa Leiko Oikawa Cardoso; Alexandre Freitas da Silva; Filipe Zimmer Dezordi; Mirleide Cordeiro dos Santos; Katia Correa de Oliveira Santos; erika Lopes Rocha Batista; Alessandro Leonardo alvares Magalhaes; Fernando Vinhal; - Brazilian Ministry of Health COVID-19 Genomic Surveillance Network; Fabio Miyajima; Helisson Faoro; Ricardo Khouri; Gabriel Luz Wallau; Edson Delatorre; Marilda Mendonca Siqueira; Paola Cristina Resende.
  • Tiago Graf; Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Brazil
  • Gonzalo Bello; Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
  • Felipe Gomes Naveca; Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia (EDTA), Leonidas e Maria Deane Institute, Fiocruz
  • Marcelo Gomes; Grupo de Metodos Analiticos em Vigilancia Epidemiologica, Programa de Computacao Cientifica (PROCC), Fiocruz, Rio de Janeiro, Brazil
  • Vanessa Leiko Oikawa Cardoso; Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Brazil.
  • Alexandre Freitas da Silva; Instituto Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife, Pernambuco, Brazil
  • Filipe Zimmer Dezordi; Instituto Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife, Pernambuco, Brazil
  • Mirleide Cordeiro dos Santos; Instituto Evandro Chagas, Belem, Para
  • Katia Correa de Oliveira Santos; Instituto Adolfo Lutz, Sao Paulo
  • erika Lopes Rocha Batista; Secretaria de Saude de Aparecida de Goiania, Goias, Brazil
  • Alessandro Leonardo alvares Magalhaes; Secretaria de Saude de Aparecida de Goiania, Goias, Brazil
  • Fernando Vinhal; Lab HLAGYN - Goiania, Goias, Brazil
  • - Brazilian Ministry of Health COVID-19 Genomic Surveillance Network; Brazilian Ministry of Health COVID-19 Genomic Surveillance Network
  • Fabio Miyajima; Fundacao Oswaldo Cruz - Fiocruz Ceara
  • Helisson Faoro; Instituto Carlos Chagas (ICC), Fiocruz-PR
  • Ricardo Khouri; Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Brazil.
  • Gabriel Luz Wallau; Instituto Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife, Pernambuco, Brazil
  • Edson Delatorre; Departamento de Biologia. Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil.
  • Marilda Mendonca Siqueira; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.
  • Paola Cristina Resende; Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21265116
ABSTRACT
The COVID-19 epidemic in Brazil experienced two major country-wide lineage replacements, the first driven by the lineage P.2, formerly classified as variant of interest (VOI) Zeta in late 2020 and the second by the variant of concern (VOC) Gamma in early 2021. To better understand how these SARS-CoV-2 lineage turnovers occurred in Brazil, we analyzed 11,724 high-quality SARS-CoV-2 whole genomes of samples collected in different country regions between September 2020 and April 2021. Our findings indicate that the spatial dispersion of both variants in Brazil was driven by short and long-distance viral transmission. The lineage P.2 harboring Spike mutation E484K probably emerged around late July 2020 in the Rio de Janeiro (RJ) state, which contributed with most ([~]50%) inter-state viral disseminations, and only became locally established in most Brazilian states by October 2020. The VOC Gamma probably arose in November 2020 in the Amazonas (AM) state, which was responsible for 60-70% of the inter-state viral dissemination, and the earliest timing of community transmission of this VOC in many Brazilian states was already traced to December 2020. We estimate that variant Gamma was 1.56-3.06 more transmissible than variant P.2 co-circulating in RJ and that the median effective reproductive number (Re) of Gamma in RJ and SP states (Re = 1.59-1.91) was lower than in AM (Re = 3.55). In summary, although the epicenter of the lineage P.2 dissemination in Brazil was the heavily interconnected Southeastern region, it displayed a slower rate of spatial spread than the VOC Gamma originated in the more isolated Northern Brazilian region. Our findings also support that the VOC Gamma was more transmissible than lineage P.2, although the viral Re of the VOC varied according to the geographic context.
Texte intégral: Disponible Collection: Preprints Base de données: medRxiv langue: Anglais Année: 2021 Type de document: Preprint
Texte intégral: Disponible Collection: Preprints Base de données: medRxiv langue: Anglais Année: 2021 Type de document: Preprint