Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

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(FIOCRUZ) Fundação Oswaldo Cruz ;  (UFMG) Universidade Federal de Minas Gerais ;  University of Campus Bio-Medico di Roma ;  (USP) Universidade de São Paulo ;  (OPAS) Organização Pan-Americana da Saúde ;  Stellenbosch University ;  (UKZN) University of KwaZulu-Natal ;  (LACEN-MG) Laboratório Central de Saúde Pública do Estado de Minas Gerais ;  (LACEN-BA) Laboratório Central do Estado da Bahia ;  (LACEN) Laboratório Central de Salud Pública ;  Universidad Nacional del Caaguazú ;  Ministerio de Salud Pública y Bienestar Social ;  (LACEN-MT) Laboratório Central de Saúde Pública do Estado de Mato Grosso ;  (LACEN-MS) Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul ;  (UFMS) Universidade Federal de Mato Grosso do Sul ;  NGS Soluções Genômicas ;  Mendelics Análise Genômica ;  Laboratório Antonello ;  (UFCSPA) Universidade Federal de Ciências da Saúde de Porto Alegre ;  (SES-MT) Vigilância em Saúde ;  (LACEN-PR) Laboratório Central do Estado do Paraná ;  (UFPR) Universidade Federal do Paraná ;  (ICC-FIOCRUZ) Instituto Carlos Chagas ;  (UNESP) Universidade Estadual Paulista Júlio de Mesquita Filho ;  (FAMERP) Faculdade de Medicina de São José do Rio Preto ;  (FIOCRUZ) Fundação Oswaldo Cruz ;  (CGLAB/SVS-MS) Coordenação Geral de Laboratórios de Saúde Pública ;  University of Oxford ;  (ULISBOA) Universidade de Lisboa ;  (CAPRISA) Centre for the AIDS Programme of Research in South Africa ;  (UW) University of Washington ;  (USYD) University of Sydney 
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The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.
Giovanetti M, Slavov SN, Fonseca V, Patané JSL, Viala VL, Lima LPO, et al. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nat Microbiol. 2022 Sep; 7:1490-1500. doi:10.1038/s41564-022-01191-z.
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