Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.
Marta GiovanettiSvetoslav Nanev SlavovVagner FonsecaEduan WilkinsonHouriiyah TegallyJosé Salvatore Leister PatanéVincent Louis VialaJames Emmanuel SanEvandra Strazza RodriguesElaine Vieira SantosFlávia Figueira AburjaileJoilson XavierHegger FritschTalita Émile Ribeiro AdelinoFelicidade PereiraArabela LealFelipe Campos de Melo IaniGlauco de Carvalho PereiraCynthia VazquezGladys Mercedes Estigarribia SanabriaElaine Cristina de OliveiraLuiz Henrique Ferraz DemarchiJulio Henrique da Rosa CrodaRafael Dos Santos BezerraLoyze Paola Oliveira de LimaAntonio Jorge MartinsClaudia Renata Dos Santos BarrosElaine Cristina MarquezeJardelina de Souza Todao BernardinoDebora Botequio MorettiRicardo Augusto BrassalotiRaquel de Lello Rocha Campos CassanoPilar Drummond Sampaio Corrêa MarianiJoão Paulo KitajimaBibiana SantosRodrigo Proto-SiqueiraVlademir Vicente CantarelliStephane TostaVanessa Brandão NardyLuciana Reboredo de Oliveira da SilvaMarcela Kelly Astete GómezJaqueline Gomes LimaAdriana Aparecida RibeiroNatália Rocha GuimarãesLuiz Takao WatanabeLuana Barbosa Da SilvaRaquel da Silva FerreiraMara Patricia F da PenhaMaría José OrtegaAndrea Gómez de la FuenteShirley VillalbaJuan ToralesMaría Liz GamarraCarolina AquinoGloria Patricia Martínez FigueredoWellington Santos FavaAna Rita C Motta-CastroJames VenturiniSandra Maria do Vale Leone de OliveiraCrhistinne Cavalheiro Maymone GonçalvesMaria do Carmo Debur RossaGuilherme Nardi BeckerMayra Presibella GiacominiNelson Quallio MarquesIrina Nastassja RiedigerSonia Maria RaboniGabriela MattosoAllan D CataneoCamila ZanlucaClaudia N Duarte Dos SantosPatricia Akemi AssatoFelipe Allan da Silva da CostaMirele Daiana PoletiJessika Cristina Chagas LesbonElisangela Chicaroni MattosCecilia Artico BanhoLívia SacchettoMarília Mazzi MoraesRejane Maria Tommasini GrottoJayme A Souza-NetoMauricio Lacerda NogueiraHeidge FukumasuLuiz Lehmann CoutinhoRodrigo Tocantins CaladoRaul Machado NetoAna Maria Bispo de FilippisRivaldo Venancio da CunhaCarla FreitasCassio Roberto Leonel PeterkaCássia de Fátima Rangel FernandesWildo Navegantes de AraújoRodrigo Fabiano do Carmo SaidCarlos Frederico Campelo de Albuquerque E MeloMaria AlmironPaul S WikramaratnaTulio de OliveiraEdward C HolmesRicardo HaddadSandra Coccuzzo SampaioMaria Carolina EliasSimone KashimaLuiz Carlos Junior AlcantaraDimas Tadeu CovasPublished in: Nature microbiology (2022)
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.