Evolution and epidemic spread of SARS-CoV-2 in Brazil.
Darlan da Silva CandidoIngra Morales ClaroJaqueline Góes de JesusWilliam Marciel de SouzaFilipe Romero Rebello MoreiraSimon DellicourThomas A MellanLouis du PlessisRafael Henrique Moraes PereiraFlávia Cristina Silva SalesErika Regina ManuliJulien ThézéLuiz Gonzaga Paula de AlmeidaMariane Talon de MenezesCarolina Moreira VolochMarcilio Jorge FumagalliThaís de Moura ColettiCamila Alves Maia da SilvaMariana Severo RamundoMariene Ribeiro AmorimHenrique H HoeltgebaumSwapnil MishraMandev S GillLuiz Max Fagundes de CarvalhoLewis Fletcher BussCarlos Augusto Prete JuniorJordan AshworthHelder Takashi Imoto NakayaPedro S PeixotoOliver J BradySamuel M NichollsAmilcar TanuriAtila Duque RossiCarlos K V BragaAlexandra Lehmkuhl GerberAna Paula de Campos GuimarãesNelson GaburoCecilia Salete AlencarAlessandro C de S FerreiraCristiano X LimaJosé Eduardo LeviCelso GranatoGiulia M FerreiraRonaldo S FranciscoFabiana GranjaMárcia Teixeira GarciaMaria Luiza MorettiMauricio Wesley Perroud JuniorTerezinha Marta Pereira Pinto CastiñeirasCarolina S LazariSarah C HillAndreza Aruska de Souza SantosCamila Lopes SimeoniJulia ForatoAndrei Carvalho SpositoAngélica Zaninelli SchreiberMagnun N N SantosCamila Zolini de SáRenan Pedra de SouzaLuciana C Resende-MoreiraMauro Martins TexeiraJosy HubnerPatrícia Falabella LemeRennan Garcias MoreiraMauricio Lacerda Nogueiranull nullNeil M FergusonSílvia Figueiredo CostaJosé Luis Proença ModenaAna Tereza Ribeiro de VasconcelosSamir BhattPhilippe LemeyChieh-Hsi WuAndrew RambautNicholas James LomanRenato Santana de AguiarOliver George PybusEster Cerdeira SabinoNuno Rodrigues FariaPublished in: Science (New York, N.Y.) (2020)
Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.