Dataset Information

Evolution and epidemic spread of SARS-CoV-2 in Brazil.

ABSTRACT: 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.

SUBMITTER: Candido DS

PROVIDER: S-EPMC7402630 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Evolution and epidemic spread of SARS-CoV-2 in Brazil.

Candido Darlan S DS Claro Ingra M IM de Jesus Jaqueline G JG Souza William M WM Moreira Filipe R R FRR Dellicour Simon S Mellan Thomas A TA du Plessis Louis L Pereira Rafael H M RHM Sales Flavia C S FCS Manuli Erika R ER Thézé Julien J Almeida Luiz L Menezes Mariane T MT Voloch Carolina M CM Fumagalli Marcilio J MJ Coletti Thaís M TM da Silva Camila A M CAM Ramundo Mariana S MS Amorim Mariene R MR Hoeltgebaum Henrique H HH Mishra Swapnil S Gill Mandev S MS Carvalho Luiz M LM Buss Lewis F LF Prete Carlos A CA Ashworth Jordan J Nakaya Helder I HI Peixoto Pedro S PS Brady Oliver J OJ Nicholls Samuel M SM Tanuri Amilcar A Rossi Átila D ÁD Braga Carlos K V CKV Gerber Alexandra L AL de C Guimarães Ana Paula AP Gaburo Nelson N Alencar Cecila Salete CS Ferreira Alessandro C S ACS Lima Cristiano X CX Levi José Eduardo JE Granato Celso C Ferreira Giulia M GM Francisco Ronaldo S RS Granja Fabiana F Garcia Marcia T MT Moretti Maria Luiza ML Perroud Mauricio W MW Castiñeiras Terezinha M P P TMPP Lazari Carolina S CS Hill Sarah C SC de Souza Santos Andreza Aruska AA Simeoni Camila L CL Forato Julia J Sposito Andrei C AC Schreiber Angelica Z AZ Santos Magnun N N MNN de Sá Camila Zolini CZ Souza Renan P RP Resende-Moreira Luciana C LC Teixeira Mauro M MM Hubner Josy J Leme Patricia A F PAF Moreira Rennan G RG Nogueira Maurício L ML Ferguson Neil M NM Costa Silvia F SF Proenca-Modena José Luiz JL Vasconcelos Ana Tereza R ATR Bhatt Samir S Lemey Philippe P Wu Chieh-Hsi CH Rambaut Andrew A Loman Nick J NJ Aguiar Renato S RS Pybus Oliver G OG Sabino Ester C EC Faria Nuno Rodrigues NR

Science (New York, N.Y.) 20200723 6508

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 representativ ...[more]

PMID: 32703910

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Project description:Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS-CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS-CoV-2 whole-genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020-February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS-CoV-2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021.

Dataset Information

Evolution and epidemic spread of SARS-CoV-2 in Brazil.

Publications

Evolution and epidemic spread of SARS-CoV-2 in Brazil.

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