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Evolution and epidemic spread of SARS-CoV-2 in Brazil
Science ( IF 44.7 ) Pub Date : 2020-07-23 , DOI: 10.1126/science.abd2161
Darlan S Candido _{1,

2} , Ingra M Claro _{2,

3} , Jaqueline G de Jesus _{2,

3} , William M Souza ₄ , Filipe R R Moreira ₅ , Simon Dellicour _{6,

7} , Thomas A Mellan ₈ , Louis du Plessis ₁ , Rafael H M Pereira ₉ , Flavia C S Sales _{2,

3} , Erika R Manuli _{2,

3} , Julien Thézé ₁₀ , Luiz Almeida ₁₁ , Mariane T Menezes ₅ , Carolina M Voloch ₅ , Marcilio J Fumagalli ₄ , Thaís M Coletti _{2,

3} , Camila A M da Silva _{2,

3} , Mariana S Ramundo _{2,

3} , Mariene R Amorim ₁₂ , Henrique H Hoeltgebaum ₁₃ , Swapnil Mishra ₈ , Mandev S Gill ₇ , Luiz M Carvalho ₁₄ , Lewis F Buss ₂ , Carlos A Prete ₁₅ , Jordan Ashworth ₁₆ , Helder I Nakaya ₁₇ , Pedro S Peixoto ₁₈ , Oliver J Brady _{19,

20} , Samuel M Nicholls ₂₁ , Amilcar Tanuri ₅ , Átila D Rossi ₅ , Carlos K V Braga ₉ , Alexandra L Gerber ₁₁ , Ana Paula de C Guimarães ₁₁ , Nelson Gaburo ₂₂ , Cecila Salete Alencar ₂₃ , Alessandro C S Ferreira ₂₄ , Cristiano X Lima _{25,

26} , José Eduardo Levi ₂₇ , Celso Granato ₂₈ , Giulia M Ferreira ₂₉ , Ronaldo S Francisco ₁₁ , Fabiana Granja _{12,

30} , Marcia T Garcia ₃₁ , Maria Luiza Moretti ₃₁ , Mauricio W Perroud ₃₂ , Terezinha M P P Castiñeiras ₃₃ , Carolina S Lazari ₃₄ , Sarah C Hill _{1,

35} , Andreza Aruska de Souza Santos ₃₆ , Camila L Simeoni ₁₂ , Julia Forato ₁₂ , Andrei C Sposito ₃₇ , Angelica Z Schreiber ₃₈ , Magnun N N Santos ₃₈ , Camila Zolini de Sá ₃₉ , Renan P Souza ₃₉ , Luciana C Resende-Moreira ₄₀ , Mauro M Teixeira ₄₁ , Josy Hubner ₄₂ , Patricia A F Leme ₄₃ , Rennan G Moreira ₄₄ , Maurício L Nogueira ₄₅ , , Neil M Ferguson ₈ , Silvia F Costa _{2,

3} , José Luiz Proenca-Modena ₁₂ , Ana Tereza R Vasconcelos ₁₁ , Samir Bhatt ₈ , Philippe Lemey ₇ , Chieh-Hsi Wu ₄₆ , Andrew Rambaut ₄₇ , Nick J Loman ₂₁ , Renato S Aguiar ₃₉ , Oliver G Pybus ₁ , Ester C Sabino _{2,

3} , Nuno Rodrigues Faria _{1,

2,

8}

Affiliation

Department of Zoology, University of Oxford, Oxford, UK.
Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
Centro de Pesquisa em Virologia, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, Brazil.
Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium.
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
Institute for Applied Economic Research, Brasília, Brazil.
Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France.
Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
Department of Mathematics, Imperial College London, London, UK.
Escola de Matemática Aplicada (EMAp), Fundação Getúlio Vargas, Rio de Janeiro, Brazil.
Department of Electronic Systems Engineering, University of São Paulo, São Paulo, Brazil.
Usher Institute, University of Edinburgh, Edinburgh, UK.
Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
Departamento de Matemática Aplicada, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil.
Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.
Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
DB Diagnósticos do Brasil, São Paulo, Brazil.
LIM 03 Laboratório de Medicina Laboratorial, Hospital das Clínicas Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
Instituto Hermes Pardini, Belo Horizonte, Brazil.
Departamento de Cirurgia, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Simile Instituto de Imunologia Aplicada Ltda, Belo Horizonte, Brazil.
Laboratório DASA, São Paulo, Brazil.
Laboratório Fleury, São Paulo, Brazil.
Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil.
Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Boa Vista, Brazil.
Divisão de Doenças Infecciosas, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, Brazil.
Hospital Estadual Sumaré, Universidade Estadual de Campinas, Campinas, Brazil.
Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
Divisão de Laboratório Central do Hospital das Clínicas, da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK.
University of Oxford, Latin American Centre, Oxford School of Global and Area Studies, Oxford, UK.
Departamento de Clínica Médica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, Brazil.
Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, Brazil.
Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Centro de Saúde da Comunidade, Universidade Estadual de Campinas, Campinas, Brazil.
Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil.
Mathematical Sciences, University of Southampton, Southampton, UK.
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.

The spread of SARS-CoV-2 in Brazil Brazil has been hard-hit by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Candido et al. combined genomic and epidemiological analyses to investigate the impact of nonpharmaceutical interventions (NPIs) in the country. By setting up a network of genomic laboratories using harmonized protocols, the researchers found a 29% positive rate for SARS-CoV-2 among collected samples. More than 100 international introductions of SARS-CoV-2 into Brazil were identified, including three clades introduced from Europe that were already well established before the implementation of NPIs and travel bans. The virus spread from urban centers to the rest of the country, along with a 25% increase in the average distance traveled by air passengers before travel bans, despite an overall drop in short-haul travel. Unfortunately, the evidence confirms that current interventions remain insufficient to keep virus transmission under control in Brazil. Science, this issue p. 1255 Large, highly connected urban centers drove virus spread across Brazil after introduction from Europe. 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.

中文翻译：

巴西 SARS-CoV-2 的演变和流行病传播

SARS-CoV-2 在巴西的传播巴西受到严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 大流行的严重打击。坎迪多等人。结合基因组和流行病学分析来调查非药物干预措施 (NPI) 在该国的影响。通过使用统一协议建立基因组实验室网络，研究人员发现收集的样本中 SARS-CoV-2 的阳性率为 29%。巴西发现了 100 多个 SARS-CoV-2 的国际传入，其中包括三个从欧洲引入的进化枝，这些进化枝在 NPI 和旅行禁令实施之前就已经很成熟。该病毒从城市中心传播到该国其他地区，尽管短途旅行总体下降，但在旅行禁令之前，航空乘客的平均旅行距离增加了 25%。不幸的是，证据证实，目前的干预措施仍然不足以控制病毒在巴西的传播。科学，本期第 14 页。 1255 从欧洲传入后，大型、高度互联的城市中心推动病毒在巴西各地传播。巴西目前是世界上严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 疫情增长最快的国家之一。由于可用数据有限，评估非药物干预措施 (NPI) 对这种病毒传播的影响仍然具有挑战性。使用流动性驱动的传播模型，我们发现非营利机构将圣保罗和里约热内卢的繁殖数从 >3 减少到 1 再到 1.6。对 427 个新基因组进行测序并对具有地理代表性的基因组数据集进行分析，确定了超过 100 种国际病毒传入巴西。我们估计，大多数（76%）巴西毒株属于2020年2月22日至3月11日期间从欧洲引入的三个分支。在流行初期，我们发现SARS-CoV-2主要在本地和州境内传播。在此期间之后，尽管航空旅行急剧减少，但我们估计大型城市中心的多次出口与国内航班平均旅行距离增加了 25%。这项研究为巴西 SARS-CoV-2 谱系的流行病传播和进化轨迹提供了新的线索，并提供证据表明当前的干预措施仍不足以控制该国的病毒传播。

更新日期：2020-07-23

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