Evolution and epidemic spread of SARS-CoV-2 in Brazil.
Darlan da Silva Candido,Darlan da Silva Candido,Ingra Morales Claro,Jaqueline Goes de Jesus,William Marciel de Souza,Filipe R. R. Moreira,Simon Dellicour,Simon Dellicour,Thomas A. Mellan,Louis du Plessis,Rafael Henrique Moraes Pereira,Flavia C. S. Sales,Erika R. Manuli,Julien Thézé,Luiz Carlos de Almeida,Mariane Talon de Menezes,Carolina M. Voloch,Marcílio Jorge Fumagalli,Thais M. Coletti,Camila A. M. Silva,Mariana S. Ramundo,Mariene R. Amorim,Henrique Hoeltgebaum,Swapnil Mishra,Mandev S. Gill,Luiz Max Carvalho,Lewis F Buss,Carlos A. Prete,Jordan Ashworth,Helder I. Nakaya,Pedro S. Peixoto,Oliver J. Brady,Samuel M. Nicholls,Amilcar Tanuri,Átila Duque Rossi,Carlos Kaue Vieira Braga,Alexandra L. Gerber,Ana Paula de C Guimarães,Nelson Gaburo,Cecila Salete Alencar,Alessandro C. S. Ferreira,Cristiano Xavier Lima,José Eduardo Levi,Celso Francisco Hernandes Granato,Giulia M. Ferreira,Ronaldo da Silva Francisco,Fabiana Granja,Fabiana Granja,Márcia Teixeira Garcia,Maria Luiza Moretti,Mauricio W. Perroud,Terezinha M. P. P. Castineiras,Carolina S. Lazari,Sarah C. Hill,Sarah C. Hill,Andreza Aruska de Souza Santos,Camila L. Simeoni,Julia Forato,Andrei C. Sposito,Angelica Zaninelli Schreiber,Magnun N. N. Santos,Camila Zolini de Sá,Renan P. Souza,Luciana C. Resende-Moreira,Mauro M. Teixeira,Josy Hubner,Patricia Asfora Falabella Leme,Rennan G. Moreira,Maurício Lacerda Nogueira,Neil M. Ferguson,Silvia Figueiredo Costa,José Luiz Proença-Módena,Ana Tereza Ribeiro de Vasconcelos,Samir Bhatt,Philippe Lemey,Chieh-Hsi Wu,Andrew Rambaut,Nicholas J. Loman,Renato Santana Aguiar,Oliver G. Pybus,Ester Cerdeira Sabino,Ester Cerdeira Sabino,Ester Cerdeira Sabino,Nuno R. Faria,Nuno R. Faria,Nuno R. Faria +85 more
TLDR
New light is shed on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and evidence that current interventions remain insufficient to keep virus transmission under control in this country is provided.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 Sao 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.read more
Citations
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Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.
Nuno R. Faria,Thomas A. Mellan,Charles Whittaker,Ingra Morales Claro,Darlan da Silva Candido,Darlan da Silva Candido,Swapnil Mishra,Myuki A E Crispim,Flavia C. S. Sales,Iwona Hawryluk,John T. McCrone,Ruben J.G. Hulswit,Lucas A M Franco,Mariana S. Ramundo,Jaqueline Goes de Jesus,Pamela S Andrade,Thais M. Coletti,Giulia M. Ferreira,Camila A. M. Silva,Erika R. Manuli,Rafael Henrique Moraes Pereira,Pedro S. Peixoto,Moritz U. G. Kraemer,Nelson Gaburo,Cecilia da C. Camilo,Henrique Hoeltgebaum,William Marciel de Souza,Esmenia C. Rocha,Leandro Marques de Souza,Mariana C. Pinho,Leonardo José Tadeu de Araújo,Frederico S V Malta,Aline B. de Lima,Joice do P. Silva,Danielle A G Zauli,Alessandro C. S. Ferreira,Ricardo P Schnekenberg,Daniel J Laydon,Patrick G T Walker,Hannah M. Schlüter,Ana L. P. dos Santos,Maria S. Vidal,Valentina S. Del Caro,Rosinaldo M. F. Filho,Helem M. dos Santos,Renato Santana Aguiar,José Luiz Proença-Módena,Bruce Walker Nelson,James A. Hay,Melodie Monod,Xenia Miscouridou,Helen Coupland,Raphael Sonabend,Michaela A. C. Vollmer,Axel Gandy,Carlos A. Prete,Vitor H. Nascimento,Marc A. Suchard,Thomas A. Bowden,Sergei L Kosakovsky Pond,Chieh-Hsi Wu,Oliver Ratmann,Neil M. Ferguson,Christopher Dye,Nicholas J. Loman,Philippe Lemey,Andrew Rambaut,Nelson Abrahim Fraiji,Maria Perpétuo Socorro Sampaio Carvalho,Oliver G. Pybus,Oliver G. Pybus,Seth Flaxman,Samir Bhatt,Samir Bhatt,Ester Cerdeira Sabino +74 more
TL;DR: In this article, the authors used a two-category dynamical model that integrates genomic and mortality data to estimate that P.1 may be 1.7-to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.
Journal ArticleDOI
Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans.
Bas B. Oude Munnink,Reina S. Sikkema,David F. Nieuwenhuijse,Robert Jan Molenaar,Emmanuelle Munger,Richard Molenkamp,Arco N. van der Spek,Paulien Tolsma,Ariene Rietveld,Miranda Brouwer,Noortje Bouwmeester-Vincken,Frank Harders,Renate Hakze-van der Honing,Marjolein C.A. Wegdam-Blans,Ruth Bouwstra,Corine H. GeurtsvanKessel,Annemiek A. van der Eijk,Francisca C. Velkers,Lidwien A.M. Smit,Arjan Stegeman,Wim H.M. van der Poel,Marion Koopmans +21 more
TL;DR: The SARS-CoV-2 virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection.
Journal ArticleDOI
The biological and clinical significance of emerging SARS-CoV-2 variants.
Kaiming Tao,Philip L Tzou,Janin Nouhin,Ravindra K. Gupta,Tulio de Oliveira,Sergei L Kosakovsky Pond,Daniela Fera,Robert W. Shafer +7 more
TL;DR: The emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic has been witnessed as mentioned in this paper.
Journal ArticleDOI
COVID-19 and the human innate immune system.
TL;DR: In this article, a conceptual framework for the interaction of the human innate immune system with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was provided to link the clinical observations with experimental findings that have been made during the first year of the pandemic.
Journal ArticleDOI
Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic.
Lewis F Buss,Carlos A. Prete,Claudia M. M. Abrahim,Alfredo Mendrone,Tassila Salomon,Cesar de Almeida-Neto,Rafael F. O. França,Maria C Belotti,Maria Perpétuo Socorro Sampaio Carvalho,Allyson Guimarães Costa,Myuki A E Crispim,Suzete C. Ferreira,Nelson Abrahim Fraiji,Susie Gurzenda,Charles Whittaker,Leonardo Tadashi Kamaura,Pedro L. Takecian,Pedro S. Peixoto,Marcio K. Oikawa,Anna S. Nishiya,Vanderson Rocha,Nanci A. Salles,Andreza Aruska de Souza Santos,Martirene A da Silva,Brian Custer,Kris V Parag,Manoel Barral-Netto,Moritz U. G. Kraemer,Rafael Henrique Moraes Pereira,Oliver G. Pybus,Michael P. Busch,Marcia C. Castro,Christopher Dye,Vitor H. Nascimento,Nuno R. Faria,Nuno R. Faria,Nuno R. Faria,Ester Cerdeira Sabino +37 more
TL;DR: The spread of COVID-19 in Manaus, Brazil, shows that a largely unmitigated epidemic can infect a high fraction of the population and cause high mortality, and confirms that when poorly controlled, CO VID-19 caninfect a large proportion of the Population, causing high mortality.
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