Marta Giovanetti, Svetoslav Nanev Slavov, Vagner Fonseca, Eduan Wilkinson, Houriiyah Tegally, José Salvatore Leister Patané, Vincent Louis Viala, James Emmanuel San, Evandra Strazza Rodrigues, Elaine Vieira Santos, Flavia Aburjaile, Joilson Xavier, Hegger Fritsch, Talita Emile Ribeiro Adelino, Felicidade Pereira, Arabela Leal, Felipe Campos de Melo Iani, Glauco de Carvalho Pereira, Cynthia Vazquez, Gladys Mercedes Estigarribia Sanabria, Elaine Cristina de Oliveira, Luiz Demarchi, Julio Croda, Rafael Dos Santos Bezerra, Loyze Paola Oliveira de Lima, Antonio Jorge Martins, Claudia Renata Dos Santos Barros, Elaine Cristina Marqueze, Jardelina de Souza Todao Bernardino, Debora Botequio Moretti, Ricardo Augusto Brassaloti, Raquel de Lello Rocha Campos Cassano, Pilar Drummond Sampaio Corrêa Mariani, João Paulo Kitajima, Bibiana Santos, Rodrigo Proto-Siqueira, Vlademir Vicente Cantarelli, Stephane Tosta, Vanessa Brandão Nardy, Luciana Reboredo de Oliveira da Silva, Marcela Kelly Astete Gómez, Jaqueline Gomes Lima, Adriana Aparecida Ribeiro, Natália Rocha Guimarães, Luiz Takao Watanabe, Luana Barbosa Da Silva, Raquel da Silva Ferreira, Mara Patricia F da Penha, María José Ortega, Andrea Gómez de la Fuente, Shirley Villalba, Juan Torales, María Liz Gamarra, Carolina Aquino, Gloria Patricia Martínez Figueredo, Wellington Santos Fava, Ana Rita C Motta-Castro, James Venturini, Sandra Maria do Vale Leone de Oliveira, Crhistinne Cavalheiro Maymone Gonçalves, Maria do Carmo Debur Rossa, Guilherme Nardi Becker, Mayra Marinho Presibella, Nelson Quallio Marques, Irina Nastassja Riediger, Sonia Raboni, Gabriela Mattoso Coelho, Allan Henrique Depieri Cataneo, Camila Zanluca, Claudia N Duarte Dos Santos, Patricia Akemi Assato, Felipe Allan da Silva da Costa, Mirele Daiana Poleti, Jessika Cristina Chagas Lesbon, Elisangela Chicaroni Mattos, Cecilia Artico Banho, Lívia Sacchetto, Marília Mazzi Moraes, Rejane Maria Tommasini Grotto, Jayme A Souza-Neto, Maurício Lacerda Nogueira, Heidge Fukumasu, Luiz Lehmann Coutinho, Rodrigo Tocantins Calado, Raul Machado Neto, Ana Maria Bispo de Filippis, Rivaldo Venancio da Cunha, Carla Freitas, Cassio Roberto Leonel Peterka, Cássia de Fátima Rangel Fernandes, Wildo Navegantes de Araújo, Rodrigo Fabiano do Carmo Said, Maria Almiron, Carlos Frederico Campelo de Albuquerque E Melo, José Lourenço, Tulio de Oliveira, Edward C Holmes, Ricardo Haddad, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Simone Kashima, Luiz Carlos Junior de Alcantara, Dimas Tadeu Covas
{"title":"Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.","authors":"Marta Giovanetti, Svetoslav Nanev Slavov, Vagner Fonseca, Eduan Wilkinson, Houriiyah Tegally, José Salvatore Leister Patané, Vincent Louis Viala, James Emmanuel San, Evandra Strazza Rodrigues, Elaine Vieira Santos, Flavia Aburjaile, Joilson Xavier, Hegger Fritsch, Talita Emile Ribeiro Adelino, Felicidade Pereira, Arabela Leal, Felipe Campos de Melo Iani, Glauco de Carvalho Pereira, Cynthia Vazquez, Gladys Mercedes Estigarribia Sanabria, Elaine Cristina de Oliveira, Luiz Demarchi, Julio Croda, Rafael Dos Santos Bezerra, Loyze Paola Oliveira de Lima, Antonio Jorge Martins, Claudia Renata Dos Santos Barros, Elaine Cristina Marqueze, Jardelina de Souza Todao Bernardino, Debora Botequio Moretti, Ricardo Augusto Brassaloti, Raquel de Lello Rocha Campos Cassano, Pilar Drummond Sampaio Corrêa Mariani, João Paulo Kitajima, Bibiana Santos, Rodrigo Proto-Siqueira, Vlademir Vicente Cantarelli, Stephane Tosta, Vanessa Brandão Nardy, Luciana Reboredo de Oliveira da Silva, Marcela Kelly Astete Gómez, Jaqueline Gomes Lima, Adriana Aparecida Ribeiro, Natália Rocha Guimarães, Luiz Takao Watanabe, Luana Barbosa Da Silva, Raquel da Silva Ferreira, Mara Patricia F da Penha, María José Ortega, Andrea Gómez de la Fuente, Shirley Villalba, Juan Torales, María Liz Gamarra, Carolina Aquino, Gloria Patricia Martínez Figueredo, Wellington Santos Fava, Ana Rita C Motta-Castro, James Venturini, Sandra Maria do Vale Leone de Oliveira, Crhistinne Cavalheiro Maymone Gonçalves, Maria do Carmo Debur Rossa, Guilherme Nardi Becker, Mayra Marinho Presibella, Nelson Quallio Marques, Irina Nastassja Riediger, Sonia Raboni, Gabriela Mattoso Coelho, Allan Henrique Depieri Cataneo, Camila Zanluca, Claudia N Duarte Dos Santos, Patricia Akemi Assato, Felipe Allan da Silva da Costa, Mirele Daiana Poleti, Jessika Cristina Chagas Lesbon, Elisangela Chicaroni Mattos, Cecilia Artico Banho, Lívia Sacchetto, Marília Mazzi Moraes, Rejane Maria Tommasini Grotto, Jayme A Souza-Neto, Maurício Lacerda Nogueira, Heidge Fukumasu, Luiz Lehmann Coutinho, Rodrigo Tocantins Calado, Raul Machado Neto, Ana Maria Bispo de Filippis, Rivaldo Venancio da Cunha, Carla Freitas, Cassio Roberto Leonel Peterka, Cássia de Fátima Rangel Fernandes, Wildo Navegantes de Araújo, Rodrigo Fabiano do Carmo Said, Maria Almiron, Carlos Frederico Campelo de Albuquerque E Melo, José Lourenço, Tulio de Oliveira, Edward C Holmes, Ricardo Haddad, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Simone Kashima, Luiz Carlos Junior de Alcantara, Dimas Tadeu Covas","doi":"10.1101/2021.10.07.21264644","DOIUrl":null,"url":null,"abstract":"<p><p>Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.</p>","PeriodicalId":43551,"journal":{"name":"Lung Cancer Management","volume":"3 1","pages":""},"PeriodicalIF":0.9000,"publicationDate":"2022-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8978948/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Lung Cancer Management","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2021.10.07.21264644","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"RESPIRATORY SYSTEM","Score":null,"Total":0}
引用次数: 0
Abstract
Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.
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