Dataset Information

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.

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.

SUBMITTER: Giovanetti M

PROVIDER: S-EPMC8978948 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.

Giovanetti Marta M Slavov Svetoslav Nanev SN Fonseca Vagner V Wilkinson Eduan E Tegally Houriiyah H Patané José Salvatore Leister JSL Viala Vincent Louis VL San James Emmanuel JE Rodrigues Evandra Strazza ES Santos Elaine Vieira EV Aburjaile Flavia F Xavier Joilson J Fritsch Hegger H Adelino Talita Emile Ribeiro TER Pereira Felicidade F Leal Arabela A de Melo Iani Felipe Campos FC de Carvalho Pereira Glauco G Vazquez Cynthia C Mercedes Estigarribia Sanabria Gladys G de Oliveira Elaine Cristina EC Demarchi Luiz L Croda Julio J Dos Santos Bezerra Rafael R de Lima Loyze Paola Oliveira LPO Martins Antonio Jorge AJ Dos Santos Barros Claudia Renata CR Marqueze Elaine Cristina EC de Souza Todao Bernardino Jardelina J Moretti Debora Botequio DB Brassaloti Ricardo Augusto RA de Lello Rocha Campos Cassano Raquel R Mariani Pilar Drummond Sampaio Corrêa PDSC Kitajima João Paulo JP Santos Bibiana B Proto-Siqueira Rodrigo R Cantarelli Vlademir Vicente VV Tosta Stephane S Nardy Vanessa Brandão VB de Oliveira da Silva Luciana Reboredo LR Kelly Astete Gómez Marcela M Lima Jaqueline Gomes JG Ribeiro Adriana Aparecida AA Guimarães Natália Rocha NR Watanabe Luiz Takao LT Da Silva Luana Barbosa LB da Silva Ferreira Raquel R da Penha Mara Patricia F MPF Ortega María José MJ de la Fuente Andrea Gómez AG Villalba Shirley S Torales Juan J Gamarra María Liz ML Aquino Carolina C Martínez Figueredo Gloria Patricia GP Fava Wellington Santos WS Motta-Castro Ana Rita C ARC Venturini James J de Oliveira Sandra Maria do Vale Leone SMDVL Gonçalves Crhistinne Cavalheiro Maymone CCM do Carmo Debur Rossa Maria M Becker Guilherme Nardi GN Presibella Mayra Marinho MM Marques Nelson Quallio NQ Riediger Irina Nastassja IN Raboni Sonia S Coelho Gabriela Mattoso GM Cataneo Allan Henrique Depieri AHD Zanluca Camila C Dos Santos Claudia N Duarte CND Assato Patricia Akemi PA da Costa Felipe Allan da Silva FADS Poleti Mirele Daiana MD Lesbon Jessika Cristina Chagas JCC Mattos Elisangela Chicaroni EC Banho Cecilia Artico CA Sacchetto Lívia L Moraes Marília Mazzi MM Grotto Rejane Maria Tommasini RMT Souza-Neto Jayme A JA Nogueira Maurício Lacerda ML Fukumasu Heidge H Coutinho Luiz Lehmann LL Calado Rodrigo Tocantins RT Neto Raul Machado RM de Filippis Ana Maria Bispo AMB da Cunha Rivaldo Venancio RV Freitas Carla C Peterka Cassio Roberto Leonel CRL de Fátima Rangel Fernandes Cássia C de Araújo Wildo Navegantes WN do Carmo Said Rodrigo Fabiano RF Almiron Maria M de Albuquerque E Melo Carlos Frederico Campelo CFC Lourenço José J de Oliveira Tulio T Holmes Edward C EC Haddad Ricardo R Sampaio Sandra Coccuzzo SC Elias Maria Carolina MC Kashima Simone S de Alcantara Luiz Carlos Junior LCJ Covas Dimas Tadeu DT

medRxiv : the preprint server for health sciences 20220328

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 ...[more]

PMID: 35378755

Similar Datasets

Project description:BackgroundAdvances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe.MethodsWe performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods.FindingsOf 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak.InterpretationInitial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies.FundingWHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.

Dataset Information

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.

Publications

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets