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Giovanetti M, Pereira LA, Santiago GA, Fonseca V, Mendoza MPG, de Oliveira C, de Moraes L, Xavier J, Tosta S, Fristch H, de Castro Barbosa E, Rodrigues ES, Figueroa-Romero D, Padilla-Rojas C, Cáceres-Rey O, Mendonça AF, de Bruycker Nogueira F, Venancio da Cunha R, de Filippis AMB, Freitas C, Peterka CRL, de Albuquerque CFC, Franco L, Méndez Rico JA, Muñoz-Jordán JL, Lemes da Silva V, Alcantara LCJ. Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Brazil. Emerg Infect Dis 2022; 28:1725-1727. [PMID: 35876608 PMCID: PMC9328905 DOI: 10.3201/eid2808.220550] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We used nanopore sequencing and phylogenetic analyses to identify a cosmopolitan genotype of dengue virus serotype 2 that was isolated from a 56-year-old male patient from the state of Goiás in Brazil. The emergence of a cosmopolitan genotype in Brazil will require risk assessment and surveillance to reduce epidemic potential.
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Alcantara LCJ, Nogueira E, Shuab G, Tosta S, Fristch H, Pimentel V, Souza-Neto JA, Coutinho LL, Fukumasu H, Sampaio SC, Elias MC, Kashima S, Slavov SN, Ciccozzi M, Cella E, Lourenco J, Fonseca V, Giovanetti M. SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves. Virus Res 2022; 315:198785. [PMID: 35461905 PMCID: PMC9022374 DOI: 10.1016/j.virusres.2022.198785] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023]
Abstract
Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. The COVID-19 epidemic in Brazil was characterised by the co-circulation of multiple variants as a consequence of multiple independent introduction events occurring through time. Here, we describe the SARS-CoV-2 variants that are currently circulating and co-circulating in the country, with the aim to highlight which variants have driven the different epidemic waves. For this purpose, we retrieved metadata information of Coronavirus sequences collected in Brazil and available at the GISAID database. SARS-CoV-2 lineages have been identified along with eleven variants, labelled as VOCs (Alpha, Gamma, Beta, Delta and Omicron) VOIs (Lambda and Mu) VUMs (B.1.1.318) and FMVs (Zeta, Eta and B.1.1.519). Here we show that, in the Brazilian context, after 24 months of sustained transmission and evolution of SARS-CoV-2, local variants (among them the B.1.1.28 and B.1.1.33) were displaced by recently introduced VOCs firstly with the Gamma, followed by Delta and more recently Omicron. The rapid spread of some of those VOCs (such as Gamma and Omicron) was also mirror by a large increase in the number of cases and deaths in the country. This in turn reinforces that, due to the emergence of variants that appear to induce a substantial evasion against neutralizing antibody response, it is important to strengthen genomic effort within the country and how vaccination still remains a critical process to protect the vulnerable population, still at risk of infection and death.
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Affiliation(s)
- Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil,Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil,Corresponding author
| | - Elisson Nogueira
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Shuab
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Hegger Fristch
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Portugal
| | - Jayme A. Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil
| | | | | | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Svetoslav Nanev Slavov
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - José Lourenco
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK,Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Portugal
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa,Corresponding author
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil,Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil,Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy,Corresponding author
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