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Emergence and Spread of the SARS-CoV-2 Variant of Concern Delta across Different Brazilian Regions.
Arantes, Ighor; Gomes Naveca, Felipe; Gräf, Tiago; Miyajima, Fábio; Faoro, Helisson; Luz Wallau, Gabriel; Delatorre, Edson; Reis Appolinario, Luciana; Cavalcante Pereira, Elisa; Venas, Tainá Moreira Martins; Sampaio Rocha, Alice; Serrano Lopes, Renata; Mendonça Siqueira, Marilda; Bello, Gonzalo; Cristina Resende, Paola.
  • Arantes I; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Gomes Naveca F; Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Gräf T; Laboratório de Ecologia de Doenças Transmissíveis da Amazônia (EDTA), Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz (FIOCRUZ), Manaus, Amazonas, Brazil.
  • Miyajima F; Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil.
  • Luz Wallau G; Analytical Competence Molecular Epidemiology Laboratory (ACME), Fundação Oswaldo Cruz (FIOCRUZ), Fortaleza, Ceará, Brazil.
  • Delatorre E; Instituto Carlos Chagas (ICC), Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Paraná, Brazil.
  • Reis Appolinario L; Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brazil.
  • Cavalcante Pereira E; Departamento de Biologia, Universidade Federal do Espirito Santo (UFES), Alegre, Espírito Santo, Brazil.
  • Venas TMM; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Sampaio Rocha A; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Serrano Lopes R; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Mendonça Siqueira M; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Bello G; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Cristina Resende P; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
Microbiol Spectr ; 10(5): e0264121, 2022 Oct 26.
Article in English | MEDLINE | ID: covidwho-2001793
ABSTRACT
The SARS-CoV-2 variant of concern (VOC) Delta was first detected in India in October 2020. The first imported cases of the Delta variant in Brazil were identified in April 2021 in the southern region, followed by more cases in different regions during the following months. By early September 2021, Delta was already the dominant variant in the southeastern (87%), southern (73%), and northeastern (52%) Brazilian regions. This study aimed to understand the spatiotemporal dissemination dynamics of Delta in Brazil. To this end, we employed a combination of maximum likelihood (ML) and Bayesian methods to reconstruct the evolutionary relationship of 2,264 VOC Delta complete genomes (482 from this study) recovered across 21 of the 27 Brazilian federal units. Our phylogeographic analyses identified three major transmission clusters of Delta in Brazil. The clade BR-I (n = 1,560) arose in Rio de Janeiro in late April 2021 and was the major cluster behind the dissemination of the VOC Delta in the southeastern, northeastern, northern, and central-western regions. The AY.101 lineage (n = 207) that arose in the Paraná state in late April 2021 and aggregated the largest fraction of sampled genomes from the southern region. Lastly, the AY.46.3 lineage emerged in Brazil in the São Paulo state in early June 2021 and remained mostly restricted to this state. In the rapid turnover of viral variants characteristic of the SARS-CoV-2 pandemic, Brazilian regions seem to occupy different stages of an increasing prevalence of the VOC Delta in their epidemic profiles. This process demands continuous genomic and epidemiological surveillance toward identifying and mitigating new introductions, limiting their dissemination, and preventing the establishment of more significant outbreaks in a population already heavily affected by the COVID-19 pandemic. IMPORTANCE Amid the SARS-CoV-2 continuously changing epidemic profile, this study details the space-time dynamics of the emergence of the Delta lineage across Brazilian territories, pointing out its multiple introductions in the country and its most prevalent sublineages. Some of these sublineages have their emergence, alongside their genomic composition and geographic distribution, detailed here for the first time. A special focus is given to the emergence process of Delta outside the country's south and southeast regions, the most populated and subjects of most published SARS-CoV-2 studies in Brazil. In summary, the study allows a better comprehension of the evolution process of a SARS-CoV-2 lineage that would be associated with a significant recrudescence of the pandemic in Brazil.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: South America / Brazil Language: English Journal: Microbiol Spectr Year: 2022 Document Type: Article Affiliation country: Spectrum.02641-21

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: South America / Brazil Language: English Journal: Microbiol Spectr Year: 2022 Document Type: Article Affiliation country: Spectrum.02641-21