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Published June 21, 2023 | Version v1
Dataset Open

Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil

Creators

  • 1. Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
  • 2. University of Oxford
  • 3. Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
  • 4. Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
  • 5. Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom
  • 6. Laboratório de Patologia Veterinária, Hospital Veterinário UFPR, PR Brazil
  • 7. Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
  • 8. Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil;
  • 9. Evandro Chagas Institute, Para, Brazil
  • 10. Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
  • 11. Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia,Goiás, Brazil
  • 12. Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasília. Brasília, DF 70636- 200, Brazil
  • 13. Environmental Health Surveillance, Directorate of the Federal District (DIVAL), DF 70790-060, Brazil.
  • 14. Veterinary Pathology Laboratory, Campus Darcy Ribeiro, University of Brasília. Brasília, DF 70636- 200, Brazil; Graduate Program in Animal Sciences, College of Agronomy and Veterinary Medicine, University of Brasília, Brasília, DF 70910-900, Brazil
  • 15. Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, DF, Brazil
  • 16. Insect Behavior Laboratory, Federal Institute of Northern Minas Gerais, Salinas 39560-000, MG, Brazil
  • 17. Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, RS, Brazil\
  • 18. Faculdade de Medicina São Leopoldo Mandic, Campinas, SP, Brazil
  • 19. Superintendência de Vigilância em Saúde – SES – Santa Catarina
  • 20. Laboratorio central de Saude Publica de Santa Catarina
  • 21. Laboratório Central de Saúde Pública do Estado do Rio Grande do Sul
  • 22. Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Porto Alegre, RS, Brasil.
  • 23. Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, 05508-000, Brazil
  • 24. Oswaldo Cruz Foundation, Biodiversity, Wildlife Health Institutional Platform (PIBSS/Fiocruz), Rio de Janeiro, Brazil
  • 25. Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil
  • 26. Laboratory of Ecology of Diseases & Forests, NUPEB/ICEB, Federal University of Ouro Preto, Minas Gerais, Brazil
  • 27. Pandemic Prevention Initiative, The Rockefeller Foundation, Washington DC, USA
  • 28. School for Data Science and Computational Thinking, Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
  • 29. Secretaria de Vigilância em Saúde, SVS, Brazilian Ministry of Health, Brasilia, Federal District, Brazil
  • 30. Oswaldo Cruz Foundation, Fiocruz, Brasilia, Federal District, Brazil
  • 31. Secretaria Estadual de Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Porto Alegre, RS, Brasil
  • 32. Plataforma Institucional Biodiversidade e Saúde Silvestre - Centro de Informação em Saúde Silvestre (CISS) - Fiocruz/RJ
  • 33. Secretaria da Saúde (São Paulo - Estado). Coordenadoria de Controle de Doenças (CCD). Instituto Pasteur (IP)
  • 34. State Department of Health of Santa Catarina, Brazil
  • 35. Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil; State Department of Health of Santa Catarina, Brazil
  • 36. Diretoria de Vigilância Epidemiológica da Secretaria de Estado da Saúde de Santa Catarina
  • 37. Secretaria de Estado da Saúde do Paraná, Brazil
  • 38. Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou—Fiocruz, Belo Horizonte 30190-002, MG, Brazil
  • 39. Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
  • 40. Fundação Oswaldo Cruz, Bio-Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
  • 41. Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington
  • 42. Pan American Health Organization/World Health Organization, Washington, DC, USA
  • 43. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
  • 44. BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa
  • 45. Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil

Description

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link the endemic north of the country with epidemic extra-Amazonian regions, are central to predicting and preventing future outbreak and epidemics. Here, we tracked the recent spread of the virus by integrating genome sequences with both epidemiological and vector data. Through a combination of phylogenetic and epidemiological models we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modelling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centres in the Southeast. Phylodynamic analysis unravelled the circulation of three distinct YFV lineages, and provided proof of the directionality of a known spatial corridor of viral spread that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology in a One Health framework can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.

Files

list_municipalities_FCOVER_map.csv

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