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Literature detail

Evolution and spillover dynamics of yellow fever at the forest-urban interface in Brazil.

Juliana Telles-de-Deus1 Ingra M Claro2,3,4,5 Mayara Bertanhe2,3,4 Charles Whittaker4,6 Márcio Port-Carvalho7,8 Esmenia C Rocha2,3,9 Thaís M Coletti2,3 Camila A M da Silva2,3 Ian Nunes Valença2,3,4 Tamara N Lima-Camara9 Márcia Bicudo de Paula9 Mariana S Cunha3,10 Jaqueline G de Jesus2,3 Pâmela Dos Santos Andrade2,3,9 Victoria Cox4 Natalia C C F de Azevedo11 Juliana M Guerra11 Juliana L Summa12 Ana Paula P Teixeira13 Eduardo S Bergo14 Mariza Pereira14 Filipe R R Moreira4,15 Alvina Clara Felix2,3 Anderson V de Paula2,3 Raissa H de Araujo Eliodoro2,3 Marissa da Silva Lima2,3 Franciane M de Oliveira2,3 Valquíria R de Souza2,3 Lucas A M Franco2,3 Marcelo S Nardi12 Thais C Sanches12 Eric T B C da Silva12 Amanda A C Coimbra12 Paulo R Dos Santos12 Katherine Lima de Gouveia16 Francisco E S P Vilela6 Sarah C Hill17 Dilmar A G Oliveira18 Hélia M Piedade18 Thaís Guimarães-Luiz18 Camila M G Abreu18 Guilherme Casoni da Rocha18 Leandro Abade19 William M de Souza5 Ben Lambert20,21 Renato Pereira de Souza22 Adriano Pinter23 Ester C Sabino2,3 Luis Filipe Mucci24 Nuno R Faria25,26,27
Affiliations 27 institutions
  1. Secretaria de Estado da Saúde de São Paulo, Instituto Pasteur, São Paulo, Brazil. [email protected].
  2. Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
  3. Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
  4. MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
  5. Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA.
  6. Division of Infectious Diseases & Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA.
  7. Conservation Biodiversity Nucleus, Environmental Research Institute, Secretariat for the Environment, Infrastructure and Logistics of São Paulo, São Paulo, Brazil.
  8. Post-Graduation Program in Biodiversity of Conservations Units, National School of Tropical Botanic, Rio de Janeiro Botanical Garden, Rio de Janeiro, Brazil.
  9. Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
  10. Centro de Virologia, Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil.
  11. Núcleo de Anatomia Patológica, Instituto Adolfo Lutz, São Paulo, Brazil.
  12. Divisão da Fauna Silvestre, Secretaria do Verde e Meio Ambiente da Prefeitura de São Paulo, São Paulo, Brazil.
  13. São Paulo Municipal Department of Health, São Paulo, Brazil.
  14. Secretaria de Estado da Saúde de São Paulo, Instituto Pasteur, São Paulo, Brazil.
  15. Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
  16. Parque Estadual Alberto Löfgren, Secretaria do Meio Ambiente do Governo do Estado de São Paulo, São Paulo, São Paulo, Brazil.
  17. Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK.
  18. Departamento de Gestão da Fauna Silvestre, Coordenadoria de Fauna Silvestre, Secretaria de Meio Ambiente, Infraestrutura e Logística do Estado de São Paulo, São Paulo, Brazil.
  19. St Mary's University, Twickenham London, Twickenham, UK.
  20. Department of Statistics, University of Oxford, Oxford, UK.
  21. Pandemic Sciences Institute, University of Oxford, Oxford, UK.
  22. Centro de Laboratório Regional XII, Núcleo de Ciências Biológicas, Instituto Adolfo Lutz, Taubaté, São Paulo, Brazil.
  23. Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil.
  24. Secretaria de Estado da Saúde de São Paulo, Instituto Pasteur, São Paulo, Brazil. [email protected].
  25. Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil. [email protected].
  26. Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil. [email protected].
  27. MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK. [email protected].
PMID 41813975 2026 Nat Microbiol eng ppublish
PubMed DOI Browse context

Article

Publication summary

Yellow fever virus (YFV) continues to threaten human and wildlife populations in the Americas, yet its transmission at the forest-urban interface remains unclear. Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018. Our analyses reveal that transmission was primarily driven by a single genetic cluster introduced during a period of high abundance of the main vector, Haemagogus leucocelaenus mosquitoes. A near-complete hepatitis A virus genome was detected in a YFV-infected howler monkey, suggesting potential co-infections at the human-wildlife interface. Phylogenetic and epidemiological modelling estimated a basic reproduction number, R<sub>0</sub>, for sylvatic yellow fever of 8.2 (95% CI 5.1-12.2), substantially higher than previous estimates for urban outbreaks. Our findings demonstrate that multisource surveillance could provide actionable early warnings in regions at risk for zoonotic spillover.

Yellow Fever Yellow fever virus Animals Brazil Cities Culicidae Disease Outbreaks Forests Genome, Viral Humans Mosquito Vectors Phylogeny Zoonoses

Structured evidence records

Evidence records

5 total
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.90
Key finding

Phylogenetic analysis identified a single genetic cluster of yellow fever virus as the main driver of the sylvatic outbreak in São Paulo, Brazil.

Virus
YFV
Location
Not specified
Supporting text

Our analyses reveal that transmission was primarily driven by a single genetic cluster introduced during a period of high abundance of the main vector, Haemagogus leucocelaenus mosquitoes.

Genes or proteins
whole genome
Analysis methods
viral metagenomics; phylogenetic analysis
Genomic Evolution Extraction confidence 0.85
Key finding

Viral metagenomics detected a near-complete hepatitis A virus genome in a YFV-infected howler monkey, indicating co-infection and multiple viral genomes in the host.

Virus
HAV
Host
Alouatta
Location
Not specified
Supporting text

A near-complete hepatitis A virus genome was detected in a YFV-infected howler monkey, suggesting potential co-infections at the human-wildlife interface.

Genes or proteins
whole genome
Analysis methods
viral metagenomics
Zoonotic Surveillance 2 records
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Mosquito surveillance and monitoring of non-human primates revealed ongoing yellow fever virus circulation in a forest fragment within metropolitan São Paulo, Brazil, during 2017–2018.

Virus
YFV
Host
Culicidae
Location
Brazil Brazil
Supporting text

Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018.

Method
mosquito surveillance; viral metagenomics
Geographic raw
metropolitan São Paulo, Brazil
Country inferred
Brazil
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Systematic monitoring of non-human primate carcasses detected yellow fever virus circulation in the Atlantic Forest fragment in metropolitan São Paulo, Brazil, during 2017–2018.

Virus
YFV
Host
Primates
Location
Brazil Brazil
Supporting text

Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018.

Method
systematic monitoring; viral metagenomics
Sample type
carcasses
Geographic raw
metropolitan São Paulo, Brazil
Country inferred
Brazil
Spillover Event 1 records
Spillover Event Extraction confidence 0.80
Key finding

A sylvatic outbreak of yellow fever virus in forest fragments near urban São Paulo indicates animal-to-human spillover risk mediated by mosquitoes and non-human primates.

Virus
YFV
Location
Brazil Brazil
Supporting text

Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018. Our findings demonstrate that multisource surveillance could provide actionable early warnings in regions at risk for zoonotic spillover.

Method
mosquito surveillance; monitoring of primate carcasses; viral metagenomics; phylogenetic analysis; epidemiological modelling
Study design
field surveillance
Transmission direction
animal-to-human
Geographic raw
metropolitan São Paulo, Brazil
Country inferred
Brazil