OmniVira

Literature detail

Genomic and epidemiological monitoring of yellow fever virus transmission potential.

N R Faria1 M U G Kraemer2,3,4 S C Hill2 J Goes de Jesus5 R S Aguiar6 F C M Iani7,8 J Xavier5 J Quick9 L du Plessis2 S Dellicour10 J Thézé2 R D O Carvalho8 G Baele10 C-H Wu11 P P Silveira6 M B Arruda6 M A Pereira7 G C Pereira7 J Lourenço2 U Obolski2 L Abade2,12 T I Vasylyeva2 M Giovanetti5,8 D Yi13 D J Weiss14 G R W Wint2 F M Shearer14 S Funk15 B Nikolay16,17 V Fonseca8,18 T E R Adelino7 M A A Oliveira7 M V F Silva7 L Sacchetto8 P O Figueiredo8 I M Rezende8 E M Mello8 R F C Said19 D A Santos19 M L Ferraz19 M G Brito19 L F Santana19 M T Menezes6 R M Brindeiro6 A Tanuri6 F C P Dos Santos20 M S Cunha20 J S Nogueira20 I M Rocco20 A C da Costa21 S C V Komninakis22,23 V Azevedo8 A O Chieppe24 E S M Araujo5 M C L Mendonça5 C C Dos Santos5 C D Dos Santos5 A M Mares-Guia5 R M R Nogueira5 P C Sequeira5 R G Abreu25 M H O Garcia25 A L Abreu26 O Okumoto26 E G Kroon8 C F C de Albuquerque27 K Lewandowski28 S T Pullan28 M Carroll29 T de Oliveira5,18,30 E C Sabino21 R P Souza20 M A Suchard31,32 P Lemey10 G S Trindade8 B P Drumond8 A M B Filippis5 N J Loman9 S Cauchemez16,17 L C J Alcantara33,8 O G Pybus1
Affiliations 33 institutions
  1. Department of Zoology, University of Oxford, Oxford, UK. [email protected] [email protected] [email protected].
  2. Department of Zoology, University of Oxford, Oxford, UK.
  3. Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA.
  4. Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
  5. Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
  6. Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
  7. Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil.
  8. Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
  9. Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  10. Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
  11. Department of Statistics, University of Oxford, Oxford, UK.
  12. The Global Health Network, University of Oxford, Oxford, UK.
  13. Department of Statistics, Harvard University, Cambridge, MA, USA.
  14. Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  15. Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
  16. Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France.
  17. CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France.
  18. KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
  19. Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
  20. Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil.
  21. Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
  22. Retrovirology Laboratory, Federal University of São Paulo, São Paulo, Brazil.
  23. School of Medicine of ABC (FMABC), Clinical Immunology Laboratory, Santo André, São Paulo, Brazil.
  24. Coordenação de Vigilância Epidemiológica do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
  25. Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil.
  26. Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil.
  27. Organização Pan - Americana da Saúde/Organização Mundial da Saúde - (OPAS/OMS), Brasília-DF, Brazil.
  28. Public Health England, National Infections Service, Porton Down, Salisbury, UK.
  29. NIHR HPRU in Emerging and Zoonotic Infections, Public Health England, London, UK.
  30. Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
  31. Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA.
  32. Department of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA.
  33. Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil. [email protected] [email protected] [email protected].
PMID 30139911 2018 Science eng ppublish
PubMed DOI Browse context

Article

Publication summary

The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian <i>Aedes</i> species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.

Epidemiological Monitoring Aedes Age Factors Animals Brazil Disease Outbreaks Evolution, Molecular Genomics Humans Phylogeny Polymerase Chain Reaction Risk Sex Factors Spatio-Temporal Analysis Yellow Fever Yellow fever virus

Structured evidence records

Evidence records

3 total
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.85
Key finding

Locally generated YFV genome sequences showed evidence of an early phase of sylvatic yellow fever virus transmission and evolutionary spread into new geographic areas in Brazil.

Virus
YFV
Location
Not specified
Supporting text

Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas.

Genes or proteins
whole genome
Analysis methods
genomic analysis; phylogenetic analysis
Spillover Event 1 records
Spillover Event Extraction confidence 0.95
Key finding

Yellow fever virus spilled over from sylvatic animal hosts to humans in Brazil during the 2016 epidemic.

Virus
YFV
Location
Brazil Brazil
Supporting text

Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016.

Method
epidemiological analysis; spatial analysis; genomic sequencing
Study design
genomic surveillance
Transmission direction
animal-to-human
Geographic raw
Brazil
Country inferred
Brazil
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.90
Key finding

Yellow fever virus was detected in Aedes mosquitoes in Brazil, prompting monitoring of potential reestablishment of urban transmission.

Virus
YFV
Host
Aedes
Location
Brazil Brazil
Supporting text

The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas.

Method
genomic approaches; epidemiological monitoring
Geographic raw
Brazil
Country inferred
Brazil