Genomic and epidemiological monitoring of yellow fever virus transmission potential

N. R. Faria*, M. U.G. Kraemer, S. C. Hill, J. Goes De Jesus, R. S. Aguiar, F. C.M. Iani, J. Xavier, J. Quick, L. Du Plessis, S. Dellicour, J. Thézé, R. D.O. Carvalho, G. Baele, C. H. Wu, P. P. Silveira, M. B. Arruda, M. A. Pereira, G. C. Pereira, J. Lourenço, U. ObolskiL. Abade, T. I. Vasylyeva, M. Giovanetti, D. Yi, D. J. Weiss, G. R.W. Wint, F. M. Shearer, S. Funk, B. Nikolay, V. Fonseca, T. E.R. Adelino, M. A.A. Oliveira, M. V.F. Silva, L. Sacchetto, P. O. Figueiredo, I. M. Rezende, E. M. Mello, R. F.C. Said, D. A. Santos, M. L. Ferraz, M. G. Brito, L. F. Santana, M. T. Menezes, R. M. Brindeiro, A. Tanuri, F. C.P. Dos Santos, M. S. Cunha, J. S. Nogueira, I. M. Rocco, A. C. Da Costa, S. C.V. Komninakis, V. Azevedo, A. O. Chieppe, E. S.M. Araujo, M. C.L. Mendonça, C. C. Dos Santos, C. D. Dos Santos, A. M. Mares-Guia, R. M.R. Nogueira, P. C. Sequeira, R. G. Abreu, M. H.O. Garcia, A. L. Abreu, O. Okumoto, E. G. Kroon, C. F.C. De Albuquerque, K. Lewandowski, S. T. Pullan, M. Carroll, T. De Oliveira, E. C. Sabino, R. P. Souza, M. A. Suchard, P. Lemey, G. S. Trindade, B. P. Drumond, A. M.B. Filippis, N. J. Loman, S. Cauchemez, L. C.J. Alcantara, O. G. Pybus

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

201 Scopus citations


The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. 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. 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.

Original languageEnglish
Pages (from-to)894-899
Number of pages6
Issue number6405
StatePublished - 31 Aug 2018
Externally publishedYes


FundersFunder number
National Institutes of HealthR01LM011965
National Institute of Child Health and Human DevelopmentT32HD040128
U.S. National Library of MedicineR01LM010812
Cystinosis Research Foundation005073
Great Lakes Regional Center of Excellence for Biodefense and Emerging Infectious Diseases ResearchANR-10-LABX-62-IBEID
Wellcome Trust206298/Z/17/Z
Horizon 2020 Framework Programme734548
H2020 European Research Council725422-ReservoirDOCS, 614725-PATHPHYLODYN
Fundação de Amparo à Pesquisa do Estado de São Paulo2016/01735-2, 2017/00021-9
Fonds Wetenschappelijk Onderzoek
Conselho Nacional de Desenvolvimento Científico e Tecnológico400354/ 2016-0
John Fell Fund, University of Oxford005166


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