Genomic and epidemiological monitoring of yellow fever virus transmission potential

Faria, N. R. and Kraemer, M. U. G. and Hill, S. C. and Goes de Jesus, J. and Aguiar, R. S. and Iani, F. C. M. and Xavier, J. and Quick, J. and du Plessis, L. and Dellicour, S. and Thézé, J. and Carvalho, R. D. O. and Baele, G. and Wu, C.-H. and Silveira, P. P. and Arruda, M. B. and Pereira, M. A. and Pereira, G. C. and Lourenço, J. and Obolski, U. and Abade, L. and Vasylyeva, T. I. and Giovanetti, M. and Yi, D. and Weiss, D. J. and Wint, G. R. W. and Shearer, F. M. and Funk, S. and Nikolay, B. and Fonseca, V. and Adelino, T. E. R. and Oliveira, M. A. A. and Silva, M. V. F. and Sacchetto, L. and Figueiredo, P. O. and Rezende, I. M. and Mello, E. M. and Said, R. F. C. and Santos, D. A. and Ferraz, M. L. and Brito, M. G. and Santana, L. F. and Menezes, M. T. and Brindeiro, R. M. and Tanuri, A. and dos Santos, F. C. P. and Cunha, M. S. and Nogueira, J. S. and Rocco, I. M. and da Costa, A. C. and Komninakis, S. C. V. and Azevedo, V. and Chieppe, A. O. and Araujo, E. S. M. and Mendonça, M. C. L. and dos Santos, C. C. and dos Santos, C. D. and Mares-Guia, A. M. and Nogueira, R. M. R. and Sequeira, P. C. and Abreu, R. G. and Garcia, M. H. O. and Abreu, A. L. and Okumoto, O. and Kroon, E. G. and de Albuquerque, C. F. C. and Lewandowski, K. and Pullan, S. T. and Carroll, M. and de Oliveira, T. and Sabino, E. C. and Souza, R. P. and Suchard, M. A. and Lemey, P. and Trindade, G. S. and Drumond, B. P. and Filippis, A. M. B. and Loman, N. J. and Cauchemez, S. and Alcantara, L. C. J. and Pybus, O. G. (2018) Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science, 361 (6405). pp. 894-899. ISSN 0036-8075

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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.

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