[Source: Science, full page: (LINK). Abstract, edited.]
Genomic and epidemiological monitoring of yellow fever virus transmission potential
N. R. Faria1,*,†, M. U. G. Kraemer1,2,3,*, S. C. Hill1,*, J. Goes de Jesus4,*, R. S. Aguiar5,*, F. C. M. Iani6,7,*, J. Xavier4, J. Quick8, L. du Plessis1, S. Dellicour9, J. Thézé1, R. D. O. Carvalho7, G. Baele9, C.-H. Wu10, P. P. Silveira5, M. B. Arruda5, M. A. Pereira6, G. C. Pereira6, J. Lourenço1, U. Obolski1, L. Abade1,11, T. I. Vasylyeva1, M. Giovanetti4,7, D. Yi12, D. J. Weiss13, G. R. W. Wint1, F. M. Shearer13, S. Funk14, B. Nikolay15,16, V. Fonseca7,17, T. E. R. Adelino6, M. A. A. Oliveira6, M. V. F. Silva6, L. Sacchetto7, P. O. Figueiredo7, I. M. Rezende7, E. M. Mello7, R. F. C. Said18, D. A. Santos18, M. L. Ferraz18, M. G. Brito18, L. F. Santana18, M. T. Menezes5, R. M. Brindeiro5, A. Tanuri5, F. C. P. dos Santos19, M. S. Cunha19, J. S. Nogueira19, I. M. Rocco19, A. C. da Costa20, S. C. V. Komninakis21,22, V. Azevedo7, A. O. Chieppe23, E. S. M. Araujo4, M. C. L. Mendonça4, C. C. dos Santos4, C. D. dos Santos4, A. M. Mares-Guia4, R. M. R. Nogueira4, P. C. Sequeira4, R. G. Abreu24, M. H. O. Garcia24, A. L. Abreu25, O. Okumoto25, E. G. Kroon7, C. F. C. de Albuquerque26, K. Lewandowski27, S. T. Pullan27, M. Carroll28, T. de Oliveira4,17,29, E. C. Sabino20, R. P. Souza19, M. A. Suchard30,31, P. Lemey9, G. S. Trindade7, B. P. Drumond7, A. M. B. Filippis4, N. J. Loman8, S. Cauchemez15,16,*, L. C. J. Alcantara4,7,*,†, O. G. Pybus1,*,†
1 Department of Zoology, University of Oxford, Oxford, UK. 2 Computational Epidemiology Lab, Boston Children’s Hospital, Boston, MA, USA. 3 Department of Pediatrics, Harvard Medical School, Boston, MA, USA. 4 Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil. 5 Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. 6 Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil. 7 Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. 8 Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK. 9 Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium. 10 Department of Statistics, University of Oxford, Oxford, UK. 11 The Global Health Network, University of Oxford, Oxford, UK. 12 Department of Statistics, Harvard University, Cambridge, MA, USA. 13 Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK. 14 Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK. 15 Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France. 16 CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France. 17 KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa. 18 Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. 19 Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil. 20 Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil. 21 Retrovirology Laboratory, Federal University of São Paulo, São Paulo, Brazil. 22 School of Medicine of ABC (FMABC), Clinical Immunology Laboratory, Santo André, São Paulo, Brazil. 23 Coordenação de Vigilância Epidemiológica do Estado do Rio de Janeiro, Rio de Janeiro, Brazil. 24 Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil. 25 Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil. 26 Organização Pan – Americana da Saúde/Organização Mundial da Saúde – (OPAS/OMS), Brasília-DF, Brazil. 27 Public Health England, National Infections Service, Porton Down, Salisbury, UK. 28 NIHR HPRU in Emerging and Zoonotic Infections, Public Health England, London, UK. 29 Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa. 30 Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA. 31 Department of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA.
†Corresponding author. Email: email@example.com (N.R.F.); firstname.lastname@example.org (L.C.J.A.); email@example.com (O.G.P.)
* These authors contributed equally to this work.
Science 31 Aug 2018: Vol. 361, Issue 6405, pp. 894-899 / DOI: 10.1126/science.aat7115
Arbovirus risk in Brazil
Despite the existence of an effective vaccine for yellow fever, there are still almost 80,000 fatalities from this infection each year. Since 2016, there has been a resurgence of cases in Africa and South America—and this at a time when the vaccine is in short supply. The worry is that yellow fever will spread from the forests to the cities, because its vector, Aedes spp. mosquitoes, are globally ubiquitous. Faria et al. integrate genomic, epidemiological, and case distribution data from Brazil to estimate patterns of geographic spread, the risks of virus exposure, and the contributions of rural versus urban transmission (see the Perspective by Barrett). Currently, the yellow fever epidemic in Brazil seems to be driven by infections acquired while visiting forested areas and indicates spillover from susceptible wild primates.
Science, this issue p. 894; see also p. 847
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.
Keywords: Yellow Fever; Aedes spp.; Brazil; Flavivirus; Wildlife; Human.