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. Obolski; L. 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

doi:10.1126/science.aat7115

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 journal › Article › peer-review

231 Scopus citations

Abstract

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 language	English
Pages (from-to)	894-899
Number of pages	6
Journal	Science
Volume	361
Issue number	6405
DOIs	https://doi.org/10.1126/science.aat7115
State	Published - 31 Aug 2018
Externally published	Yes

Funding

Funders	Funder number
National Institute of Child Health and Human Development
Fonds Wetenschappelijk Onderzoek
National Institutes of Health
European Commission
U.S. National Library of Medicine	R01LM010812, R01LM011965
Cystinosis Research Foundation	005073
Conselho Nacional de Desenvolvimento Científico e Tecnológico	400354/ 2016-0
Fundação de Amparo à Pesquisa do Estado de São Paulo	2016/01735-2, 2017/00021-9
Eunice Kennedy Shriver National Institute of Child Health and Human Development	T32HD040128
Wellcome Trust	206298, 206298/Z/17/Z
H2020 European Research Council	614725, 725422
Medical Research Council	MC_PC_15100, MR/M501621/1, MR/L015080/1
Great Lakes Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research	ANR-10-LABX-62-IBEID
John Fell Fund, University of Oxford	005166
Horizon 2020 Framework Programme	734548

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1126/science.aat7115

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Faria, N. R., Kraemer, M. U. G., Hill, S. C., De Jesus, J. G., Aguiar, R. S., Iani, F. C. M., Xavier, J., Quick, J., Du Plessis, L., Dellicour, S., Thézé, J., Carvalho, R. D. O., Baele, G., Wu, C. H., Silveira, P. P., Arruda, M. B., Pereira, M. A., Pereira, G. C., Lourenço, J., ... Pybus, O. G. (2018). Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science, 361(6405), 894-899. https://doi.org/10.1126/science.aat7115

@article{a42ae56392fb47d79e9cf8bbcfebbe34,

title = "Genomic and epidemiological monitoring of yellow fever virus transmission potential",

abstract = "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.",

author = "Faria, {N. R.} and Kraemer, {M. U.G.} and Hill, {S. C.} and {De Jesus}, {J. Goes} and Aguiar, {R. S.} and Iani, {F. C.M.} and J. Xavier and J. Quick and {Du Plessis}, L. and S. Dellicour and J. Th{\'e}z{\'e} and Carvalho, {R. D.O.} and G. Baele and Wu, {C. H.} and Silveira, {P. P.} and Arruda, {M. B.} and Pereira, {M. A.} and Pereira, {G. C.} and J. Louren{\c c}o and U. Obolski and L. Abade and Vasylyeva, {T. I.} and M. Giovanetti and D. Yi and Weiss, {D. J.} and Wint, {G. R.W.} and Shearer, {F. M.} and S. Funk and B. Nikolay and V. Fonseca and Adelino, {T. E.R.} and Oliveira, {M. A.A.} and Silva, {M. V.F.} and L. Sacchetto 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 A. Tanuri 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 V. Azevedo and Chieppe, {A. O.} and Araujo, {E. S.M.} and Mendon{\c c}a, {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 O. Okumoto and Kroon, {E. G.} and {De Albuquerque}, {C. F.C.} and K. Lewandowski and Pullan, {S. T.} and M. Carroll and {De Oliveira}, T. and Sabino, {E. C.} and Souza, {R. P.} and Suchard, {M. A.} and P. Lemey and Trindade, {G. S.} and Drumond, {B. P.} and Filippis, {A. M.B.} and Loman, {N. J.} and S. Cauchemez and Alcantara, {L. C.J.} and Pybus, {O. G.}",

note = "Publisher Copyright: 2017 {\textcopyright} The Authors,",

year = "2018",

month = aug,

day = "31",

doi = "10.1126/science.aat7115",

language = "אנגלית",

volume = "361",

pages = "894--899",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6405",

}

Faria, NR, Kraemer, MUG, Hill, SC, De Jesus, JG, Aguiar, RS, Iani, FCM, Xavier, J, Quick, J, Du Plessis, L, Dellicour, S, Thézé, J, Carvalho, RDO, Baele, G, Wu, CH, Silveira, PP, Arruda, MB, Pereira, MA, Pereira, GC, Lourenço, J, Obolski, U, Abade, L, Vasylyeva, TI, Giovanetti, M, Yi, D, Weiss, DJ, Wint, GRW, Shearer, FM, Funk, S, Nikolay, B, Fonseca, V, Adelino, TER, Oliveira, MAA, Silva, MVF, Sacchetto, L, Figueiredo, PO, Rezende, IM, Mello, EM, Said, RFC, Santos, DA, Ferraz, ML, Brito, MG, Santana, LF, Menezes, MT, Brindeiro, RM, Tanuri, A, Dos Santos, FCP, Cunha, MS, Nogueira, JS, Rocco, IM, Da Costa, AC, Komninakis, SCV, Azevedo, V, Chieppe, AO, Araujo, ESM, Mendonça, MCL, Dos Santos, CC, Dos Santos, CD, Mares-Guia, AM, Nogueira, RMR, Sequeira, PC, Abreu, RG, Garcia, MHO, Abreu, AL, Okumoto, O, Kroon, EG, De Albuquerque, CFC, Lewandowski, K, Pullan, ST, Carroll, M, De Oliveira, T, Sabino, EC, Souza, RP, Suchard, MA, Lemey, P, Trindade, GS, Drumond, BP, Filippis, AMB, Loman, NJ, Cauchemez, S, Alcantara, LCJ & Pybus, OG 2018, 'Genomic and epidemiological monitoring of yellow fever virus transmission potential', Science, vol. 361, no. 6405, pp. 894-899. https://doi.org/10.1126/science.aat7115

TY - JOUR

T1 - Genomic and epidemiological monitoring of yellow fever virus transmission potential

AU - Faria, N. R.

AU - Kraemer, M. U.G.

AU - Hill, S. C.

AU - De Jesus, J. Goes

AU - Aguiar, R. S.

AU - Iani, F. C.M.

AU - Xavier, J.

AU - Quick, J.

AU - Du Plessis, L.

AU - Dellicour, S.

AU - Thézé, J.

AU - Carvalho, R. D.O.

AU - Baele, G.

AU - Wu, C. H.

AU - Silveira, P. P.

AU - Arruda, M. B.

AU - Pereira, M. A.

AU - Pereira, G. C.

AU - Lourenço, J.

AU - Obolski, U.

AU - Abade, L.

AU - Vasylyeva, T. I.

AU - Giovanetti, M.

AU - Yi, D.

AU - Weiss, D. J.

AU - Wint, G. R.W.

AU - Shearer, F. M.

AU - Funk, S.

AU - Nikolay, B.

AU - Fonseca, V.

AU - Adelino, T. E.R.

AU - Oliveira, M. A.A.

AU - Silva, M. V.F.

AU - Sacchetto, L.

AU - Figueiredo, P. O.

AU - Rezende, I. M.

AU - Mello, E. M.

AU - Said, R. F.C.

AU - Santos, D. A.

AU - Ferraz, M. L.

AU - Brito, M. G.

AU - Santana, L. F.

AU - Menezes, M. T.

AU - Brindeiro, R. M.

AU - Tanuri, A.

AU - Dos Santos, F. C.P.

AU - Cunha, M. S.

AU - Nogueira, J. S.

AU - Rocco, I. M.

AU - Da Costa, A. C.

AU - Komninakis, S. C.V.

AU - Azevedo, V.

AU - Chieppe, A. O.

AU - Araujo, E. S.M.

AU - Mendonça, M. C.L.

AU - Dos Santos, C. C.

AU - Dos Santos, C. D.

AU - Mares-Guia, A. M.

AU - Nogueira, R. M.R.

AU - Sequeira, P. C.

AU - Abreu, R. G.

AU - Garcia, M. H.O.

AU - Abreu, A. L.

AU - Okumoto, O.

AU - Kroon, E. G.

AU - De Albuquerque, C. F.C.

AU - Lewandowski, K.

AU - Pullan, S. T.

AU - Carroll, M.

AU - De Oliveira, T.

AU - Sabino, E. C.

AU - Souza, R. P.

AU - Suchard, M. A.

AU - Lemey, P.

AU - Trindade, G. S.

AU - Drumond, B. P.

AU - Filippis, A. M.B.

AU - Loman, N. J.

AU - Cauchemez, S.

AU - Alcantara, L. C.J.

AU - Pybus, O. G.

PY - 2018/8/31

Y1 - 2018/8/31

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85052626601&partnerID=8YFLogxK

U2 - 10.1126/science.aat7115

DO - 10.1126/science.aat7115

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 30139911

AN - SCOPUS:85052626601

SN - 0036-8075

VL - 361

SP - 894

EP - 899

JO - Science

JF - Science

IS - 6405

ER -

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Abstract

Funding

UN SDGs

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