Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Faria, N. R. and Quick, J. and Claro, I.M. and Thézé, J. and de Jesus, J. G. and Giovanetti, M. and Kraemer, M. U. G. and Hill, S. C. and Black, A. and da Costa, A. C. and Franco, L. C. and Silva, S. P. and Wu, C.-H. and Raghwani, J. and Cauchemez, S. and du Plessis, L. and Verotti, M. P. and de Oliveira, W. K. and Carmo, E. H. and Coelho, G. E. and Santelli, A. C. F. S. and Vinhal, L. C. and Henriques, C. M. and Simpson, J. T. and Loose, M. and Andersen, K. G. and Grubaugh, N. D. and Somasekar, S. and Chiu, C. Y. and Muñoz-Medina, J. E. and Gonzalez-Bonilla, C. R. and Arias, C. F. and Lewis-Ximenez, L. L. and Baylis, S. A. and Chieppe, A. O. and Aguiar, S. F. and Fernandes, C. A. and Lemos, P. S. and Nascimento, B. L. S. and Monteiro, H. A. O. and Siqueira, I. C. and de Queiroz, M. G. and de Souza, T. R. and Bezerra, J. F. and Lemos, M. R. and Pereira, G. F. and Loudal, D. and Moura, L. C. and Dhalia, R. and França, R. F. and Magalhães, T. and Marques, E. T. and Jaenisch, T. and Wallau, G. L. and de Lima, M. C. and Nascimento, V. and de Cerqueira, E. M. and de Lima, M. M. and Mascarenhas, D. L. and Neto, J. P. Moura and Levin, A. S. and Tozetto-Mendoza, T. R. and Fonseca, S. N. and Mendes-Correa, M. C. and Milagres, F. P. and Segurado, A. and Holmes, E. C. and Rambaut, A. and Bedford, T. and Nunes, M. R. T. and Sabino, E. C. and Alcantara, L. C. J. and Loman, N. J. and Pybus, O. G. (2017) Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Springer.

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Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil1 . Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 20162 ) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 20162 ). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease3 . However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus.

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