Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
Faria NR., Quick J., Claro IM., Thézé J., de Jesus JG., Giovanetti M., Kraemer MUG., Hill SC., Black A., da Costa AC., Franco LC., Silva SP., Wu C-H., Raghwani J., Cauchemez S., du Plessis L., Verotti MP., de Oliveira WK., Carmo EH., Coelho GE., Santelli ACFS., Vinhal LC., Henriques CM., Simpson JT., Loose M., Andersen KG., Grubaugh ND., Somasekar S., Chiu CY., Muñoz-Medina JE., Gonzalez-Bonilla CR., Arias CF., Lewis-Ximenez LL., Baylis SA., Chieppe AO., Aguiar SF., Fernandes CA., Lemos PS., Nascimento BLS., Monteiro HAO., Siqueira IC., de Queiroz MG., de Souza TR., Bezerra JF., Lemos MR., Pereira GF., Loudal D., Moura LC., Dhalia R., França RF., Magalhães T., Marques ET., Jaenisch T., Wallau GL., de Lima MC., Nascimento V., de Cerqueira EM., de Lima MM., Mascarenhas DL., Neto JPM., Levin AS., Tozetto-Mendoza TR., Fonseca SN., Mendes-Correa MC., Milagres FP., Segurado A., Holmes EC., Rambaut A., Bedford T., Nunes MRT., Sabino EC., Alcantara LCJ., Loman NJ., Pybus OG.
Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 2016) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 2016). 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 disease. 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.