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Science. 2016 Apr 15;352(6283):345-349. doi: 10.1126/science.aaf5036. Epub 2016 Mar 24.

Zika virus in the Americas: Early epidemiological and genetic findings.

Author information

Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
Instituto Adolfo Lutz, University of São Paulo, Brazil.
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Metabiota, San Francisco, California 94104, USA.
Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil.
Centre of Post Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil.
Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.
Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.
Department of Medicine, Division of Infectious Diseases, University of Toronto, Canada.
Dalla Lana School of Public Health, University of Toronto, Canada.
Brazilian Ministry of Health, Brasília, Brazil.
Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
Contributed equally


Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however, no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this correlation does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology of this emerging virus in the Americas.

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