BACKGROUND: The outbreak of Zika virus (ZIKV) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern. Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis. Determining genomic sequences of clinical viral isolates and characterization of elements within these are an important prerequisite to advance our understanding of viral replicative processes and virus-host interactions. METHODOLOGY/PRINCIPAL FINDINGS: We obtained a ZIKV isolate from a patient who presented with classical ZIKV-associated symptoms, and used high throughput sequencing and other molecular biology approaches to determine its full genome sequence, including non-coding regions. Genome regions were characterized and compared to the sequences of other isolates where available. Furthermore, we identified a subgenomic flavivirus RNA (sfRNA) in ZIKV-infected cells that has antagonist activity against RIG-I induced type I interferon induction, with a lesser effect on MDA-5 mediated action. CONCLUSIONS/SIGNIFICANCE: The full-length genome sequence including non-coding regions of a South American ZIKV isolate from a patient with classical symptoms will support efforts to develop genetic tools for this virus. Detection of sfRNA that counteracts interferon responses is likely to be important for further understanding of pathogenesis and virus-host interactions.

Boyd Orr Centre for Population and Ecosystem Health Institute of Biodiversity Animal Health and Comparative Medicine College of Medical Veterinary and Life Sciences University of Glasgow Glasgow Scotland United Kingdom

Department of Microbial Pathogenesis Yale University New Haven Connecticut United States of America

Faculty of Science University of South Bohemia České Budějovice Czech Republic Institute of Parasitology Biology Centre of the Academy of Sciences of the Czech Republic České Budějovice Czech Republic

Fundação Oswaldo Cruz PE Centro de Pesquisas Aggeu Magalhães Departamento de Virologia Campus da UFPE Cidade Universitária Recife PE Brasil

Medical Research Council Human Immunology Unit Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine University of Oxford Oxford England United Kingdom

MRC University of Glasgow Centre for Virus Research Glasgow Scotland United Kingdom

Pole de Virologie Unité des arbovirus et virus des fièvres hémorragiques Institut Pasteur de Dakar Dakar Senegal

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