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Zika virus in the Americas: Early epidemiological and genetic findings
Science 24 Mar 2016:
DOI: 10.1126/science.aaf5036
Abstract
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. Using next generation sequencing we generated 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. Phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, estimated to have occurred between May-Dec 2013, more than 12 months prior to the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV endemic areas, and with reported outbreaks in 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 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 in the Americas of this emerging virus.
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Zika virus in the Americas: Early epidemiological and genetic findings
- Nuno Rodrigues Faria1,2,*,
- Raimunda do Socorro da Silva Azevedo3,*,
- Moritz U. G. Kraemer2,
- Renato Souza4,
- Mariana Sequetin Cunha4,
- Sarah C. Hill2,
- Julien Th?z?2,
- Michael B. Bonsall2,
- Thomas A. Bowden5,
- Ilona Rissanen5,
- Iray Maria Rocco4,
- Juliana Silva Nogueira4,
- Adriana Yurika Maeda4,
- Fernanda Giseli da Silva Vasami4,
- Fernando Luiz de Lima Macedo4,
- Akemi Suzuki4,
- Sueli Guerreiro Rodrigues3,
- Ana Cecilia Ribeiro Cruz3,
- Bruno Tardeli Nunes3,
- Daniele Barbosa de Almeida Medeiros3,
- Daniela Sueli Guerreiro Rodrigues3,
- Alice Louize Nunes Queiroz3,
- Eliana Vieira Pinto da Silva3,
- Daniele Freitas Henriques3,
- Elisabeth Salbe Travassos da Rosa3,
- Consuelo Silva de Oliveira3,
- Livia Caricio Martins3,
- Helena Baldez Vasconcelos3,
- Livia Medeiros Neves Casseb3,
- Darlene de Brito Simith3,
- Jane P. Messina2,6,
- Leandro Abade2,
- Jos? Louren?o2,
- Luiz Carlos Junior Alcantara7,
- Maric?lia Maia de Lima8,
- Marta Giovanetti7,
- Simon I. Hay9,5,
- Rodrigo Santos de Oliveira1,
- Poliana da Silva Lemos1,
- Layanna Freitas de Oliveira1,
- Clayton Pereira Silva de Lima1,
- Sandro Patroca da Silva1,
- Janaina Mota de Vasconcelos1,
- Luciano Franco1,
- Jedson Ferreira Cardoso1,
- Jo?o L?dio da Silva Gon?alves Vianez-J?nior1,
- Daiana Mir10,
- Gonzalo Bello10,
- Edson Delatorre10,
- Kamran Khan11,12,
- Marisa Creatore13,
- Giovanini Evelim Coelho14,
- Wanderson Kleber de Oliveira14,
- Robert Tesh15,
- Oliver G. Pybus2,6,?,?,
- Marcio R. T. Nunes1,15,?,?,
- Pedro F. C. Vasconcelos3,?,?
- 1Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
- 2Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
- 3Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Par? State, Brazil.
- 4Instituto Adolfo Lutz, University of S?o Paulo, Brazil.
- 5Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- 6Metabiota, San Francisco, CA 94104, USA.
- 7Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil.
- 8Centre of Post Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil.
- 9Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.
- 10Laborat?rio de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
- 11Li Ka Shing Knowledge Institute, St. Michael?s Hospital, Toronto, Canada.
- 12Department of Medicine, Division of Infectious Diseases, University of Toronto, Canada.
- 13Dalla Lana School of Public Health, University of Toronto, Canada.
- 14Brazilian Ministry of Health, Bras?lia, Brazil.
- 15Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
- ↵?Correspondening author. E-mail: oliver.pybus@zoo.ox.ac.uk (O.G.P.); marcionunesbrasil@yahoo.com.br(M.R.T.N.); pedrovasconcelos@iec.pa.gov.br (P.F.C.V.)
- ↵* These authors contributed equally to this work.
- ↵? These authors contributed equally to this work.
Science 24 Mar 2016:
DOI: 10.1126/science.aaf5036
Abstract
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. Using next generation sequencing we generated 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. Phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, estimated to have occurred between May-Dec 2013, more than 12 months prior to the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV endemic areas, and with reported outbreaks in 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 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 in the Americas of this emerging virus.
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