title: Zika virus in the Americas: Early epidemiological and genetic findings.
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. 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.
authors.affiliation: 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.
authors.forename: Nuno Rodrigues
authors.initials: NR
authors.lastname: Faria
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Raimunda do Socorro da Silva
authors.initials: RDSDS
authors.lastname: Azevedo
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
authors.forename: Moritz U G
authors.initials: MUG
authors.lastname: Kraemer
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Renato
authors.initials: R
authors.lastname: Souza
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Mariana Sequetin
authors.initials: MS
authors.lastname: Cunha
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
authors.forename: Sarah C
authors.initials: SC
authors.lastname: Hill
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
authors.forename: Julien
authors.initials: J
authors.lastname: Thézé
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Bonsall
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Bowden
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Ilona
authors.initials: I
authors.lastname: Rissanen
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Iray Maria
authors.initials: IM
authors.lastname: Rocco
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Juliana Silva
authors.initials: JS
authors.lastname: Nogueira
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Adriana Yurika
authors.initials: AY
authors.lastname: Maeda
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Fernanda Giseli da Silva
authors.initials: FGDS
authors.lastname: Vasami
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Fernando Luiz de Lima
authors.initials: FLL
authors.lastname: Macedo
authors.affiliation: Instituto Adolfo Lutz, University of São Paulo, Brazil.
authors.forename: Akemi
authors.initials: A
authors.lastname: Suzuki
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Sueli Guerreiro
authors.initials: SG
authors.lastname: Rodrigues
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Ana Cecilia Ribeiro
authors.initials: ACR
authors.lastname: Cruz
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Bruno Tardeli
authors.initials: BT
authors.lastname: Nunes
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Daniele Barbosa de Almeida
authors.initials: DBA
authors.lastname: Medeiros
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Daniela Sueli Guerreiro
authors.initials: DSG
authors.lastname: Rodrigues
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Alice Louize Nunes
authors.initials: ALN
authors.lastname: Queiroz
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Eliana Vieira Pinto
authors.initials: EVP
authors.lastname: da Silva
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Daniele Freitas
authors.initials: DF
authors.lastname: Henriques
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Elisabeth Salbe Travassos
authors.initials: EST
authors.lastname: da Rosa
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Consuelo Silva
authors.initials: CS
authors.lastname: de Oliveira
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Livia Caricio
authors.initials: LC
authors.lastname: Martins
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Helena Baldez
authors.initials: HB
authors.lastname: Vasconcelos
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Livia Medeiros Neves
authors.initials: LMN
authors.lastname: Casseb
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
authors.forename: Darlene de Brito
authors.initials: DB
authors.lastname: Simith
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.|Metabiota, San Francisco, California 94104, USA.
authors.forename: Jane P
authors.initials: JP
authors.lastname: Messina
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
authors.forename: Leandro
authors.initials: L
authors.lastname: Abade
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.
authors.forename: José
authors.initials: J
authors.lastname: Lourenço
authors.affiliation: Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil.
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authors.initials: LCJ
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authors.forename: Maricélia Maia
authors.initials: MM
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authors.affiliation: Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil.
authors.forename: Marta
authors.initials: M
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authors.affiliation: Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.|Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Simon I
authors.initials: SI
authors.lastname: Hay
authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
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authors.initials: RS
authors.lastname: de Oliveira
authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
authors.forename: Poliana da Silva
authors.initials: PDS
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authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
authors.forename: Layanna Freitas
authors.initials: LF
authors.lastname: de Oliveira
authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
authors.forename: Clayton Pereira Silva
authors.initials: CPS
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authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
authors.forename: Sandro Patroca
authors.initials: SP
authors.lastname: da Silva
authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
authors.forename: Janaina Mota
authors.initials: JM
authors.lastname: de Vasconcelos
authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
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authors.initials: L
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authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
authors.forename: Jedson Ferreira
authors.initials: JF
authors.lastname: Cardoso
authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
authors.forename: João Lídio da Silva Gonçalves
authors.initials: JLDSG
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authors.affiliation: Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
authors.forename: Daiana
authors.initials: D
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authors.affiliation: Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
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authors.initials: G
authors.lastname: Bello
authors.affiliation: Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
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authors.initials: E
authors.lastname: Delatorre
authors.affiliation: Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.|Department of Medicine, Division of Infectious Diseases, University of Toronto, Canada.
authors.forename: Kamran
authors.initials: K
authors.lastname: Khan
authors.affiliation: Dalla Lana School of Public Health, University of Toronto, Canada.
authors.forename: Marisa
authors.initials: M
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authors.affiliation: Brazilian Ministry of Health, Brasília, Brazil.
authors.forename: Giovanini Evelim
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authors.affiliation: Brazilian Ministry of Health, Brasília, Brazil.
authors.forename: Wanderson Kleber
authors.initials: WK
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authors.affiliation: Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
authors.forename: Robert
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authors.lastname: Tesh
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.|Metabiota, San Francisco, California 94104, USA.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.|Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
authors.forename: Marcio R T
authors.initials: MRT
authors.lastname: Nunes
authors.affiliation: Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil.
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authors.initials: PFC
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mesh_terms: D000330:Aedes / Q000821:virology; D000569:Americas / Q000453:epidemiology; D000818:Animals; D004196:Disease Outbreaks; D005260:Female; D016679:Genome, Viral / Q000235:genetics; D006801:Humans; D015994:Incidence; D007303:Insect Vectors / Q000821:virology; D008831:Microcephaly / Q000453:epidemiology* / Q000821:virology; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D009154:Mutation; D010139:Pacific Islands / Q000453:epidemiology; D010802:Phylogeny; D011247:Pregnancy; D012367:RNA, Viral / Q000235:genetics; D017423:Sequence Analysis, RNA; D014195:Travel; D000071244:Zika Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D000071243:Zika Virus Infection / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*
chemical_list: D012367:RNA, Viral