Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Research output: Contribution to journalArticle


  • N R Faria
  • I M Claro
  • J Thézé
  • J G de Jesus
  • M Giovanetti
  • M U G Kraemer
  • S C Hill
  • A Black
  • A C da Costa
  • L C Franco
  • S P Silva
  • C-H Wu
  • J Raghwani
  • S Cauchemez
  • L du Plessis
  • M P Verotti
  • W K de Oliveira
  • E H Carmo
  • G E Coelho
  • A C F S Santelli
  • L C Vinhal
  • C M Henriques
  • J T Simpson
  • M Loose
  • K G Andersen
  • N D Grubaugh
  • S Somasekar
  • C Y Chiu
  • J E Muñoz-Medina
  • C R Gonzalez-Bonilla
  • C F Arias
  • L L Lewis-Ximenez
  • S A Baylis
  • A O Chieppe
  • S F Aguiar
  • C A Fernandes
  • P S Lemos
  • B L S Nascimento
  • H A O Monteiro
  • I C Siqueira
  • M G de Queiroz
  • T R de Souza
  • J F Bezerra
  • M R Lemos
  • G F Pereira
  • D Loudal
  • L C Moura
  • R Dhalia
  • R F França
  • T Magalhães
  • E T Marques
  • T Jaenisch
  • G L Wallau
  • M C de Lima
  • V Nascimento
  • E M de Cerqueira
  • M M de Lima
  • D L Mascarenhas
  • J P Moura Neto
  • A S Levin
  • T R Tozetto-Mendoza
  • S N Fonseca
  • M C Mendes-Correa
  • F P Milagres
  • A Segurado
  • E C Holmes
  • A Rambaut
  • T Bedford
  • M R T Nunes
  • E C Sabino
  • L C J Alcantara
  • O G Pybus

Colleges, School and Institutes

External organisations

  • Department of Zoology, University of Oxford, Oxford OX1 3SY, UK.
  • Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil.
  • Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil.
  • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
  • Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.
  • Department of Statistics, University of Oxford, Oxford OX1 3LB, UK.
  • Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France.
  • Coordenação dos Laboratórios de Saúde (CGLAB/DEVIT/SVS), Ministry of Health, Brasília, Brazil.
  • Coordenação Geral de Vigilância e Resposta às Emergências em Saúde Pública (CGVR/DEVIT), Ministry of Health, Brasília, Brazil.
  • Departamento de Vigilância das Doenças Transmissíveis, Ministry of Health, Brasilia, Brazil.
  • Coordenação Geral dos Programas de Controle e Prevenção da Malária e das Doenças Transmitidas pelo Aedes, Ministry of Health, Brasília, Brazil.
  • Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.
  • University of Nottingham
  • The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, California 92037, USA.
  • Departments of Laboratory Medicine and Medicine &Infectious Diseases, University of California, San Francisco, California, USA.
  • División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico.
  • Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
  • Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.
  • Paul-Ehrlich-Institut, Langen, Germany.
  • Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro, Brazil.
  • Laboratório Central de Saúde Pública do Estado do Rio Grande do Norte, Natal, Brazil.
  • Laboratório Central de Saúde Pública do Estado da Paraíba, João Pessoa, Brazil.
  • Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brazil.
  • Section Clinical Tropical Medicine, Department for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany.
  • Laboratório Central de Saúde Pública do Estado de Alagoas, Maceió, Brazil.
  • Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil.
  • Secretaria de Saúde de Feira de Santana, Feira de Santana, Bahia, Brazil.
  • Universidade Federal do Amazonas, Manaus, Brazil.
  • Hospital São Francisco, Ribeirão Preto, Brazil.
  • Universidade Federal do Tocantins, Palmas, Brazil.
  • University of Western Sydney, Sydney, Australia
  • Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.


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.


Original languageEnglish
Pages (from-to)406-410
Number of pages5
Issue number7658
Publication statusPublished - 24 May 2017