Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico

Julien Thézé, Tony Li, Louis du Plessis, Jerome Bouquet, Moritz U.G. Kraemer, Sneha Somasekar, Guixia Yu, Mariateresa de Cesare, Angel Balmaseda, Guillermina Kuan, Eva Harris, Chieh hsi Wu, M. Azim Ansari, Rory Bowden, Nuno R. Faria, Shigeo Yagi, Sharon Messenger, Trevor Brooks, Mars Stone, Evan M. BlochMichael Busch, José E. Muñoz-Medina, Cesar R. González-Bonilla, Steven Wolinsky, Susana López, Carlos F. Arias, David Bonsall, Charles Y. Chiu*, Oliver G. Pybus

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

60 Scopus citations


The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures. Thézé et al. examine the genomic epidemiology of Zika virus in Central America and Mexico. Following its likely introduction to Honduras in 2014, the virus spread undetected in the region. Genetic and epidemiological data indicate that biannual transmission peaks occurred, and could potentially be explained by local variation in mosquito abundance.

Original languageEnglish (US)
Pages (from-to)855-864.e7
JournalCell Host and Microbe
Issue number6
StatePublished - Jun 13 2018


  • Central America
  • Mexico
  • Zika virus
  • bait capture enrichment
  • effective reproductive number
  • genomics
  • metagenomic sequencing
  • phylodynamics
  • transmission
  • “spiked” primer enrichment

ASJC Scopus subject areas

  • Virology
  • Parasitology
  • Microbiology


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