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Cell Host Microbe. 2018 Jun 13;23(6):855-864.e7. doi: 10.1016/j.chom.2018.04.017. Epub 2018 May 24.

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

Author information

1
Department of Zoology, University of Oxford, Oxford, UK.
2
Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
3
Department of Zoology, University of Oxford, Oxford, UK; Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA.
4
Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
5
Laboratory Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua.
6
Centro de Salud Sócrates Flores Vivas, Ministerio de Salud, Managua, Nicaragua.
7
Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA.
8
Department of Statistics, University of Oxford, Oxford, UK.
9
Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
10
California Department of Public Health, Richmond, CA, USA.
11
Blood Systems Research Institute, San Francisco, CA, USA.
12
Department of Pathology, Johns Hopkins University School of Medcine, Baltimore, MD, USA.
13
División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico.
14
Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
15
Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
16
Nuffield Department of Medicine, University of Oxford, Oxford, UK.
17
Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA. Electronic address: charles.chiu@ucsf.edu.
18
Department of Zoology, University of Oxford, Oxford, UK. Electronic address: oliver.pybus@zoo.ox.ac.uk.

Abstract

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.

KEYWORDS:

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

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