Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico
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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.
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A hybrid enrichment method using metagenomic sequencing with spiked primers combines targeted and untargeted sequencing with panels of 100-10,000 short primers to enrich specific target organisms while retaining breadth for off-target organisms.
“Combining targeted with untargeted sequencing, the method uses variably sized panels (100–10,000) of short primers that are added (‘spiked’) into reaction mixtures to enrich for specific target organisms while retaining the breadth of metagenomic sequencing for off-target organisms.”
From Clinical metagenomics (2019) · cites this paper as [46]
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Self-citation
- Authors
- Thézé, J., Li, T., du Plessis, L., Bouquet, J., Kraemer, M. U. G., Somasekar, S., Yu, G., de Cesare, M., Balmaseda, A., Kuan, G., Harris, E., Wu, C.-H., Ansari, M. A., Bowden, R., Faria, N. R., Yagi, S., Messenger, S., Brooks, T., Stone, M., Bloch, E. M., Busch, M., Muñoz-Medina, J. E., González-Bonilla, C. R., Wolinsky, S., López, S., Arias, C. F., Bonsall, D., Chiu, C. Y., & Pybus, O. G.
- Affiliations
- University of Oxford (GB)
- University of California, San Francisco (US)
- Boston Children's Hospital (US)
- Ministerio de Salud (NI)
- University of California, Berkeley (US)
- Centre for Human Genetics (GB)
- California Department of Public Health (US)
- Blood Systems Research Institute (US)
- Johns Hopkins University (US)
- Northwestern University (US)
- Universidad Nacional Autónoma de México (MX)
- Corresponding author
- Chiu, Charles Y.
- Pybus, Oliver G.
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2018-06
- Volume
- 23
- Issue
- 6
- Pages
- 855-864.e7
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC6006413
- OpenAlex
- W2803998769
- Cited by
- 106
- References
- 69
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 7 · 2023: 7 · 2022: 7 · 2021: 23 · 2020: 19 · 2019: 26 · 2018: 7 · 2017: 1
- FWCI
- 17.88
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell Host & Microbe (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- HAL (submittedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- National Heart, Lung, and Blood Institute (203141/Z/16/Z)
- Branco Weiss Fellowship â Society in Science
- European Research Council
- National Institute of Child Health and Human Development (T32HD040128)
- National Institute of Allergy and Infectious Diseases (R01 HL105704)
- Eidgenössische Technische Hochschule Zürich
- Royal Society (204311/Z/16/Z)
- Wellcome Trust
- National Institutes of Health (R21AI129455, R01AI099631, U19 AI118610, P01AI106695)
- Abbott Laboratories
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mosquito-borne diseases and control
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Vectors
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Outbreaks Research
- Keywords
- Zika virus, virus introduction, Central America, Mexico, phylogenetic analysis, metagenomic sequencing, mosquito vectors, herd immunity, seasonal transmission, arbovirus surveillance, microcephaly
- MeSH terms
- Zika Virus Infection, Zika Virus, Mosquito Vectors, Adolescent, Adult, Brazil, Central America, Child, Child, Preschool, Humans, Mexico, Phylogeny, Genome, Viral, Sequence Analysis, RNA, Immunity, Herd, Metagenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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