Large-scale complete-genome sequencing and phylodynamic analysis of eastern equine encephalitis virus reveals source-sink transmission dynamics in the United States

Yi Tan, Tommy Tsan Yuk Lam, Lea A. Heberlein-Larson, Sandra C. Smole, Albert J. Auguste, Scott Hennigan, Rebecca A. Halpin, Nadia Fedorova, Vinita Puri, Timothy B. Stockwell, Meghan H. Shilts, Theodore Andreadis, Philip M. Armstrong, Robert B. Tesh, Scott C. Weaver, Thomas R. Unnasch, Alexander T. Ciota, Laura D. Kramer, Suman R. Das

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

Eastern equine encephalitis virus (EEEV) has a high case-fatality rate in horses and humans, and Florida has been hypothesized to be the source of EEEV epidemics for the northeastern United States. To test this hypothesis, we sequenced complete genomes of 433 EEEV strains collected within the United States from 1934 to 2014. Phylogenetic analysis suggested EEEV evolves relatively slowly and that transmission is enzootic in Florida, characterized by higher genetic diversity and long-term local persistence. In contrast, EEEV strains in New York and Massachusetts were characterized by lower genetic diversity, multiple introductions, and shorter local persistence. Our phylogeographic analysis supported a source-sink model in which Florida is the major source of EEEV compared to the other localities sampled. In sum, this study revealed the complex epidemiological dynamics of EEEV in different geographic regions in the United States and provided general insights into the evolution and transmission of other avian mosquito-borne viruses in this region.

Original languageEnglish (US)
Article numbere00074-18
JournalJournal of virology
Volume92
Issue number12
DOIs
StatePublished - Jun 1 2018

Keywords

  • EEEV
  • Evolution
  • NGS
  • Next-generation sequencing
  • Phylodynamics
  • Phylogeography
  • Source-sink dynamics

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

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    Tan, Y., Lam, T. T. Y., Heberlein-Larson, L. A., Smole, S. C., Auguste, A. J., Hennigan, S., Halpin, R. A., Fedorova, N., Puri, V., Stockwell, T. B., Shilts, M. H., Andreadis, T., Armstrong, P. M., Tesh, R. B., Weaver, S. C., Unnasch, T. R., Ciota, A. T., Kramer, L. D., & Das, S. R. (2018). Large-scale complete-genome sequencing and phylodynamic analysis of eastern equine encephalitis virus reveals source-sink transmission dynamics in the United States. Journal of virology, 92(12), [e00074-18]. https://doi.org/10.1128/JVI.00074-18