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

doi:10.1128/JVI.00074-18

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

Microbiology And Immunology

Research output: Contribution to journal › Article › peer-review

31 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 language	English (US)
Article number	e00074-18
Journal	Journal of virology
Volume	92
Issue number	12
DOIs	https://doi.org/10.1128/JVI.00074-18
State	Published - 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), Article e00074-18. https://doi.org/10.1128/JVI.00074-18

Tan, Y, Lam, TTY, Heberlein-Larson, LA, Smole, SC, Auguste, AJ, Hennigan, S, Halpin, RA, Fedorova, N, Puri, V, Stockwell, TB, Shilts, MH, Andreadis, T, Armstrong, PM, Tesh, RB, Weaver, SC, Unnasch, TR, Ciota, AT, Kramer, LD & Das, SR 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, vol. 92, no. 12, e00074-18. https://doi.org/10.1128/JVI.00074-18

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

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.",

keywords = "EEEV, Evolution, NGS, Next-generation sequencing, Phylodynamics, Phylogeography, Source-sink dynamics",

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

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doi = "10.1128/JVI.00074-18",

language = "English (US)",

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AU - Tan, Yi

AU - Lam, Tommy Tsan Yuk

AU - Heberlein-Larson, Lea A.

AU - Smole, Sandra C.

AU - Auguste, Albert J.

AU - Hennigan, Scott

AU - Halpin, Rebecca A.

AU - Fedorova, Nadia

AU - Puri, Vinita

AU - Stockwell, Timothy B.

AU - Shilts, Meghan H.

AU - Andreadis, Theodore

AU - Armstrong, Philip M.

AU - Tesh, Robert B.

AU - Weaver, Scott C.

AU - Unnasch, Thomas R.

AU - Ciota, Alexander T.

AU - Kramer, Laura D.

AU - Das, Suman R.

PY - 2018/6/1

Y1 - 2018/6/1

N2 - 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.

AB - 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.

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KW - Phylodynamics

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

Abstract

Keywords

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