Characterization of genetic variability of venezuelan equine encephalitis viruses

Shea N. Gardner, Kevin McLoughlin, Nicholas A. Be, Jonathan Allen, Scott Weaver, Naomi Forrester, Mathilde Guerbois, Crystal Jaing

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic potential, and predict human virulence phenotype. We performed whole genome single nucleotide polymorphism (SNP) analysis of all available VEE antigenic complex genomes, verified that a SNP-based phylogeny accurately captured the features of a phylogenetic tree based on multiple sequence alignment, and developed a high resolution genome-wide SNP microarray.We used the microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array- And sequence-based SNP calls, genotyped unsequenced isolates, and placed them on a phylogeny with sequenced genomes. The microarray successfully genotyped VEEV directly from tissue samples of an infected mouse, bypassing the need for viral isolation, culture and genomic sequencing. Finally, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype.

Original languageEnglish (US)
Article numbere0152604
JournalPLoS One
Volume11
Issue number4
DOIs
StatePublished - Apr 1 2016

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Venezuelan Equine Encephalitis Viruses
Venezuelan equine encephalitis virus
Polymorphism
Viruses
single nucleotide polymorphism
Single Nucleotide Polymorphism
Microarrays
Nucleotides
Genes
Genome
genetic variation
genome
Phylogeny
Horses
phylogeny
Alphavirus
Phenotype
genomics
horses
phenotype

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Gardner, S. N., McLoughlin, K., Be, N. A., Allen, J., Weaver, S., Forrester, N., ... Jaing, C. (2016). Characterization of genetic variability of venezuelan equine encephalitis viruses. PLoS One, 11(4), [e0152604]. https://doi.org/10.1371/journal.pone.0152604

Characterization of genetic variability of venezuelan equine encephalitis viruses. / Gardner, Shea N.; McLoughlin, Kevin; Be, Nicholas A.; Allen, Jonathan; Weaver, Scott; Forrester, Naomi; Guerbois, Mathilde; Jaing, Crystal.

In: PLoS One, Vol. 11, No. 4, e0152604, 01.04.2016.

Research output: Contribution to journalArticle

Gardner, SN, McLoughlin, K, Be, NA, Allen, J, Weaver, S, Forrester, N, Guerbois, M & Jaing, C 2016, 'Characterization of genetic variability of venezuelan equine encephalitis viruses', PLoS One, vol. 11, no. 4, e0152604. https://doi.org/10.1371/journal.pone.0152604
Gardner, Shea N. ; McLoughlin, Kevin ; Be, Nicholas A. ; Allen, Jonathan ; Weaver, Scott ; Forrester, Naomi ; Guerbois, Mathilde ; Jaing, Crystal. / Characterization of genetic variability of venezuelan equine encephalitis viruses. In: PLoS One. 2016 ; Vol. 11, No. 4.
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