Characterization of genetic variability of Venezuelan equine encephalitis viruses

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

doi:10.1371/journal.pone.0152604

Characterization of genetic variability of Venezuelan equine encephalitis viruses

Journal Article · Thu Apr 07 00:00:00 EDT 2016 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0152604· OSTI ID:1248287

Gardner, Shea N. ^[1]; McLoughlin, Kevin ^[1]; Be, Nicholas A. ^[1]; Allen, Jonathan ^[1]; Weaver, Scott C. ^[2]; Forrester, Naomi ^[2]; Guerbois, Mathilde ^[2]; Jaing, Crystal ^[1]

Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Univ. of Texas, Galveston, TX (United States)

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. Lastly, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1248287

Report Number(s):: LLNL-JRNL--687422

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 4 Vol. 11; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Venezuelan equine encephalitis virus
decision trees
genome analysis
genome complexity
genotype
mammalian genomics
microarray
microarrays
multiple alignment calculation
pathogen
phenotype
phylogenetic analysis
sequence alignment
single nucleotide polymorphism

Characterization of genetic variability of Venezuelan equine encephalitis viruses

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