JVI Accepts, published online ahead of print on 4 November 2009

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J. Virol. doi:10.1128/JVI.01586-09
Copyright (c) 2009, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Evolutionary Patterns of Eastern Equine Encephalitis Virus in North versus South America Suggest Ecological Differences and Taxonomic Revision

Nicole C. Arrigo, A. Paige Adams, and Scott C. Weaver^*

Department of Pathology and WHO Collaborating Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609

^* To whom correspondence should be addressed. Email: sweaver{at}utmb.edu.

The eastern equine encephalitis (EEE) complex consists of 4 distinct genetic lineages; one that circulates in North America (NA EEEV) and the Caribbean, and 3 that circulate in Central and South America (SA EEEV). Differences in their geographic, pathogenic, and epidemiologic profiles prompted evaluation of their genetic diversity and evolutionary histories. The structural polyprotein open reading frames of all available SA EEEV and recent NA EEEV isolates were sequenced and used in evolutionary and phylogenetic analyses. The nucleotide substitution rate per year for SA EEEV (1.2x10^-4) was slower and more consistent than for NA EEEV (2.7x10^-4), which exhibited considerable rate variation among constituent clades. Estimates for times since divergence varied widely depending upon the sequences used, with NA and SA EEEV diverging ca. 922 to 4,856 years ago and the 2 main SA EEEV lineages ca. 577 to 2,927 years ago. The single, monophyletic NA EEEV lineage mainly exhibited temporally associated relationships and was highly conserved throughout its geographic range. In contrast, SA EEEV comprised 3 divergent lineages, two consisting of highly conserved geographic groupings that completely lacked temporal associations. Phylogenetic comparison of SA EEEV and Venezuelan equine encephalitis viruses (VEEV) demonstrated similar genetic and evolutionary patterns, consistent with the well-documented use of mammalian reservoir hosts by VEEV. Our results emphasize the evolutionary and genetic divergence between members of the NA and SA EEEV lineages, consistent with major differences in pathogenicity and ecology, and propose that NA and SA EEEV be reclassified as distinct species in the EEE complex.