Genetic and phenotypic changes accompanying the emergence of epizootic subtype IC Venezuelan equine encephalitis viruses from an enzootic subtype ID progenitor

Abstract

Recent studies have indicated that epizootic Venezuelan equine encephalitis (VEE) viruses can evolve from enzootic, subtype ID strains that circulate continuously in lowland tropical forests (A. M. Powers, M. S. Oberste, A. C. Brault, R. Rico-Hesse, S. M. Schmura, J. F. Smith, W. Kang, W. P. Sweeney, and S. C. Weaver, J. Virol. 71:6697-6705, 1997). To identify mutations associated with the phenotypic changes leading to epizootics, we sequenced the entire genomes of two subtype IC epizootic VEE virus strains isolated during a 1992-1993 Venezuelan outbreak and four sympatric, subtype ID enzootic strains closely related to the predicted epizootic progenitor. Analysis by maximum-parsimony phylogenetic methods revealed 25 nucleotide differences which were predicted to have accompanied the 1992 epizootic emergence; 7 of these encoded amino acid changes in the nsP1, nsP3, capsid, and E2 envelope glycoprotein, and 2 were mutations in the 3' untranslated genome region. Comparisons with the genomic sequences of IAB and other IC epizootic VEE virus strains revealed that only one of the seven amino acid changes associated with the 1992 emergence, a threonine-to-methionine change at position 360 of the nsP3 protein, accompanied another VEE virus emergence event. Two changes in the E2 envelope glycoprotein region believed to include the major antigenic determinants, both involving replacement of uncharged residues with arginine, are also candidates for epizootic determinants.

FIG. 1

Summary of variable amino acids among 1992–1993 epizootic Venezuelan IC and sympatric enzootic ID viruses. Dots indicate same amino acid as is present in strain 66637.

FIG. 2

Maximum-parsimony phylogenetic tree, derived from complete nonstructural and structural polyprotein amino acid sequences, showing relationships among VEE virus strains. Branches are labeled to reflect predicted ancestral epidemiological phenotypes (enzootic or epizootic) obtained by minimizing changes in the tree. Numbers represent amino acid changes in terminal branches representing epizootic virus emergence. Diagonal lines show two pairs of amino acid changes shared by two epizootic emergence events. Bootstrap values were 100% for all nodes in the tree of identical topology obtained by nucleotide sequence analysis.