Evolutionary relationships and systematics of the alphaviruses

Abstract

Partial E1 envelope glycoprotein gene sequences and complete structural polyprotein sequences were used to compare divergence and construct phylogenetic trees for the genus Alphavirus. Tree topologies indicated that the mosquito-borne alphaviruses could have arisen in either the Old or the New World, with at least two transoceanic introductions to account for their current distribution. The time frame for alphavirus diversification could not be estimated because maximum-likelihood analyses indicated that the nucleotide substitution rate varies considerably across sites within the genome. While most trees showed evolutionary relationships consistent with current antigenic complexes and species, several changes to the current classification are proposed. The recently identified fish alphaviruses salmon pancreas disease virus and sleeping disease virus appear to be variants or subtypes of a new alphavirus species. Southern elephant seal virus is also a new alphavirus distantly related to all of the others analyzed. Tonate virus and Venezuelan equine encephalitis virus strain 78V3531 also appear to be distinct alphavirus species based on genetic, antigenic, and ecological criteria. Trocara virus, isolated from mosquitoes in Brazil and Peru, also represents a new species and probably a new alphavirus complex.

FIG. 1

Organization of the Alphavirus genome. Gene products and associated functions are indicated.

FIG. 2

Phylogenetic tree of all Alphavirus species, and selected subtypes and variants, generated from partial E1 envelope glycoprotein gene sequences by using the neighbor-joining program with the F84 distance formula (61). Virus abbreviations are found in Table 1, footnote 6. Numbers refer to bootstrap values for clades defined by the adjacent node. The topology of Cabassou virus (CABV) and Pixuna virus (PIXV) within the VEEV complex was constrained based on the more robust results of the complete structural polyprotein sequence analysis (see Fig. 3), and this topology was not significantly less likely based on maximum-likelihood analyses with the E1 gene sequences. The open circle adjacent to a branch indicates hypothetical Old to New World introduction, and the closed circle indicates New to Old World introduction, assuming a New World origin; the open square indicates Old to New World introduction, and the closed square indicates New to Old World introduction, assuming an Old World origin of the nonfish Alphavirus clade.

FIG. 3

Unrooted phylogenetic tree of Alphavirus species generated from complete structural polyprotein amino acid sequences by using the neighbor-joining program (61). Virus abbreviations are found in Table 1, footnote 6. Numbers refer to bootstrap values for clades defined by the indicated node.