Orthologs of the vaccinia A13L and A36R virion membrane protein genes display diversity in species of the genus Orthopoxvirus.

Alignment of vaccinia and variola virus genomes has highlighted some targets that display diversity. We have investigated the sequence diversity of two viral membrane protein genes from 36 different orthopoxvirus (OPV) strains to evaluate the suitability of these loci to differentiate between OPV species. Orthologs of the vaccinia virus Copenhagen A13L gene were all predicted to have functional genes that ranged between 201-213 bps in length. Whereas the N- and C-termini of each protein were relatively well conserved within the genus, a central proline-rich domain displayed characteristic species-specific amino acid motifs. Orthologs of the A36R gene displayed considerable sequence variation between species and strains. The majority of variation was localised to the last 100 bps of the gene. Multiple-alignment of these sequences identified the presence of gaps, insertions or frame-shift mutations among the samples examined. Nearly all strains of cowpox virus contained different nucleotide sequences at this locus. Phylogenetic analysis of the aligned sequences showed that variola and camelpox viruses shared a common ancestry with cowpox virus, whereas ectromelia viruses were divergent from all the other OPVs examined. Phylogeny generated with A13L sequences distributed the OPV species in a manner that correlated to their known properties.