Pulford D J, Meyer H, Ulaeto D
Biomedical Sciences, Dstl, Salisbury, Wiltshire, UK.
Arch Virol. 2002 May;147(5):995-1015. doi: 10.1007/s00705-001-0777-z.
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.
痘苗病毒和天花病毒基因组的比对突出了一些具有多样性的靶点。我们研究了来自36种不同正痘病毒（OPV）毒株的两个病毒膜蛋白基因的序列多样性，以评估这些基因座区分OPV物种的适用性。痘苗病毒哥本哈根株A13L基因的直系同源基因均被预测具有功能基因，长度在201-213个碱基对之间。虽然每种蛋白质的N端和C端在该属内相对保守，但富含脯氨酸的中央结构域显示出特征性的物种特异性氨基酸基序。A36R基因的直系同源基因在物种和毒株之间表现出相当大的序列变异。大部分变异集中在基因的最后100个碱基对。这些序列的多重比对确定了所检测样本中存在缺口、插入或移码突变。几乎所有牛痘病毒毒株在该基因座都含有不同的核苷酸序列。对齐序列的系统发育分析表明，天花病毒和骆驼痘病毒与牛痘病毒有共同的祖先，而埃可病毒与所有其他检测过的OPV不同。用A13L序列生成的系统发育树以一种与其已知特性相关的方式分布了OPV物种。
