Genomes of the parapoxviruses ORF virus and bovine papular stomatitis virus

Abstract

Bovine papular stomatitis virus (BPSV) and orf virus (ORFV), members of the genus Parapoxvirus of the Poxviridae, are etiologic agents of worldwide diseases affecting cattle and small ruminants, respectively. Here we report the genomic sequences and comparative analysis of BPSV strain BV-AR02 and ORFV strains OV-SA00, isolated from a goat, and OV-IA82, isolated from a sheep. Parapoxvirus (PPV) BV-AR02, OV-SA00, and OV-IA82 genomes range in size from 134 to 139 kbp, with an average nucleotide composition of 64% G+C. BPSV and ORFV genomes contain 131 and 130 putative genes, respectively, and share colinearity over 127 genes, 88 of which are conserved in all characterized chordopoxviruses. BPSV and ORFV contain 15 and 16 open reading frames (ORFs), respectively, which lack similarity to other poxvirus or cellular proteins. All genes with putative roles in pathogenesis, including a vascular endothelial growth factor (VEGF)-like gene, are present in both viruses; however, BPSV contains two extra ankyrin repeat genes absent in ORFV. Interspecies sequence variability is observed in all functional classes of genes but is highest in putative virulence/host range genes, including genes unique to PPV. At the amino acid level, OV-SA00 is 94% identical to OV-IA82 and 71% identical to BV-AR02. Notably, ORFV 006/132, 103, 109, 110, and 116 genes (VEGF, homologues of vaccinia virus A26L, A33R, and A34R, and a novel PPV ORF) show an unusual degree of intraspecies variability. These genomic differences are consistent with the classification of BPSV and ORFV as two PPV species. Compared to other mammalian chordopoxviruses, PPV shares unique genomic features with molluscum contagiosum virus, including a G+C-rich nucleotide composition, three orthologous genes, and a paucity of nucleotide metabolism genes. Together, these data provide a comparative view of PPV genomics.

FIG. 1.

Phylogenetic analysis of PPV proteins. PPV025 DNA polymerase and homologous sequences were aligned using ClustalW. Unrooted trees were generated using the neighbor-joining algorithm with Poisson correction for multiple substitutions. Bootstrap values greater than 95% after 1,000 replicates are indicated at appropriate nodes. Homologous protein sequences from the following viruses and accession numbers were compared: ORFV, AY386264; MOCV, MCU60315; VACV, M35027; yaba-like disease virus (YLDV), YDI293568; lumpy skin disease virus (LSDV), AF325528; myxoma virus (MYXV), AF170726; and swinepox virus (SWPV), AF410153. Similar results were obtained for 16 additional conserved PPV proteins, with 15 maintaining 100% bootstrap support for separation of PPV and MOCV from other mammalian ChPVs. Similar results were also obtained for these 17 proteins using the maximum likelihood algorithm with Dayhoff correction for multiple substitutions and for whole genomic nucleotide alignment utilizing amino acid translation as implemented by using Dialign (54).