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Background  Papillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infecting primates. PVs associated to lesions in economically important ruminant species have been isolated from cattle and sheep.    Methods  Potential PV DNA from teat lesions of a Damascus goat was isolated, cloned and sequenced. The PV genome was analyzed using bioinformatics approaches to detect open reading frames and to predict potential features of encoded proteins as well as putative regulatory elements. Sequence comparison and phylogenetic analyses using the concatenated  E1E2L2L1  nucleotide and amino acid alignments was used to reveal the relationship of the new PV to the known PV diversity and its closest relevants.    Results  We isolated and characterized the full-genome of novel  Capra hircus papillomavirus.  We identified the E6, E7, E1, E2, L2, L1 open reading frames with protein coding potential and putative active elements in the ChPV2 proteins and putative regulatory genome elements. Sequence similarities of  L1  and phylogenetic analyses using concatenated  E1E2L2L1  nucleotide and amino acid alignments suggest the classification as a new PV type designated ChPV2 with a phylogenetic position within the  XiPV  genus, basal to the XiPV1 species. ChPV2 is not closely related to ChPV1, the other known goat PV isolated from healthy skin, although both of them belong confidently into a clade composed of PVs infecting cervids and bovids. Interestingly, ChPV2 contains an  E6  open reading frame whereas all closely related PVs do not    Conclusion  ChPV2 is a novel goat PV closely related to the Xi-PV1 species infecting bovines. Phylogenetic relationships and genome architecture of ChPV2 and closely related PV types suggest at least two independent  E6  losses within the  XiPV  clade.

Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines