Identification of two novel equine papillomavirus sequences suggests three genera in one cluster

The number of recognized papillomavirus (PV) species and potential PV genera has dramatically been increasing throughout the past decade. It seems that every host species might potentially harbour a large set of PVs, while the PVs of each species appear to belong to only a few genera. In horses at least three conditions beside the equine sarcoid have been described, being supposedly PV induced namely classical equine papillomas, genital papillomas and aural plaques. We were able to identify the DNA of novel equine PVs (EcPVs) in the two latter disorders where PV involvement had been predicted. Both PV genomes were entirely cloned and sequenced. Both EcPV genomes, one derived from a penile papilloma, the other derived from an ear papilloma contain the characteristic open reading frames (ORFs) E6, E7, E1, E2, L2 and L1, a large non-coding region between the late and early region as well as a small non-coding region between the early and the late region. The viruses were consequently designated as EcPV2 and EcPV3. The genomes of the three equine PVs were analysed and compared with each other and further PVs. Upon phylogenetic analyses the equine PVs group well together. Pairwise alignment of the L1 nucleotide sequences reveals that EcPV1 shares 54.9% identities with EcPV2 and 53.2% with EcPV3. EcPV2 and EcPV3 share 51.3% identities. As the three EcPVs share less than 60% of nucleotide identities in L1, they may be regarded as belonging to different genera.