Novel snake papillomavirus does not cluster with other non-mammalian papillomaviruses. Part 3
Furthermore, Needle alignments which reflect global alignments of the entire genes in contrast to the alignment used for the tree were made. Upon these pairwise alignments on the nucleotide level of the L1 ORF the highest percentage of sequence identities was found with a human PV (HPV5; 57.9%) and with TmPV1 on the E1 ORF (55.6%). Consequently MsPV1 may be regarded as rather a close to the root prototype of a new PV clade that might establish a new genus regarding to the guidelines of PV classification.
While many PVs have been described in humans and other mammalian species, the number of known PVs infecting non-mammalian species is limited. The described MsPV1 genome represents the first PV isolated from a snake. It contains the characteristic ORFs E6, E7, E1, E2, L1 and L2, a large non-coding region between L1 and E6 as well as a small non-coding region between E2 and L2. The size of the viral genome (7048 bp) is comparable with the two turtle PV genomes (CcPV1; 7020 bp and CmPV1; 6953 bp), which are all relatively small. However, while the latter two viruses have short versions of E1, E2, L2 and E6 ORFs as well as the NCR, the small size of MsPV1 is primarily due to comparably short E2 and L2 ORFs and also comparably short NCRs.
The genomic sequences of the PVs from three bird and two turtle species have previously been published. According to our and other’s phylogenetic analysis, they cluster together. However, our newly discovered PV genome isolated from the snake did not at all cluster with the five other sauropsid PVs (CcPV1, CmPV1, FcPV1, FlPV1 and PePV1). Upon pairwise alignment of individual ORFs, MsPV1 shares much higher percentage of sequence identities with mammalian PVs than with any of the known sauropsid PVs. This finding raises interesting questions in the context of PV evolution. While co-evolution with the host has been suggested and demonstrated to play a role in PV evolution it has also been shown that PV evolution is probably a complex matter and other mechanism such as crossing of species barriers and adaptive radiation have to be considered as well.
Turtles as putative representatives of the Anapsida and snakes as representatives of the Diapsida are phylogenetically distinct with a common ancestor dating back more than 200 million years. However, the three PVs isolated from birds (FcPV1, FlPV1 and PePV1), which also belong to the Diapsida, are phylogenetically much closer to the turtle PVs (CcPV1, CmPV1) than to MsPV1. As the snake PV appears closer to mammalian PVs, one explanation could be that it belongs to a lineage of PVs, which existed already in Amniota species, that lived before the split of Synapsida (mammals and mammal-like reptiles) and Sauropsida. The five other sauropsid PVs could under these circumstances go back to a second distinct ancestral lineage. However, an alternative explanation could be that some ancestor of this virus had been able to cross species barriers between the Sauropsida and the Synapsida, even long after their separation.