Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data

Human papillomaviruses (HPV) of the β-group seem to be involved in the pathogenesis of non-melanoma skin cancer. Papillomaviruses are host specific and are considered closely co-evolving with their hosts. Evolutionary incongruence between early genes and late genes has been reported among oncogenic genital α-papillomaviruses and considerably challenge phylogenetic reconstructions. We investigated the relationships of 29 β-HPV (25 types plus four putative new types, subtypes, or variants) as inferred from codon aligned and amino acid sequence data of the genes E1, E2, E6, E7, L1, and L2 using likelihood, distance, and parsimony approaches. An analysis of a L1 fragment included additional nucleotide and amino acid sequences from seven non-human β-papillomaviruses. Early genes and late genes evolution did not conflict significantly in β-papillomaviruses based on partition homogeneity tests (p ⩾ 0.001). As inferred from the complete genome analyses, β-papillomaviruses were monophyletic and segregated into four highly supported monophyletic assemblages corresponding to the species 1, 2, 3, and fused 4/5. They basically split into the species 1 and the remainder of β-papillomaviruses, whose species 3, 4, and 5 constituted the sistergroup of species 2. β-Papillomaviruses have been isolated from humans, apes, and monkeys, and phylogenetic analyses of the L1 fragment showed non-human papillomaviruses highly polyphyletic nesting within the HPV species. Thus, host and virus phylogenies were not congruent in β-papillomaviruses, and multiple invasions across species borders may contribute (additionally to host-linked evolution) to their diversification.