Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments

Abstract

We present an expansion of the classification of the family Papillomaviridae, which now contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non-human mammals, birds and reptiles (64, 3 and 2 types, respectively). To accommodate the number of PV genera exceeding the Greek alphabet, the prefix "dyo" is used, continuing after the Omega-PVs with Dyodelta-PVs. The current set of human PVs is contained within five genera, whereas mammalian, avian and reptile PVs are contained within 20, 3 and 1 genera, respectively. We propose standardizations to the names of a number of animal PVs. As prerequisite for a coherent nomenclature of animal PVs, we propose founding a reference center for animal PVs. We discuss that based on emerging species concepts derived from genome sequences, PV types could be promoted to the taxonomic level of species, but we do not recommend implementing this change at the current time.

Fig. 1. Distribution of pairwise L1 nucleotide sequence comparisons of 189 Papillomaviruses

L1 nucleotide global multiple sequence alignments were guided by amino acid alignment using MUSCLE v3.7 (Edgar, 2004) and Seaview v4.1 (Galtier et al., 1996) software. A matrix of 189 L1 regions compared to each other, resulted in a total of 17766 percent identity values. Gaps were included and counted as one position. The Y-axis represents the percent of the total number of comparisons. The X-axis shows the L1 nucleotide sequence percent identity. The figure has a predominantly bimodal distribution with overlap at around 60% nucleotide sequence identity.

Fig. 2. Specific Intergeneric, Interspecies and Intraspecies L1 nucleotide sequence comparisons based on the multiple sequence alignment matrix

L1 nucleotide global multiple sequence alignment was created as described in the legend to Figure 1. The same matrix was used to evaluate the distribution of- Intraspecies: comparisons of PV types within the same species (161 PV types within 49 species, 558 comparisons); Interspecies: comparisons of PV types within the same genus (161 PV types within 10 genera, 3207 comparisons); Intergeneric: comparisons of all PV types within different genera (189 PVs in 30 genera, 14001 comparison). The Y-axis represents the percent of the total number of comparisons. The X-axis shows the L1 nucleotide sequence percent identity.

Fig. 3. Phylogenetic tree inferred from the L1 nucleotide sequences of 189 papillomaviruses

The phylogeny analysis is based on the multiple L1 nucleotide sequence alignment of 189 PV types that was used in Figures 1 and 2. MrBayes v3.1.2 (Huelsenbeck and Ronquist, 2001; Ronquist and Huelsenbeck, 2003) with 10,000,000 cycles for the Markov chain Monte Carlo (MCMC) algorithm was used to generate a phylogenetic tree. For Bayesian tree construction, the computer program ModelTest v3.7 (Posada and Crandall, 1998) identified the best evolutionary model. The identified gamma model was set for among-site rate variation and allowed all substitution rates of aligned sequence to be different.