Diverse papillomaviruses identified in Weddell seals

Abstract

Papillomaviridae is a diverse family of circular, double-stranded DNA (dsDNA) viruses that infect a broad range of mammalian, avian and fish hosts. While papillomaviruses have been characterized most extensively in humans, the study of non-human papillomaviruses has contributed greatly to our understanding of their pathogenicity and evolution. Using high-throughput sequencing approaches, we identified 7 novel papillomaviruses from vaginal swabs collected from 81 adult female Weddell seals (Leptonychotes weddellii) in the Ross Sea of Antarctica between 2014-2017. These seven papillomavirus genomes were amplified from seven individual seals, and six of the seven genomes represented novel species with distinct evolutionary lineages. This highlights the diversity of papillomaviruses among the relatively small number of Weddell seal samples tested. Viruses associated with large vertebrates are poorly studied in Antarctica, and this study adds information about papillomaviruses associated with Weddell seals and contributes to our understanding of the evolutionary history of papillomaviruses.

Keywords: Antarctic; Carnivora; Leptonychotes weddellii; papillomavirus.

Fig. 1.

(a) Neighbour-joining phylogenetic tree of the tree inferred from the aligned genome sequences of LwPV1-7 with the genome organization for each genotype showing E6, E7, E2, L2 and L1 ORFs coupled with genome size. (b) Pairwise identity plot with percentage pairwise identities provided in coloured boxes for the genome and the L1 nucleotide sequences.

Fig. 2.

(a) blastp results for each of the proteins encoded by LwPV1-7 with Weddell seal papillomaviruses highlighted in red and California sea lion papillomavirus 1 (ZcPV1) given in pink. Protein sequence of first (b) and second (c) zinc-binding motifs (CX₂CX_21–23CX₂C) present in the L6 ORF of LwPV1-7. (d) Protein sequence of pRB-binding motif (Lx[C/S]xE) and zinc-binding motif in E7 ORF of LwPV1-5.

Fig. 3.

Maximum-likelihood phylogenetic tree inferred using concatenated protein sequences of E1, E2 and L1. LwPV1-7 are highlighted in red and California sea lion papillomavirus 1 (ZcPV1) is highlighted in pink. Branches in black indicate lineages that have no recognizable E7 ORF. Branches with <0.75 aLRT branch support have been collapsed. Branch support values are given in purple circle size gradients. Papillomaviruses marked with asterisks are unclassified.

Fig. 4.

Co-evolution of carnivore papillomaviruses from Omega-, Lambda-, Triesta-, Tau-, Dyonu-, Chi- and Dyothetapapillomaviruses. Clades of concatenated E1–E2–L1 maximum-likelihood phylogenetic tree (see Fig. 3). All Carnivora papillomaviruses known to date are present in the six clades and these are linked to their host phylogenies.