Novel Bovine Papillomavirus Type Discovered by Rolling-Circle Amplification Coupled with Next-Generation Sequencing

<div><p>Currently, fifteen bovine papillomavirus (BPV) types have been identified and classified into four genera: <i>Deltapapillomavirus</i>, <i>Epsilonpapillomavirus</i>, <i>Dyoxipapillomavirus</i>, and <i>Xipapillomavirus</i>. Here, the complete genome sequence of a new BPV type (BPV 04AC14) recovered from a papillomatous lesion is reported. The genome is 7,282 bp in length and exhibits the classic genetic organization and motifs of the members of <i>Papillomaviridae</i>. Maximum likelihood phylogenetic analyses revealed that BPV 04AC14 clusters with members of the <i>Xipapillomavirus</i> genus. The nucleotide sequence of the L1 capsid protein of the novel BPV is closely related to its counterpart, BPV3, with which it shares 79% similarity. These findings suggest that this virus is a new BPV type of the <i>Xipapillomavirus</i> genus.</p></div

Features of the BPV 04AC14 non-coding region and E7 protein.

<p>(A) Non-coding region: coloured boxes display the genomic locations of the E2 binding site (ACCN₅GGT), polyadenylation site (AATAAA), and TATA box (TATAAA). (B) Amino acid alignment of E7 proteins with corresponding proteins of closely related types from <i>Xipapillomavirus 1</i> and <i>2</i>. The location of the pRb-binding core sequence (LXCXE) is marked with a red box, and the location of the zinc-binding domain (CX₂CX₂₉CX₂C) is indicated by a blue box. Multiple sequence alignments were performed in MUSCLE, and the figure was drawn in GeneDoc.</p

Genomic organization of BPV 04AC14.

<p>The first position of the BPV 04AC14 genome was set as the first ATG of the E8 ORF. The ORFs were identified with the aid of the ORF Finder (NCBI). The figure was drawn in Geneious 8.1.4.</p

Main features of the BPV 04AC14 genome.

<p>Main features of the BPV 04AC14 genome.</p

Maximum likelihood phylogenetic trees.

<p><b>(A)</b> Maximum likelihood phylogenetic tree of <i>L1</i> gene sequences of genus-representative papillomaviruses. Nucleotide sequences were compared to those of 54 papillomavirus sequences, representing all known papillomavirus genera. The sequences were retrieved from GenBank. Bootstrap values are indicated above the branches. The putative new BPV type introduced here is indicated with a black diamond. (B) Maximum likelihood phylogenetic tree of the <i>Xipapillomavirus</i> genus. Nucleotide sequences of the <i>L1</i> gene were compared to those of nine bovine <i>Xipapillomavirus</i> sequences, representing the three known <i>Xipapillomavirus</i> species. The sequences were retrieved from GenBank. Bootstrap values are indicated above the branches. The putative new BPV type is indicated with a black diamond.</p