Characterization of a novel polyomavirus isolated from a fibroma on the trunk of an African elephant (Loxodonta africana)

Abstract

Viruses of the family Polyomaviridae infect a wide variety of avian and mammalian hosts with a broad spectrum of outcomes including asymptomatic infection, acute systemic disease, and tumor induction. In this study a novel polyomavirus, the African elephant polyomavirus 1 (AelPyV-1) found in a protruding hyperplastic fibrous lesion on the trunk of an African elephant (Loxodonta africana) was characterized. The AelPyV-1 genome is 5722 bp in size and is one of the largest polyomaviruses characterized to date. Analysis of the AelPyV-1 genome reveals five putative open-reading frames coding for the classic small and large T antigens in the early region, and the VP1, VP2 and VP3 capsid proteins in the late region. In the area preceding the VP2 start codon three putative open-reading frames, possibly coding for an agnoprotein, could be localized. A regulatory, non-coding region separates the 2 coding regions. Unique for polyomaviruses is the presence of a second 854 bp long non-coding region between the end of the early region and the end of the late region. Based on maximum likelihood phylogenetic analyses of the large T antigen of the AelPyV-1 and 61 other polyomavirus sequences, AelPyV-1 clusters within a heterogeneous group of polyomaviruses that have been isolated from bats, new world primates and rodents.

Figure 1. Lesions found on the trunks of the elephants.

(a) Nodular lesion as seen on the trunks of three elephants; (b) Protruding ulcerated fibroma, from which the biopsy was taken; (c) Interface between the fibroblastic mass and proliferative dermis; (d) Whirling fibroblasts with prominent collagen deposits.

Figure 2. Schematic of the African elephant polyomavirus 1 (AelPyV-1) genome organization.

Figure 3. Nucleotide-based maximum likelihood phylogenetic analysis of the large T antigen open-reading frame of AelPyV-1 and 61 other polyomaviruses.

The numbers at the internal nodes represent significant bootstrap support values, determined from 10,000 iterations. The scale bar indicates the genetic distance in nucleotide substitutions per site.

Figure 4. Amino acid-based neighbor-joining analysis of (A) the major capsid protein VP1, (B) the minor capsid protein VP2, (C) the large T antigen, and (D) the small T antigen.

The numbers at the internal nodes represent significant bootstrap support values determined from 10,000 iterations. The scale bar indicates the genetic distance in amino acid substitutions per site. Genbank accession numbers: African green monkey polyomavirus, NC_004763; Bovine polyomavirus, NC_001442; Cebus albifrons polyomavirus 1, NC_019854; Crow polyomavirus, NC_007922; Finch polyomavirus, NC_007923; Hamster polyomavirus, NC_001663; Human polyomavirus 2 (JC), NC_001699; Human polyomavirus 3 (KI), NC_009238; Human polyomavirus 4 (WU), NC_009539; Human polyomavirus 5 (Merkel cell), JQ479318; Human polyomavirus 7, NC_014407; Human polyomavirus 9, NC_015150; Murine pneumotropic virus, NC_001505; Pteronotus polyomavirus, NC_020070; Squirrel monkey polyomavirus, NC_009951; Vervet monkey polyomavirus 1, NC_019844. PyV: Polyomavirus.