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Isoodon Obesulus) in Western Australia Virology 376 (2008) 173–182 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Genomic characterization of a novel virus found in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus) in Western Australia Mark D. Bennett a,⁎, Lucy Woolford a, Hans Stevens b, Marc Van Ranst b, Timothy Oldfield c, Michael Slaven a, Amanda J. O'Hara a, Kristin S. Warren a, Philip K. Nicholls a a School of Veterinary and Biomedical Sciences, Murdoch University, Perth, Western Australia, 6150, Australia b Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10 B-3000, Leuven, Belgium c Wattle Grove Veterinary Hospital, 791 Welshpool Road, Wattle Grove, Western Australia, 6107, Australia article info abstract Article history: The genome of a novel virus, tentatively named bandicoot papillomatosis carcinomatosis virus type 2 (BPCV2), Received 21 January 2008 obtained from multicentric papillomatous lesions from an adult male southern brown bandicoot (Isoodon Returned to author for revision obesulus) was sequenced in its entirety. BPCV2 had a circular double-stranded DNA genome consisting of 3 March 2008 7277 bp and open reading frames encoding putative L1 and L2 structural proteins and putative large T antigen Accepted 14 March 2008 and small t antigen transforming proteins. These genomic features, intermediate between Papillomaviridae Available online 25 April 2008 and Polyomaviridae are most similar to BPCV1, recently described from papillomas and carcinomas in the endangered western barred bandicoot (Perameles bougainville). This study also employed in situ hybridization Keywords: to definitively demonstrate BPCV2 DNA within lesion biopsies. The discovery of BPCV2 provides evidence of Peramelidae – Marsupial virus host co-speciation between BPCVs and marsupial bandicoots and has important implications for the Isoodon obesulus phylogeny and taxonomy of circular double-stranded DNA viruses infecting vertebrates. Virus–host co-speciation © 2008 Elsevier Inc. All rights reserved. Papillomatosis Bandicoot papillomatosis carcinomatosis virus type 2 In situ hybridization Introduction skin scraping was performed, but no ectoparasites or fungal pathogens The southern brown bandicoot, Isoodon obesulus (Shaw, 1797), is were identified. Initial treatment performed at Kanyana Wildlife an Australian peramelid marsupial species that inhabits areas of Rehabilitation Centre included weekly oral Ivomec® (Ivermectin, Merial) southern mainland Australia, Tasmania and also several islands off the and Malaseb (miconazole nitrate and chlorhexidine gluconate, DVM) southern coast of Australia. A sub-species, Isoodon obesulus peninsulae baths. During this treatment, the bandicoot's weight and level of activity occurs on the northern tip of the Cape York Peninsula, Queensland, increased. General improvement of the skin condition was noted at a Australia (Braithwaite, 2002). I. obesulus is nocturnal, omnivorous and follow up veterinary examination, but the raised plaques persisted. adults typically weigh 400–1600 g. In Western Australia, this species is BPCV1 was recently discovered in western barred bandicoots commonly known as the ‘quenda’, the name given to I. obesulus by (Perameles bougainville) in association with papillomatous and carcino- local indigenous Australians (Braithwaite, 2002). matous epithelial lesions grossly similar to the lesions evident on the An adult male I. obesulus in poor health was found at Lesmurdie, southern brown bandicoot (Woolford et al., 2007; Woolford et al., 2008). Western Australia (32° 00′S, 116° 02′E) in April 2007 and taken to Significantly, BPCV1 had certain genomic characteristics typical of Pa- Kanyana Wildlife Rehabilitation Centre. During initial examination, pillomaviridae and other genomic features classically associated with multifocal to coalescing irregular, raised, alopecic and erythematous Polyomaviridae (Woolford et al., 2007). The 7295 bp double-stranded, plaques were observed over the skin of the flanks, face and limbs. Routine circular DNA genome of BPCV1 was similar in size to known papil- lomaviruses (PVs), and it encoded putative structural proteins with ⁎ Corresponding author. Fax: +618 9310 4144. greatest nucleotide and amino acid sequence similarity to the L1 and L2 E-mail addresses: [email protected] (M.D. Bennett), capsid proteins of established PV types (Woolford et al., 2007). The [email protected] (L. Woolford), [email protected] putative transforming protein-encoding open reading frames (ORFs), (H. Stevens), [email protected] (M. Van Ranst), [email protected] most similar to large T antigen (LTag) and small t antigen (stag) occurred (T. Oldfield), [email protected] (M. Slaven), [email protected] on the opposite DNA strand to the structural protein-encoding ORFs: (A.J. O'Hara), [email protected] (K.S. Warren), [email protected] (P.K. Nicholls). features characteristic of the Polyomaviridae (Woolford et al., 2007). 0042-6822/$ – see front matter © 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.virol.2008.03.014 174 M.D. Bennett et al. / Virology 376 (2008) 173–182 Formerly, PVs and polyomaviruses (PyVs) were classified within a Hepatozoon sp. gamonts were seen in blood smears, but nonetheless, single family, Papovaviridae, but the current taxonomic paradigm the bandicoot was in excellent body condition and appeared other- recognizes the distinct phylogenies of PVs and PyVs by classifying wise healthy. them separately at the family level (de Villiers et al., 2004; Howley and Lowy, 2007; Imperiale and Major, 2007). Theoretically, PVs and PyVs Microscopy may have evolved from a common ancestor virus (Van Ranst et al., 1995), and the discovery of BPCV1 suggested that a third lineage Routine histopathology revealed locally extensive epidermal descended from this theoretical ancestor virus may exist today hyperplasia of the strata spinosum and granulosum, with moderate (Woolford et al., 2007). Alternatively, BPCV1 may have arisen in anisokaryosis and anisocytosis of keratinocytes. There were also mild more recent evolutionary history from a recombination event multifocal neutrophilic infiltrates in the superficial dermis and between a PV and a PyV (Woolford et al., 2007). epidermis and mild dermal oedema. Rare suprabasilar mitotic figures The discovery of BPCV2 provides context and a point of comparison were detected, occasionally the cytoplasm of stratum spinosum kera- with BPCV1 to better elucidate their evolutionary histories and also tinocytes appeared vacuolated (koilocytosis) and there were fewer provides additional information on the genomic features of these hair follicles than normal (Fig. 1D). No parasitic, bacterial or fungal novel circular double-stranded DNA viruses that appear to have co- infections were demonstrable using routine or special histochemical speciated with Australian marsupial bandicoot hosts. stains. No PV capsid antigens were detected using indirect immuno- histochemistry on biopsies of I. obesulus papillomatous lesions, Results though the positive control tissue section from a canine oral papillomavirus-infected tissue stained strongly positive. No virions Clinical examination were visualized in the skin fragments processed for transmission electron microscopy studies, though neither were intranuclear The southern brown bandicoot was referred to the Murdoch inclusions identified by light microscopy of histopathology sections. University School of Veterinary and Biomedical Sciences and there, a clinical examination revealed numerous multifocal to coalescing flat Restriction enzyme analysis alopecic skin plaques involving approximately 10–15% of the total skin surface area (Figs. 1A–C). These lesions were evident on the fore- and The restriction endonuclease KpnI produced 1 band at ~7.3 kb. hindpaws, fore- and hindlegs, thorax, flanks, lips, chin and face. The Sal1 did not cut the DNA sample at all. BglII cut the genome twice, but claw of the left lateral digit was overgrown and deformed medially produced only 1 very strong band ~3.6 kb. EcoRI produced 2 bands at across the palmar aspect of the left forepaw (Fig. 1B). Low numbers of ~5.1 kb, ~2.2 kb; BamHI produced 3 fragments, ~5.1 kb, ~2.1 kb, and Fig. 1. A–C Photographs of a 2 kg adult male southern brown bandicoot (Isoodon obesulus) affected by multicentric papillomatosis. The multifocal to coalescing red–black flat, alopecic plaques were found on the face (A), forelimbs (B), hindlimbs, thorax and abdomen (C). The claw of the lateral digit of the left forelimb (B) was elongated and had deviated medially to lie across the palmar aspect of the manus. (D) Photomicrograph of a haematoxylin and eosin stained slide of a skin biopsy from the southern brown bandicoot. There is mild orthokeratotic hyperkeratosis with a hyperplastic stratum basale. The strata spinosum and granulosum are hyperplastic and display anisocytosis, anisokaryosis and occasional suprabasilar mitoses (arrow). There is also a mild neutrophilic inflammatory infiltrate in the superficial dermis. Bar=50 μm. M.D. Bennett et al. / Virology 376 (2008) 173–182 175 ~0.1 kb; and HindIII produced 6 bands ~3.4 kb, ~1.7 kb, ~1 kb, ~0.7 kb, Table 1 ~0.3 kb and ~0.1 kb. Comparisons of aligned amino acid sequences from BPCV2 to BPCV1, polyomaviruses and selected papillomavirus types Polymerase chain reaction Type LTag stag Type Genus
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