Characterisation of the first complete genome sequence of the roe deer (Capreolus capreolus) papillomavirus

Genetic characterization of Sus scrofa papillomavirus type 1 from domestic pigs in Guangxi Province, China

Sus scrofa papillomatosis (SsP) is a tumour caused by Sus scrofa papillomaviruses (SsPVs). To investigate the presence of SsPVs in China, 354 domestic pig skin samples collected from Guangxi Province were examined for SsPV DNA by PCR. Three SsPV1s (GX12, GX14, and GX18) were identified with a prevalence of 0.847% (3/354). Sequence analysis showed that L1 of SsPV1/GX12 and SsPV1/GX14 had 99.7% and 99.6% nucleotide identify with the reference SsPV1a, respectively. Phylogenetic and evolutionary analyses showed that SsPV1/GX12 and SsPV1/14 clustered into SsPV1a and that SsPV1/GX18 clustered into SsPV1b. Compared with other SsPV L1 and L2 proteins, we found that the SsPV1/GX18 and SsPV1b strains shared the same unique substitutions, and SsPV1/GX12, SsPV1/GX14, and SsPV1a shared almost identical amino acid sequences. This study reports the first detection of SsPV DNA in China based on whole genome information and provides a scientific basis for the development of SsPV pathogenic biology, epidemiology, and prevention, as well as control technology research.

Identification of a Novel Papillomavirus Type (MfoiPV1) Associated with Acrochordon in a Stone Marten (Martes foina)

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosal infections in humans and various domestic and wild animals. Nevertheless, there is limited knowledge about PVs in wildlife hosts, including mustelid species. This study describes a case in stone marten (Martes foina) with a clinical manifestation of skin tumor, which is rather atypical for infections with PVs. The result of the papillomavirus PCR performed on the skin tumor sample was positive, and the complete PV genome was determined in the studied sample using next-generation sequencing technology. The analysis of the PV genome revealed infection of the stone marten with a putative new PV type belonging to the Dyonupapillomavirus genus. The proposed new stone marten PV type was named MfoiPV1.

A Comprehensive Study of Cutaneous Fibropapillomatosis in Free-Ranging Roe Deer (Capreolus capreolus) and Red Deer (Cervus elaphus): from Clinical Manifestations to Whole-Genome Sequencing of Papillomaviruses

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosa infections in humans and various animals. In roe deer and red deer, most PVs belong to the Deltapapillomavirus genus and cause neoplastic changes that are generally described as fibropapillomas. Despite the wide distribution of roe and red deer throughout Europe and beyond, the data in the scientific literature regarding the widespread distribution of PVs and the genetic variability of PV genomes in these species are rather scarce. This study describes cutaneous fibropapillomatosis cases in roe and red deer with clinical manifestations that are typical of infections with PVs. In all cases, the presence of PV DNA was confirmed using PCR, followed by Sanger sequencing of the partial L1 gene. The complete PV genomes were determined in all the investigated samples using next-generation sequencing technology, revealing infections of roe deer with the CcaPV1-type and red deer with the CePV1v-type variant. A comparison of the complete CcaPV1-type and CePV1v-type variant genome sequences reported here with already available complete genome sequences in GenBank revealed their great genetic stability across time and space.

Epitheliotropic Infections in Wildlife Ruminants From the Central Alps and Stelvio National Park

The mountain chain of the Alps, represents the habitat of alpine fauna where the red deer (Cervus elaphus) population is the outmost numerous, followed by the chamois (Rupicapra rupicapra) and the alpine ibex (Capra ibex) at higher altitudes. Previous reports showed the circulation of epitheliotropic viruses, belonging to the families Papillomaviridae and Poxviridae, causing skin and mucosal lesions in wild ruminants of the Stelvio National Park, situated in the area. To deepen our knowledge on the natural dynamics of the infections, a passive surveillance on all the cases of proliferative skin and mucosal lesions in wild ruminants was performed. Twenty-seven samples (11 chamois, 10 red deer and 6 ibex) collected from 2008 to 2018 were analyzed by negative staining electron microscopy, histology, and PCR followed by genome sequencing and phylogenetic analyses. Results confirmed the spread of Parapoxvirus of Red Deer in New Zealand (PVNZ) in Italy, and its ability to cause severe lesions i.e., erosions and ulcers in the mouth. We showed for the first time a PVNZ/CePV1v (C. elaphus papillomavirus 1 variant) co-infection identified in one red deer. This result supports previous evidence on the ability of papillomavirus and parapoxvirus to mutually infect the same host tissue. Interestingly two ibex and one chamois showing orf virus (OV) skin lesions were shown to be co-infected with bovine papillomavirus type 1 and 2. The presence of bovine papillomavirus, in orf virus induced lesions of chamois and ibex raises the question of its pathogenetic role in these animal species. For the first time, OV/CePV1v co-infection was demonstrated in another chamois. CePV1v is sporadically reported in red deer throughout Europe and is considered species specific, its identification in a chamois suggests its ability of cross-infecting different animal species. Poxviruses and papillomavirus have been simultaneously detected also in the skin lesions of cattle, bird and human suggesting a possible advantageous interaction between these viruses. Taken together, our findings add further information on the epidemiology and pathogenetic role of epitheliotropic viruses in wild ruminants living in the central Alps and in Stelvio National Park.

Mandibular Ossifying Fibroma and Multiple Oral Papillomas in a Roe Deer (Capreolus capreolus)

An emaciated, adult, free-ranging roe deer (Capreolus capreolus) presenting a large mandibular mass, was shot by a game warden in Sissach, Switzerland. The head of the roe deer was submitted to the Center for Fish and Wildlife Health for examination. Grossly, the mass consisted of a 6 × 7 × 4 cm mandibular exophytic growth, associated with loss of incisors teeth. On cut section, a hard, light-tan core was rimmed by a thick layer of soft tissue. Computed tomography examination confirmed the mandibular origin of the mass. Histologically, the mass consisted of an unencapsulated fibro-osseous neoplasm. The bony portion was composed of multiple haphazardly arranged spicules rimmed by osteoblasts with no associated periosteal layer. Embedding the bony spicules were short anastomosing and branching streams and bundles of spindled cells. The overlaying partially ulcerated mucosa, showed prominent rete ridges deepening into the submucosa. In addition to the mandibular mass, multiple soft cauliflower-like proliferations were expanding from the gingival surface. Histologically, these masses were arranged in papillary elements composed of pluristratified squamous epithelium with long rete ridges extending into a rich underlying fibrovascular supportive stroma. Neither papillomaviral DNA nor antigen could be identified in association with the oral masses. The gross, histological and radiological features of the mandibular mass are consistent with an ossifying fibroma, while the cauliflower oral masses were diagnosed as papillomas.

Cutaneous Fibropapilloma in a Red Deer (Cervus elaphus) Associated with Cervus elaphus Papillomavirus in Portugal

A pedunculated cauliflower-like mass was detected on the left posterior limb of a subadult male red deer (Cervus elaphus) after a hunt in Portugal. Histologically the lesion was classified as cutaneous fibropapilloma. The identification of Cervus elaphus papillomavirus (CePV-1 variant) was based on sequencing of the L1 gene. The L2 sequence revealed a nine-nucleotide deletion, as already reported in the Italian and Hungarian CePV-1, further supporting the theory that this is a distinctive genomic characteristic of this viral variant, as this feature has been found in distinct cases from geographically distant countries. In addition, a coinfection with bovine papillomavirus was evidenced by amplification and sequencing of the E5 gene, confirming the ability of Delta papillomaviruses to cross-infect different animal species and providing more evidence that wildlife may act as reservoir for papillomaviruses affecting domestic species. Papillomavirus infection in red deer has been sporadically described in different European countries; in this work, we describe the identification of a CePV-1 variant infection associated with a red deer fibropapilloma in Portugal.

A teat papillomatosis case in a Damascus goat (Shami goat) in Hatay province, Turkey: a new putative papillomavirus?

Papillomaviruses (PVs) are epitheliotropic viruses that cause benign proliferative lesions in the skin (warts or papillomas) and mucous membranes of their natural hosts. Recently, new PVs have been found in many animal species. The most common current approach for identifying novel PV types is based on PCR, using various consensus or degenerated primer (broad-range primers), designed on the basis of the multiple alignment of nucleotide or amino acid sequences of a large number of different human papillomaviruses (HPV). PVs have been classified according to the sequence similarity of one of their capsid proteins, L1, without taking into account other regions of the genome and without considering the phenotypic characteristics of the viral infection. In this study, we performed molecular detection and typing of a PV in a goat with teat papillomatosis. Firstly, PCR was performed using the FAP59/FAP64 and MY09/MY11 primer pairs for the L1 gene region. The PV DNA was found to be positive only with the FAP59/FAP64 primer pair. PV DNA was then tested with three primer sets in four different combinations (L2Bf/FAP64, L2Bf/L1Br, FAP59/FAP64, L1Bf/LCRBr) for the gene region encoding the L1, L2 and LCR proteins. The goat teat papilloma sample was amplified using FAP59/FAP64 primers and two primer pairs (L2Bf/FAP64 and L2Bf/L1Br). We obtained products matching approximately 604 bp of the L1 region of the virus. PV DNA was used for typing using sequence analysis/PCR with some type-specific primers for bovids, caprids and cervids. The results of the sequence analysis suggested one new putative PV type with sequence identity ranging from 46.45 to 80.09% to other known papillomaviruses, including Capra hircus papillomavirus (ChPV-2), bovine papillomavirus (BPV) 6, 7, 10, 11 and 12, Rangifer tarandus papillomavirus 3 (RtPV-3) and BPV-7Z (Alpine wild ruminant papillomavirus; Cervus elaphus papillomavirus). We therefore propose that this is the first identification of a new putative type, MG523274 (HTY-goat-TR2016), in a goat with teat papillomatosis. It is essential to identify PV types in different animal species and investigate their prevalence/distribution and clinical consequences in order to develop appropriate prophylactic and/or therapeutic procedures and to determine the interspecies transmission potential and evolution of PVs.

Genomic characterization of a novel Epsilonpapillomavirus associated with pigmented papillomas in a red deer (Cervus elaphus)

Two of a group of 15 farmed European red (Cervus elaphus elaphus) X wapiti (C. e. canadensis) deer stags developed multiple persistent pigmented squamous papillomas (warts) on their chins. DNA was extracted from a papilloma and a short section of DNA from a novel papillomavirus (PV) was amplified. This short sequence was used to design 'outward facing' primers to amplify the remainder of the circular PV DNA. The PCR product was sequenced using next-generation sequencing and the full genome of the PV, consisting of 8082 bp, was assembled and analysed. The novel PV was designated Cervus elaphus papillomavirus (CePV) type 2. The putative coding regions of CePV2 were predicted to produce four early and two late proteins with two other potential ORFs also noted. Phylogenetic analysis of ORF L1 revealed greater than 60 %, but less than 70 % similarity, to Bos taurus papillomavirus (BPV) types -5 and -7. As both BPV5 and BPV7 are Epsilonpapillomavirus 1, CePV2 is proposed as the first Epsilonpapillomavirus 2 PV type. This is the first EpsilonPV to be identified in a non-bovine species and the first non-DeltaPV to be identified as a cause of disease in any deer species.

Rusa alfredi papillomavirus 1 - a novel deltapapillomavirus inducing endemic papillomatosis in the endangered Visayan spotted deer

We describe a novel papillomavirus - Rusa alfredi papillomavirus 1 (RalPV1) - which causes endemic fibropapillomatosis in the European conservation breeding population of the highly endangered Visayan spotted deer (Rusa alfredi). Degenerated papillomavirus-specific primers were used to amplify and sequence parts of the viral DNA. Subsequently, the complete genomic DNA was cloned and the sequence was determined. The RalPV1 genome has a length of 8029 bp, encodes the early proteins E6, E7, E1, E2 and E5, the two late proteins L1 and L2 and contains an upstream regulatory region. Highest sequence identities were observed with two deltapapillomaviruses, the Capreolus capreolus PV1 and Cervus elaphus PV1. Pairwise comparisons and phylogenetic analysis based on the ORF L1 suggested that RalPV1 is a putative new type of the papillomavirus species Deltapapillomavirus 5.

PAPILLOMAVIRUS IN HEALTHY SKIN AND MUCOSA OF WILD RUMINANTS IN THE ITALIAN ALPS

We investigated healthy skin and mucosal specimens of wild ruminants in the Italian Alps. We identified bovine papillomavirus (BPV)-2 DNA in the healthy skin of wild ruminants and documented coinfection of BPV-1 and Cervus elaphus papillomavirus (CePV)-1 in a healthy red deer (Cervus elaphus). We also demonstrated cross-infections of BPVs of the genus Xipapillomavirus, both as single virus infection and also in association with Deltapapillomavirus types 1 and 2, confirming that host tropism of papillomaviruses is not as species-specific as previously thought. Our results suggest that subclinical infections could be linked to the presence of domestic ruminants sharing the same habitat with wild species and that the wildlife may act as a reservoir for papillomaviruses affecting domestic species.

Papillomavirus infection of roe deer in the Czech Republic and fibropapilloma-associated levels of metallothionein, zinc, and oxidative stress

The present study aimed at the aetiological diagnosis of skin tumours of roe deer (Capreolus capreolus) in the Czech Republic. A total of 33 roe deer specimens showing skin masses were sampled for histopathology, virus detection and identification using polymerase chain reaction (PCR) and deoxyribonucleic acid sequence (DNA) analysis, and to investigate fibropapilloma-associated levels of metallothionein, zinc and oxidative stress in 2012 and 2013. Ticks (Ixodes ricinus) and deer keds (Lipoptena cervi) were also collected and pooled from sampled game specimens. Ticks found on dogs in hunting grounds under study were pooled into another sample. Skin tumours, ranging from 2 to 10 per inspected specimen and 2 to 5 cm in size, were classified as fibropapillomas by histopathology. All 33 viral-infection-suspected skin samples from roe deer in South Moravia and South Bohemia were PCR positive. The nucleotide sequences of PCR products were 100% homologous to the Western roe deer papillomavirus 1 isolate CcPV-1. Ticks and deer keds from positive roe deer and ticks from dogs were PCR and DNA sequence positive for the roe deer papillomavirus. Viral DNA was also demonstrated in one blood sample from a roe deer female. Differences in metallothionein, zinc, taurine and electrochemical index among samples from lesions and normal skin of affected roe deer and negative controls from papillomavirus-non-infected animals were non-significant. While we have demonstrated circulation of specific roe deer papillomavirus in the Czech Republic that results in multiple fibropapillomatous skin tumours, many ecological and epidemiological issues of this wildlife disease still remain unanswered.

Pigmented chin papillomas in red (Cervus elaphus) x wapiti (Cervus canadensis) stags associated with a novel papillomavirus

CASE HISTORY

Lesions were observed on the chins of two 2- to 3-year-old red (Cervus elaphus)  x wapiti (Cervus canadensis) stags from the lower North Island of New Zealand during velvet removal.

CLINICAL FINDINGS

Both stags had numerous, coalescing, darkly pigmented plaques and nodules on the skin of the chin and lower lips that were 3-10 mm in diameter. Re-examination after 12 months of initial detection revealed no appreciable change in the lesions. A biopsy sample from one lesion was submitted for histopathological examination.

HISTOPATHOLOGY

Sections revealed lesions consistent with pigmented viral papillomas, characterised by marked epidermal hyperplasia forming papillary fronds, prominent clumping of keratohyalin granules, keratinocytes with dilated grey-blue cytoplasm, shrunken nuclei surrounded by a clear halo (koilocytes), and presumptive viral intranuclear inclusions. Papillomavirus DNA was amplified by PCR from a fresh tissue sample from the same papilloma. Comparison of the partial nucleotide sequence amplified to previously reported papillomaviruses suggested the presence of a novel papillomavirus type.

DIAGNOSIS

A presumptive diagnosis of pigmented viral papilloma was made.

CLINICAL RELEVANCE

While the papillomas described in these two cases do not appear to cause major clinical disease, they are visually unappealing and have the potential to spread to other valuable deer.

Animal papillomaviruses

We provide an overview of the host range, taxonomic classification and genomic diversity of animal papillomaviruses. The complete genomes of 112 non-human papillomavirus types, recovered from 54 different host species, are currently available in GenBank. The recent characterizations of reptilian papillomaviruses extend the host range of the Papillomaviridae to include all amniotes. Although the genetically diverse papillomaviruses have a highly conserved genomic lay-out, deviations from this prototypic genome organization are observed in several animal papillomaviruses, and only the core ORFs E1, E2, L2 and L1 are present in all characterized papillomavirus genomes. The discovery of papilloma-polyoma hybrids BPCV1 and BPCV2, containing a papillomaviral late region but an early region encoding typical polyomaviral nonstructural proteins, and the detection of recombination breakpoints between the early and late coding regions of cetacean papillomaviruses, could indicate that early and late gene cassettes of papillomaviruses are relatively independent entities that can be interchanged by recombination.

Bos grunniens papillomavirus type 1: a novel deltapapillomavirus associated with fibropapilloma in yak

Papillomaviruses (PVs) have been widely identified among vertebrates, but have not yet been reported to infect yaks. We report, for the first time, a novel deltapapillomavirus that was associated with fibropapilloma in yak herds on the Qinghai–Tibetan Plateau. Six skin papilloma samples were collected and examined using histopathology, immunohistochemistry and PCR assays. The samples were identified as fibropapilloma and were found to contain PV antigens. Sequencing of diagnostic PCR products and the full-length genome revealed that all samples were infected with the same PV type. The whole virus genome was 7946 bp in length and possessed the common PV genomic organization. The virus was identified as a novel PV type and designated Bos grunniens papillomavirus type 1 (BgPV-1) based on the nucleotide sequence alignment of the L1 ORF. It is classified in the Delta-4 species of the genus Deltapapillomavirus based on phylogenetic analysis of the L1 ORF. Identification of this novel PV type provides further information about the pathology, development of diagnostic methods and evolutionary studies of the family Papillomaviridae.

Characterization of the complete genomes of Camelus dromedarius papillomavirus types 1 and 2

Camel papillomatosis has been described previously, but the genome of the suspected papillomavirus (PV) has not been identified. An outbreak of papillomatosis occurred in a dromedary farm of 55 animals in Sudan during August 2009. The disease was only present in young animals aged about 3-7 months, of which 44 % (11/25) were affected with lesions, mainly on the lips and lower jaw. This study reports for the first time the complete genomes of Camelus dromedarius papillomavirus types 1 (CdPV1) and 2 (CdPV2), isolated from a cauliflower-like nodule and a round oval raised nodule, respectively. Pairwise comparisons of their L1 nucleotide sequences revealed 69.2 % identity, and phylogenetic analyses suggested that these two PV types are grouped within the genus Deltapapillomavirus. Both viruses were isolated from fibropapillomas, although no putative E5 proteins homologous to that of bovine papillomavirus type 1 were identified. The genetic information will be useful for evolutionary studies of the family Papillomaviridae, as well as for the development of diagnostic methods for surveillance of the disease in dromedaries.

Novel betapapillomavirus associated with hand and foot papillomas in a cynomolgus macaque

Betapapillomavirus is a genus of papillomaviruses (PVs) commonly found in human skin and associated with both benign and malignant skin lesions. Only 2 previous beta-PVs have been fully characterized in nonhuman species. This report describes a novel beta-PV, named Macaca fascicularis PV type 2 (MfPV2), isolated from exophytic skin papillomas on the hands and feet of a 2-year-old male cynomolgus monkey (M. fascicularis). On histology the papillomas were composed of diffusely thickened epidermis with superficial foci of cytomegaly, cytoplasmic pallor, marginalized chromatin, and rare eosinophilic intranuclear inclusion bodies. Positive immunostaining for p16 and the proliferation marker Ki67 was present multifocally within affected epidermis, most prominently within basal-type cells. Complete sequence identity (100%) was noted between PV genomes fully sequenced from hand and foot lesions. The MfPV2 genome was 7632 base pairs in length and included putative open reading frames (ORFs) for E1, E2, E4, E6, E7, L1, and L2 genes, similar to other PVs. The closest relatives to MfPV2 based on the L1 ORF sequence were all beta-PVs. These included human PV (HPV) 9, HPV115, HPV76, HPV75, and MfPV1 (60-70% pairwise identity for all), the latter of which was also isolated from hand and foot papillomas in a cynomolgus macaque. Phylogenetic analysis placed MfPV2 in a new species group (beta-6), distinct from HPVs (beta-1 to beta-5) and MfPV1 (beta-1). These findings characterize a new nonhuman beta-PV and provide additional support for the idea that tissue tropism among ancestral primate PVs developed prior to divergence of certain Old World primate lineages.

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

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.

Papillomavirus-associated fibropapillomas of red deer ( Cervus elaphus )

Oval, firm, cutaneous tumours with a rough, hairless, pigmented surface, exhibiting a moderately pronounced papillary structure were detected on the abdominal skin of two young red deer ( Cervus elaphus ). One animal was shot in Lower Austria in 2004, the other at a deer farm in Hungary in 2007. Histological examination of both samples classified the tumours as fibropapillomas, showing marked proliferation of fibroblasts and connective tissue, accompanied by hyperkeratosis, parakeratosis and acanthosis of the overlaying epidermis, and occasional foci of inflammation. The distribution of cytokeratin and vimentin was characterised in the lesion. The presence of papillomavirus (PV) antigen was demonstrated by immunohistochemistry in both cases. Papillomavirus-specific DNA was successfully amplified by PCR from one sample. The obtained partial nucleotide sequence of the L2 ORF exhibited the highest critical identity values with the homologous regions of Delta-papillomaviruses, especially the Roe deer papillomavirus (93%). Phylogenetic analysis of the partial L2 ORF sequence alignment of 10 papillomaviruses by both neighbour-joining and maximum parsimony method confirmed that the Red deer PV is very closely related to the Western roe deer papillomavirus (CcPV1).

Endemic papillomavirus infection of roe deer (Capreolus capreolus)

Roe deer papillomavirus (CcPV1) infection has been identified as an endemic disease in roe deer populations of the Carpathian basin in Central Europe (Hungary, Austria and Croatia). The disease is characterised by easily recognizable skin tumours similar to deer papillomavirus infection of North American deer species. In 2006, a questionnaire study was conducted among all Hungarian game management units (GMUs) in order to assess the distribution of the disease and its major epidemiological features. Categorical information was collected about disease occurrence, trend and frequency of detection, on primarily affected age classes in both sexes, and association of lesions with mortality. Replies were received from 539 GMUs representing 50.9% of total GMU territory and disease presence was reported by 295 (54.7%) GMUs. Older age classes of both sexes were found to be more affected. Association of various environmental factors with disease occurrence was evaluated and data were collected on the occurrence of similar skin lesions in other European countries. Pathological features of CcPV1 infection were described and the localisation of both CcPV1 antigen and DNA was characterised by immunohistochemistry and in situ DNA hybridisation in skin lesions. Virus presence was also demonstrated by PCR and PCR product sequencing.