Identification of two novel equine papillomavirus sequences suggests three genera in one cluster

Equus caballus papillomavirus Type 7 is a rare cause of equine penile squamous cell carcinomas

Penile squamous cell carcinomas (SCCs) are common, potentially life-threatening neoplasms of horses. They are well-recognized to be caused by Equus caballus papillomavirus (EcPV) type 2, although EcPV2 cannot be detected in all cases. A 23-year-old standardbred gelding developed multiple penile in situ and invasive SCCs that contained histological evidence of PV infection. By using both consensus and specific PCR primers, these lesions were found to contain EcPV7 DNA, but not DNA from EcPV2 or any other PV type. To determine how frequently EcPV7 is present in equine penile SCCs, specific primers were used to detect EcPV2 and EcPV7 in a series of 20 archived samples. EcPV7 was the only PV detected in one, both EcPV2 and 7 were detected in five, and only EcPV2 was detected in 14 SCCs. EcPV7 DNA was also detected in three of 10 archived oropharyngeal SCCs, although only as a co- infection with EcPV2. This is the first report of EcPV7 causing disease in horses. These results suggest EcPV7 could cause a subset of equine penile SCCs, and this is the first evidence that PV types other than EcPV2 can cause these neoplasms. The detection of EcPV7 in the oropharyngeal SCCs suggests a potential role of this PV type in the development of these SCCs. There were no clinical or histological features that differentiated lesions containing EcPV7 DNA from those containing EcPV2 DNA. If EcPV7 causes a proportion of equine penile SCCs, vaccines to prevent EcPV2 infection may not prevent all equine penile SCCs.

Detection of Equus caballus Papillomavirus in Equine Aural Plaque Samples

Aural plaques have been linked to Equus caballus papillomavirus (EcPV). Ten types of EcPVs have already been described; however, only EcPVs 1, 3, 4, 5, and 6 have been observed in association with aural plaques. Accordingly, the objective of this study was to evaluate the presence of EcPVs in equine aural plaque samples. A total of 29 aural plaque samples (from 15 horses) were collected and assessed for the presence of the DNA of these EcPVs by PCR. Additionally, 108 aural plaque samples used in previous research were evaluated for the presence of EcPVs 8 and 9. Previously described primers were used for PCR to detect EcPVs 1 to 8, and specific primers were designed for EcPV 9. Minigenes were synthesized and used as a positive control in the PCRs for the undetected EcPVs. EcPVs 2, 7, 8, and 9 were not detected in any of the evaluated samples, suggesting that these viral types are not involved in the etiology of the equine aural plaque in Brazil. EcPV 6 was the most prevalent (81%), followed by EcPVs 3 (72%), 4 (63%) and 5 (47%), which reinforces the idea that these viruses play an important role in the etiology of the equine aural plaque in Brazil.

Cutaneous plaques associated with a putative novel papillomavirus type in a horse

CASE HISTORY AND CLINICAL FINDINGS

A 6-year-old Thoroughbred mare developed multiple flat plaques, < 1 cm in diameter, on the left front fetlock. These were treated topically using 5-fluorouracil and resolved after 4 weeks. However, additional similar plaques developed on the left front pastern 5 months later. These lesions resolved within 3 months without treatment.

PATHOLOGICAL AND MOLECULAR FINDINGS

One plaque that developed initially and one plaque that developed later were examined histologically. Both consisted of well-demarcated foci of moderate epidermal hyperplasia. Scattered throughout both plaques were cells showing evidence of papillomavirus-induced cell changes and the same papillomaviral DNA sequence was amplified from both lesions using PCR. As the novel sequence had 79.1% similarity to a partial sequence previously amplified from an equine cutaneous wart and 67.9% similarity to Equus caballus papillomavirus type 1, these results indicate detection of a putative novel papillomavirus type.

DIAGNOSIS

Multiple cutaneous plaques due to infection by a novel papillomavirus type.

CLINICAL RELEVANCE

Unlike more typical equine cutaneous warts which generally appear as pedunculated and filiform masses, the lesions in this horse appeared as raised plaques. With the exception of aural plaques that are confined to the ears, localised clusters of papillomaviral plaques have not been previously described in horses. The lesions contained subtle histological evidence of papillomavirus infection and careful examination is required to differentiate these plaques from pre-neoplastic lesions. The plaques contained a putative novel papillomavirus type. These results increase the spectrum of papillomavirus-induced skin disease in horses.

Papillomaviral skin diseases of humans, dogs, cats and horses: A comparative review. Part 2: Pre-neoplastic and neoplastic diseases

Papillomaviruses (PVs) are well recognized to cause pre-neoplastic and neoplastic diseases in humans. Similarly, there is increasing evidence that PVs play a significant role in the development of pre-neoplastic and neoplastic diseases of the haired skin of dogs and cats, and the mucosa of horses. As the mechanisms by which PVs cause neoplasia are well studied in humans, it is valuable to compare the PV-induced neoplasms of humans with similar PV-associated neoplasms in the companion animal species. In the second part of this comparative review, the pre-neoplastic and neoplastic diseases thought to be caused by PVs in humans, dogs, cats, and horses are described. This includes PV-induced cutaneous plaques, cutaneous squamous cell carcinomas (SCCs) and mucosal SCCs within the four species. The review concludes with a discussion about the potential use of vaccines to prevent PV-induced diseases of dogs, cats, and horses.

Tumor Cell Plasticity in Equine Papillomavirus-Positive Versus-Negative Squamous Cell Carcinoma of the Head and Neck

Squamous cell carcinoma of the head and neck (HNSCC) is a common malignant tumor in humans and animals. In humans, papillomavirus (PV)-induced HNSCCs have a better prognosis than papillomavirus-unrelated HNSCCs. The ability of tumor cells to switch from epithelial to mesenchymal, endothelial, or therapy-resistant stem-cell-like phenotypes promotes disease progression and metastasis. In equine HNSCC, PV-association and tumor cell phenotype switching are poorly understood. We screened 49 equine HNSCCs for equine PV (EcPV) type 2, 3 and 5 infection. Subsequently, PV-positive versus -negative lesions were analyzed for expression of selected epithelial (keratins, β-catenin), mesenchymal (vimentin), endothelial (COX-2), and stem-cell markers (CD271, CD44) by immunohistochemistry (IHC) and immunofluorescence (IF; keratins/vimentin, CD44/CD271 double-staining) to address tumor cell plasticity in relation to PV infection. Only EcPV2 PCR scored positive for 11/49 equine HNSCCs. IHC and IF from 11 EcPV2-positive and 11 EcPV2-negative tumors revealed epithelial-to-mesenchymal transition events, with vimentin-positive cells ranging between <10 and >50%. CD44- and CD271-staining disclosed the intralesional presence of infiltrative tumor cell fronts and double-positive tumor cell subsets independently of the PV infection status. Our findings are indicative of (partial) epithelial–mesenchymal transition events giving rise to hybrid epithelial/mesenchymal and stem-cell-like tumor cell phenotypes in equine HNSCCs and suggest CD44 and CD271 as potential malignancy markers that merit to be further explored in the horse.

Detection of a Putative Novel Papillomavirus Type within a Large Exophytic Papilloma on the Fetlock of a Horse

A 10-year-old horse presented with two 3-cm diameter exophytic masses over the fetlock. Histology was consistent with a hyperplastic squamous papilloma and numerous cell changes consistent with papillomavirus (PV) infection were visible. Partial sequences of PV L1 and E1 ORFs were amplified using consensus PCR primers. The sequences were most similar to Equus caballus type 1 (EcPV1). However, as the sequences were only around 73% similar to EcPV1, they appear to be from a novel PV type that is likely to be within the Zetapapillomavirus genus. The papillomas were treated with topical imiquimod and resolved within 14 weeks. The clinical presentation of the papillomas in the present case had marked differences to the clinical presentation of EcPV-1-induced papillomas, which are typically small, numerous and around the face. Observations from the present case increase the clinical spectrum of PV-induced lesions in this species as well as providing evidence of an additional novel papillomavirus that is able to cause disease in horses.

Paving the way for more precise diagnosis of EcPV2-associated equine penile lesions

Background

There is growing evidence that equine papillomavirus type 2 (EcPV2) infection is causally associated with the development of equine genital squamous cell carcinomas (SCCs). Early stages of disease present clinically as plaques or wart-like lesions which can gradually progress to tumoural lesions. Histologically these lesions are inconsistently described as benign hyperplasia, papilloma, penile intraepithelial neoplasia (PIN), carcinoma in situ (CIS) or SCC. Guidelines for histological classification of early SCC precursor lesions are not precisely defined, leading to potential misdiagnosis. The aim of this study was to identify histologic criteria and diagnostic markers allowing for a more accurate diagnosis of EcPV2-associated equine penile lesions.

Results

A total of 61 archived equine penile lesions were histologically re-assessed and classified as benign hyperplasia, papilloma, CIS or SCC. From these, 19 representative lesions and adjacent normal skin were comparatively analysed for the presence of EcPV2 DNA and transcripts using PCR and RNA in situ hybridisation (RISH). All lesional samples were positive by EcPV2 PCR and RISH, while adjacent normal skin was negative. RISH analysis yielded signal distribution patterns that allowed distinction of early (hyperplasia, papilloma) from late stage lesions (CIS, SCC). Subsequently, the 19 lesions were further assessed for expression of p53, Ki67, MCM7 and MMP1 by immunohistochemistry (IHC). All four proteins were expressed in both normal and lesional tissue. However, p53 expression was up-regulated in basal keratinocyte layers of papillomas, CIS and SCCs, as well as in upper keratinocyte layers of CIS and SCCs. MCM7 expression was only up-regulated in upper proliferating keratinocyte layers of papillomas, CIS and SCCs.

Conclusion

This study proposes combining a refined histological protocol for analysis of equine penile lesions with PCR- and/or RISH based EcPV2-screening and p53/MCM7 IHC to more accurately determine the type of lesion. This may help to guide the choice of optimum treatment strategy, especially at early stages of disease.

Identification of a Novel Equine Papillomavirus in Semen from a Thoroughbred Stallion with a Penile Lesion

Papillomaviruses (PVs) have been identified in a wide range of animal species and are associated with a variety of disease syndromes including classical papillomatosis, aural plaques, and genital papillomas. In horses, 13 PVs have been described to date, falling into six genera. Using total RNA sequencing (meta-transcriptomics) we identified a novel equine papillomavirus in semen taken from a thoroughbred stallion suffering a genital lesion, which was confirmed by nested RT-PCR. We designate this novel virus Equus caballus papillomavirus 9 (EcPV9). The complete 7656 bp genome of EcPV9 exhibited similar characteristics to those of other horse papillomaviruses. Phylogenetic analysis based on concatenated E1-E2-L2-L1 amino acid sequences revealed that EcPV9 clustered with EcPV2, EcPV4, and EcPV5, although was distinct enough to represent a new viral species within the genus Dyoiotapapillomavirus (69.35%, 59.25%, and 58.00% nucleotide similarity to EcPV2, EcPV4, and EcPV5, respectively). In sum, we demonstrate the presence of a novel equine papillomavirus for which more detailed studies of disease association are merited.

RNA-seq analysis in equine papillomavirus type 2-positive carcinomas identifies affected pathways and potential cancer markers as well as viral gene expression and splicing events

Equine papillomavirus type 2 (EcPV2) was discovered only recently, but it is found consistently in the context of genital squamous cell carcinomas (SCCs). Since neither cell cultures nor animal models exist, the characterization of this potential disease agent relies on the analysis of patient materials. To analyse the host and viral transcriptome in EcPV2-affected horses, genital tissue samples were collected from horses with EcPV2-positive lesions as well as from healthy EcPV2-negative horses. It was determined by RNA-seq analysis that there were 1957 differentially expressed (DE) host genes between the SCC and control samples. These genes were most abundantly related to DNA replication, cell cycle, extracellular matrix (ECM)-receptor interaction and focal adhesion. By comparison to other cancer studies, MMP1 and IL8 appeared to be potential marker genes for the development of SCCs. Analysis of the viral reads revealed the transcriptional activity of EcPV2 in all SCC samples. While few reads mapped to the structural viral genes, the majority of reads mapped to the non-structural early (E) genes, in particular to E6, E7 and E2/E4. Within these reads a distinct pattern of splicing events, which are essential for the expression of different genes in PV infections, was observed. Additionally, in one sample the integration of EcPV2 DNA into the host genome was detected by DNA-seq and confirmed by PCR. In conclusion, while host MMP1 and IL8 expression and the presence of EcPV2 may be useful markers in genital SCCs, further research on EcPV2-related pathomechanisms may focus on cell cycle-related genes, the viral genes E6, E7 and E2/E4, and integration events.

Frequency of Equus caballus papillomavirus in equine aural plaques

Despite the reported association between aural plaques and the presence of Equus caballus papillomavirus (EcPV), there are few data regarding the distribution of viral types in different geographic regions or possible correlations for different papillomaviruses and lesion characteristics. We detected the presence and frequency of EcPV (1-7) DNA in aural plaque biopsies of horses from different regions of Brazil and identified the patterns of these infections or coinfections and their possible association with lesion severity. A total of 108 aural plaque biopsies from horses in the 5 geopolitical regions of Brazil were examined. We performed PCR to detect EcPV DNA in the biopsies. At least 1 type of EcPV was detected in 97% of the samples. EcPV coinfection was observed in 59% of the samples. Compared to the other viruses, EcPV-4 was found at the highest frequency in coinfection (84%) or individually identified (32%). EcPV-2 and -7 were not detected. No significant association was found between lesion characteristics (type and distribution) and either the viral type detected or the presence of coinfection. EcPV is widely distributed in Brazil, both isolated and in coinfection; the viral type does not appear to influence the clinical characteristics of equine aural plaques.

Isolation of equine papillomavirus type 1 from racing horse in Japan

Although many studies have been conducted worldwide for Equus caballus papillomavirus (EcPV), limited information is available on the virus in Japan. We recently collected one classical viral papillomatosis sample (E150904) from a racing horse in Japan. Papillomavirus infection was confirmed by histopathology, immunohistochemistry and PCR assays, and the sample was diagnosed as epithelial papilloma. Full-length genome of the virus was cloned and sequenced. It was 7,613 bp in length and had the same genome organization with reported EcPV-1. Moreover, phylogenetic analysis based on L1 gene revealed that the infection was caused by a variant of EcPV-1. This is the first report of EcPV infection in Japan, and would further contribute to the molecular epidemiological and pathological studies for EcPV.

Generalized papillomatosis in three horses associated with a novel equine papillomavirus (EcPV8)

BACKGROUND

Currently, seven equine papillomaviruses (PV) are known and are associated with one of three different and distinct clinical presentations.

HYPOTHESIS/OBJECTIVES

To report the clinical, histopathological and immunohistochemical findings in horses with generalized papillomatosis associated with a novel equine PV, Equus caballus papillomavirus 8 (EcPV8).

ANIMALS

Three client-owned quarter horses.

METHODS

Case report, retrospective.

RESULTS

Dozens to thousands of papillomas involved the axilla, inguinal area and proximal limbs as well as the ventral and lateral neck, thorax and abdomen. Lesions were sometimes confluent in ventral areas. Fewer lesions were on the face, ears, distal limbs and genitalia. Plaque-type papillomas were small, 0.5 to 1.5 cm in diameter and hyperkeratotic. Histologically, plaque-type papillomas prominently involved follicular infundibula. Immunohistochemical findings demonstrated PV antigen in superficial keratinocyte nuclei. PCR using degenerate primers for the PV L1 gene and sequencing of amplicons revealed PV DNA sequences that were 98% identical for all three cases, but shared <70% identity to other PVs. Horses were otherwise healthy; serum immunoglobulin levels and peripheral blood lymphocyte phenotyping did not identify a known immunodeficiency syndrome. Lesions nearly completely resolved after 1.5 years in one horse and persisted for two years in another, despite intralesional human IFN-alpha treatment. The oldest horse was lost to follow-up.

CONCLUSION AND CLINICAL IMPORTANCE

A novel equine papillomavirus (EcPV8) is associated with a distinct, plaque-type, generalized papillomatosis. Papillomas persisted for months to years, with or without treatment.

Papillomavirus infection and squamous cell carcinoma in horses

Squamous cell carcinoma (SCC) is a common disease that seriously impairs the health and welfare of affected horses and other equids. In humans, almost all cervical carcinomas, a high percentage of anogenital SCCs and a subset of SCCs of the head and neck are caused by high-risk human papillomavirus (hrHPV) infection. Since hrHPV-induced human cancers and equine SCC have similar cytological and histopathological features, it has been hypothesised that equine SCCs could also be induced by papillomaviruses. This review provides an overview of the current evidence for an aetiological association between papillomavirus infections and equine SCCs and SCC precursor lesions. SCC of apparently papillomavirus-unrelated aetiology are also discussed, as are recent advances in equine SCC prophylaxis.

Pododermatitis in Captive and Free-Ranging Greater Flamingos (Phoenicopterus roseus)

Pododermatitis is frequent in captive flamingos worldwide, but little is known about the associated histopathologic lesions. Involvement of a papillomavirus or herpesvirus has been suspected. Histopathologic evaluation and viral assessment of biopsies from 19 live and 10 dead captive greater flamingos were performed. Selected samples were further examined by transmission electron microscopy and immunohistochemistry. Feet from 10 dead free-ranging greater flamingos were also evaluated. The histologic appearance of lesions of flamingos of increasing age was interpreted as the progression of pododermatitis. Mild histologic lesions were seen in a 3-week-old flamingo chick with no macroscopic lesions, and these were characterized by Micrococcus-like bacteria in the stratum corneum associated with exocytosis of heterophils. The inflammation associated with these bacteria may lead to further histologic changes: irregular columnar proliferations, papillary squirting, and dyskeratosis. In more chronic lesions, hydropic degeneration of keratinocytes, epidermal hyperplasia, and dyskeratosis were seen at the epidermis, as well as proliferation of new blood vessels and increased intercellular matrix in the dermis. Papillomavirus DNA was not identified in any of the samples, while herpesvirus DNA was seen only in a few cases; therefore, these viruses were not thought to be the cause of the lesions. Poor skin health through suboptimal husbandry may weaken the epidermal barrier and predispose the skin to invasion of Micrococcus-like bacteria. Histologic lesions were identified in very young flamingos with no macroscopic lesions; this is likely to be an early stage lesion that may progress to macroscopic lesions.

Expression of p53, Ki67, EcPV2- and EcPV3 DNA, and viral genes in relation to metastasis and outcome in equine penile and preputial squamous cell carcinoma

REASONS FOR PERFORMING STUDY

Equine penile and preputial squamous cell carcinoma (SCC) is a potentially lethal disease of which little is known regarding the relationship between tumour characteristics and prognosis.

OBJECTIVES

To assess the relationship between tumour differentiation grade (tumour subtype), presence of papillomaviruses, expression of viral genes (E2, E6, L1), nuclear proteins p53 and Ki67 and metastasis in equine penile and preputial SCC and to assess the relationship of tumour subtype, presence of papillomavirus type 2, p53 and Ki67 with survival.

STUDY DESIGN

Retrospective case-control study using archived material.

METHODS

Samples (n = 103) from 87 horses with penile and/or preputial intraepithelial neoplasia (PIN), papilloma or SCC and corresponding case files were evaluated. Tumours were graded microscopically and p53 and Ki67 expression evaluated immunohistochemically. Equine papillomavirus (EcPV) types 2 and 3 DNA was detected by conventional PCR. Real-time PCR was used for quantification of E2, E6 and L1 mRNA.

RESULTS

Equine papillomavirus type 2 DNA was detected in 89.4% and EcPV3 in 1.5% of horses. No differences in quantitative expression of E2, E6 and L1 oncogenes between subtypes were found. Expression of p53 and occurrence of metastasis were positively correlated to a less differentiated subtype (r = 0.429, P<0.001 and r = 0.769, P = 0.001, respectively). Differences in survival between subtypes were significant (log Rank P<0.001); horses with less differentiated tumours were more likely to die of the disease (papilloma 8.3%; G1 26.1%; G2 26.3%; G3 63.3%).

CONCLUSIONS

In equine penile and preputial SCC, tumour grading is an important prognosticator for survival and a predictor for presence of metastases. Expression of p53 and Ki67 and presence or expression of EcPV2 and EcPV3 do not appear to be important prognosticators.

Equus asinus papillomavirus (EaPV1) provides new insights into equine papillomavirus diversity

We detected a novel papillomavirus (EaPV1) from healthy skin and from sun associated cutaneous lesions of an Asinara (Sardinia, Italy) white donkey reared in captivity in a wildlife recovery centre. The entire genome of EaPV1 was cloned, sequenced, and characterised. Genome is 7467 bp long, and shows some characteristic elements of horse papillomaviruses, including a small untranslated region between the early and late regions and the lack of the retinoblastoma tumour suppressor binding domain LXCXE in E7. Additionally, a typical E6 ORF is missing. EaPV1 DNA was detected in low copies in normal skin of white and grey donkeys of the Asinara Island, and does not transform rodent fibroblasts in standard transformation assays. Pairwise nucleotide alignments and phylogenetic analyses based on concatenated E1-E2-L1 amino acid sequences revealed the highest similarity with the Equine papillomavirus type 1. The discovery of EaPV1, the prototype of a novel genus and the first papillomavirus isolated in donkeys, confirms a broad diversity in Equidae papillomaviruses. Taken together, data suggest that EaPV1 is a non-malignant papillomavirus adapted to healthy skin of donkeys.

Four novel papillomavirus sequences support a broad diversity among equine papillomaviruses

Papillomaviruses appear to be species-specific pathogens, and it was suggested that each animal species might harbour its own set of papillomaviruses. However, all approaches addressing the underlying evolutionary phenomena still suffer from very limited data about animal papillomaviruses. In case of the horse for example, only three equine papillomaviruses (EcPVs) have been identified. To further address the situation in this host, suspected papillomavirus-associated lesions were tested for EcPV DNA. Four novel EcPV types were detected and their genomes entirely cloned and sequenced. They display the characteristic organization, with early (E) and late (L) regions harbouring the seven classical open reading frames divided by non-coding regions. They were named EcPVs 4, 5, 6 and 7, according to their dissimilarity to other papillomaviruses. Most L1 nucleotide identities were shared with EcPV2 in case of EcPV4 (62 %) and EcPV5 (60 %) or with EcPV3 in case of EcPV6 (70 %) and EcPV7 (71 %). Thus, EcPVs 4 and 5 may establish novel species within the genus Dyoiota, while EcPVs 6 and 7 might fit into the genus Dyorho and belong to the same species as EcPV3. They were found in genital plaques (EcPV4), aural plaques (EcPV5, EcPV6) or penile masses (EcPV7). Interestingly, PCR analysis revealed the DNA of EcPV2 and EcPV4 as well as of EcPV3 and EcPV6 together in the same tissue samples, respectively. In conclusion, the DNA of four novel EcPV types was identified and cloned. They cluster with the known types and support broad genetic EcPV diversity in at least two of the known clades. Furthermore, PCR assays also provide evidence for EcPV co-infections in horses.

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.

Multiple evolutionary origins of bat papillomaviruses

Infection by papillomaviruses (PVs) has been linked to different types of neoplasias, in both human and non-human hosts. Knowledge about PV diversity is essential to reliably infer the evolutionary history of these pathogens and to elucidate the link between infection and disease. We cloned and sequenced the complete genome of a novel PV, EhelPV1, isolated from hair bulbs from a captive straw-colored fruit bat Eidolon helvum (Pteropodidae, Chiroptera). We also retrieved partial sequences of the E1 and L1 genes from hair bulbs from a captive Indian flying fox Pteropus giganteus (Pteropodidae, Chiroptera). The detected virus (PgigPV1) presumably corresponded to a novel type as well. Maximum likelihood phylogenetic analyses were conducted using a representative collection of 132 PVs. EhelPV1 belonged to the Lambda+Mu-PV crown group and was most closely related to another bat PV, MschPV2. Both fragments of PgigPV1 were placed alongside with EhelPV1. The novel PVs were phylogenetically distant from other previously described bat PVs, namely MrPV1, MschPV1 and RaPV1. We have further characterized the sequence patterns of the E2-binding sites occurring in the upstream regulatory region of Lambda+Mu-PVs. Common fingerprints within this region are shared by certain PVs. However, there is not a sharp correspondence between the repertoire of transcription factor binding sites in the viral regulatory region and host range, tissue tropism or viral life style. Our results reinforce the hypothesis that PVs have undergone an initial radiation prior to the divergence of the mammalian hosts, giving rise to the present-day PV crown groups.

Characterisation of early and late bovine papillomavirus protein expression in equine sarcoids

Sarcoids are common skin tumours of horses and donkeys that are characterised by persistent proliferation of dermal fibroblasts associated with the presence of bovine papillomavirus (BPV) DNA. Some early BPV proteins have been demonstrated within sarcoids and RNA containing both early and late transcripts is present, yet it remains unclear whether late replication of BPV, culminating in the production of infectious virus particles, can occur in equids. Here we report that BPV1 RNA isolated from equine sarcoids encodes a unique deletion of four residues within the L2 protein suggesting a novel variant of virus has evolved in equines. Such viral evolution would require the production and transmission of virus particles among horses with sarcoids. Quantitative RT-PCR demonstrated the presence of mRNA transcripts containing early gene message in sarcoid tissues and BPV-E2 early virus antigen was detected by immunofluorescence in the nuclei of dermal fibroblasts, but no E2 expression could be detected within the overlying epidermis where productive virus replication would be expected to occur. Although immunohistochemistry clearly detected late virus proteins in the nuclei of dermal cells from samples of bovine papillomas, no late protein expression was detected in formalin-fixed tissue from equine sarcoids; either in the dermis or epidermis. Moreover, quantitative RT-PCR demonstrated that late gene mRNA represented <0.3% of the transcribed BPV RNA. We conclude that BPV does not undergo productive infection in the epidermis overlying equine sarcoids at levels comparable with that occurring in its natural bovine host.

EcPV2 DNA in equine papillomas and in situ and invasive squamous cell carcinomas supports papillomavirus etiology

Equine penile papillomas, in situ carcinomas, and invasive carcinomas are hypothesized to belong to a continuum of papillomavirus-induced diseases. The former ones clinically present as small grey papules, while the latter 2 lesions are more hyperplasic or alternatively ulcerated. To test the hypothesis that these lesions are papillomavirus-induced, samples of 24 horses with characteristic clinical and histologic findings of penile papillomas or in situ or invasive squamous cell carcinomas were collected. As controls, 11 horses with various lesions--namely, Balanoposthitis (6 cases), melanoma (3 cases), follicular cyst (1 case), and amyloidosis (1 case)--were included. DNA was extracted and polymerase chain reaction applied to amplify papillomavirus DNA. The respective primers were designed to amplify DNA of the recently discovered equine papillomavirus EcPV2. All tested papilloma and squamous cell carcinoma samples were found to contain DNA of either of 2 previously published EcPV2 variants. Among the other samples 6 of 11 were found to contain EcPV2 DNA. To further support the findings and to determine where the papillomavirus DNA was located within the lesions, an in situ hybridization for the detection of EcPV2 DNA was established. The samples tested by this technique were found to clearly contain papillomavirus nucleic acid concentrated in the nucleus of the koilocytes. The findings of this study support previous data and the hypothesis that papillomaviruses induce the described penile lesions in horses.

Phylogenetic and structural studies of a novel equine papillomavirus identified from aural plaques

Papillomaviruses (PVs) infect a wide range of animal species and show great genetic diversity. To date, excluding equine sarcoids, only three species of PVs were identified associated with lesions in horses: Equus caballus papillomavirus 1 (EcPV1-cutaneous), EcPV2 (genital) and EcPV3 (aural plaques). In this study, we identified a novel equine PV from aural plaques, which we designated EcPV4. Cutaneous samples from horses with lesions that were microscopically diagnosed as aural plaques were subjected to DNA extraction, amplification and sequencing. Rolling circle amplification and inverse PCR with specific primers confirmed the presence of an approximately 8 kb circular genome. The full-length EcPV4 L1 major capsid protein sequence has 1488 nucleotides (495 amino acids). EcPV4 had a sequence identity of only 53.3%, 60.2% and 51.7% when compared with the published sequences for EcPV1, EcPV2 and EcPV3, respectively. A Bayesian phylogenetic analysis indicated that EcPV4 clusters with EcPV2, but not with EcPV1 and EcPV3. Using the current PV classification system that is based on the nucleotide sequence of L1, we could not define the genus of the newly identified virus. Therefore, a structural analysis of the L1 protein was carried out to aid in this classification because EcPV4 cause lesion similar to the lesion caused by EcPV3. A comparison of the superficial loops demonstrated a distinct amino acid conservation pattern between EcPV4/EcPV2 and EcPV4/EcPV3. These results demonstrate the presence of a new equine PV species and that structural studies could be useful in the classification of PVs.

Novel animal papillomavirus sequences and accurate phylogenetic placement

All amniotes are probably infected by specific papillomaviruses (PVs), but knowledge about PV diversity remains sparse. An insufficient taxon sampling, and a focus on humans as hosts, may perturb phylogenetic analyses leading to wrong conclusions about PV evolution. We performed a systematic approach to explore the diversity of PVs combining rolling circle amplification with the use of "universal" primers to search for the presence of novel PV sequences in animal samples. We communicate 12 sequences putatively corresponding to novel PVs gained from 10 host species in eight mammal families: Bovidae, Canidae, Cervidae, Equidae, Hominidae, Phocoenidae, Procyonidae and Pteropodidae. The phylogenetic position of the new sequences was inferred with an evolutionary placement algorithm under a Maximum Likelihood framework using a pre-computed, well-resolved tree constructed with the E1-E2-L1 gene sequences as a backbone. The new sequences were phylogenetically diverse and could be respectively placed with confidence within all four PV crown groups. The prevailing presence of sequences from the crown groups Alpha+Omikron-PVs and Beta+Xi-PVs may correspond to an increased viral diversity in these taxa, or rather reflect a combination of anthropocentric bias and preferential amplification from commonly used "universal" primers. Our results combined with literature data support the view that the number and diversity of animal PVs is overwhelmingly large.

EcPV2 DNA in equine genital squamous cell carcinomas and normal genital mucosa

Squamous cell carcinoma (SCC) represents the most common genital malignant tumor in horses. Similar to humans, papillomaviruses (PVs) have been proposed as etiological agents and recently Equine papillomavirus type 2 (EcPV2) has been identified in a subset of genital SCCs. The goals of this study were (1) to determine the prevalence of EcPV2 DNA in tissue samples from equine genital SCCs, penile intraepithelial neoplasia (PIN) and penile papillomas, using EcPV2-specific PCR, (2) to examine the prevalence of latent EcPV2 infection in healthy genital mucosa and (3) to determine genetic variability within EcPV2 and to disentangle phylogenetic relationships of EcPV2 among PVs. EcPV2 DNA was detected in all but one penile SCC (15/16), in all PIN lesions (8/8) and penile papillomas (4/4). Additionally, EcPV2 DNA was demonstrated in one of two metastasized lymph nodes, one contact metastasis in the mouth, two vaginal and one anal lesion. In healthy horses, EcPV2 DNA was detected in 10% (4/39) of penile swabs but in none of vulvovaginal swabs (0/20). This study confirms the presence of EcPV2 DNA in equine genital SCCs and shows its involvement in anal lesions, a lymph node and contact metastases. Latent EcPV2 presence was also shown in normal male genital mucosa. We found that different EcPV2 variants cocirculate among horses and that EcPV2 is related to the Delta+Zeta PVs and is only a very distant relative of high-risk human PVs causing genital cancer. Thus, similar viral tropism and similar malignant outcome of the infection do not imply close evolutionary relationship.