Incidental finding of a human-like tusavirus in a lamb with lip lesions and fatal pneumonia

Tusaviruses in the genus Protoparvovirus of family Parvoviridae were first identified in a diarrhoeic Tunisian child in 2014. Thereafter, high prevalence of a genetically similar virus was demonstrated in faeces from caprine and ovine species in Hungary. Here, we describe an investigation into the cause of scabby lip lesions in a 6 month-old lamb, submitted from a farm experiencing weight loss and scouring in lambs in England. Transmission electron microscopy visualised small circular particles of 18 and 22 nm in diameter in lip lesions identified as tusavirus and flumine parvovirus by Next Generation Sequencing. Liver, kidney, lung, small intestine content and faeces were also strongly positive for the tusavirus DNA as well as 10 % of faecal samples of the flock collected 2 months after the initial lip sampling. NS1 and VP1 amino acid sequences of this tusavirus displayed 99.5 and 92.89 % identity to those of a human tusavirus, respectively. These amino acid identities were at 95.5 and 89.68 % when compared to those of a goat tusavirus. Phylogenetic analysis of the NS1 and VP1 also grouped the virus in the genus Protoparvovirus and close to tusaviruses detected in human, ovine and caprine species. Wider surveillance of the virus indicated a broader geographical distribution for the virus in England. Histology of the lip tissue revealed localised areas of epidermal hyperplasia and hyperkeratosis affecting haired skin, with mild leucocyte infiltration of the subjacent dermis, but no changes to implicate virus involvement. Flumine parvovirus was concluded to be an environment contaminant. Broader studies in prevalence of these virus in UK sheep flocks and human population, animal models and experimental infections could provide insights into the pathogenesis of these novel viruses and their zoonotic potential.

Significant Association of Cutavirus With Parapsoriasis en Plaques: High Prevalence Both in Skin Swab and Biopsy Samples

Cutavirus (CuV) is associated with cutaneous T-cell lymphoma (CTCL), of which parapsoriasis is a precursor. Our study reveals a significantly higher CuV-DNA prevalence in skin swabs of parapsoriasis patients (6/13; 46.2%) versus those of healthy adults (1/51; 1.96%). Eight patients (8/12; 66.7%) had CuV DNA in biopsied skin, and 4 developed CTCL.

Newlavirus, a Novel, Highly Prevalent, and Highly Diverse Protoparvovirus of Foxes (Vulpes spp.)

The genus Protoparvovirus (family Parvoviridae) includes several viruses of carnivores. We describe a novel fox protoparvovirus, which we named Newlavirus as it was discovered in samples from Newfoundland and Labrador, Canada. Analysis of the full non-structural protein (NS1) sequence indicates that this virus is a previously uncharacterized species. Newlavirus showed high prevalence in foxes from both the mainland (Labrador, 54/137, 39.4%) and the island of Newfoundland (22/50, 44%) but was not detected in samples from other carnivores, including coyotes (n = 92), lynx (n = 58), martens (n = 146), mink (n = 47), ermines (n = 17), dogs (n = 48), and ringed (n = 4), harp (n = 6), bearded (n = 6), and harbor (n = 2) seals. Newlavirus was found at similar rates in stool and spleen (24/80, 30% vs. 59/152, 38.8%, p = 0.2) but at lower rates in lymph nodes (2/37, 5.4%, p < 0.01). Sequencing a fragment of approximately 750 nt of the capsid protein gene from 53 samples showed a high frequency of co-infection by more than one strain (33.9%), high genetic diversity with 13 genotypes with low sequence identities (70.5-87.8%), and no geographic segregation of strains. Given the high prevalence, high diversity, and the lack of identification in other species, foxes are likely the natural reservoir of Newlavirus, and further studies should investigate its distribution.

Genetic heterogeneity of canine bufaviruses

Canine bufavirus (CBuV) is a protoparvovirus, genetically related to human and non-human primate bufaviruses and distantly related to canine parvovirus type 2 (CPV-2). CBuV was initially identified from young dogs with respiratory signs but subsequent studies revealed that this virus is also a common component of the canine enteric virome. In this survey, by assessing archival and recent collections of dogs faecal samples, CBuV DNA was detected with a higher prevalence rate (8.8%) in animals with enteritis than in control animals (5.0%), although this difference was not statistically significant. The rate of co-infections with other enteric viruses in diarrhoeic dogs was high (84.6%), mostly in association with canine parvovirus CPV-2 (90.1%). The complete ORF2 gene was determined in five samples, and the nearly full-length genome was reconstructed for three strains, 62/2017/ITA, 9AS/2005/ITA and 35/2018/ITA. Upon sequence comparison, the viruses appeared highly conserved in the NS1 (97.2%-97.9% nt and 97.5%-98.1% aa identities). In the complete VP2 coding region, three strains were similar to the prototype viruses (99.7-99.8 nt and 99.6%-99.8% aa) whilst strains 9AS/2005/ITA and 35/2016/ITA were distantly related (87.6%-89.3% nt and 93.9%-95.1% aa identities). Interestingly, genetic diversification occurred downstream conserved regions such as the VP1/VP2 splicing signals and/or the G-rich motif in the N terminus of the VP2, suggesting a potential recombination nature. Upon phylogenetic analysis, the two divergent CBuV strains formed a distinct cluster/genotype.

Cutavirus DNA in Malignant and Nonmalignant Skin of Cutaneous T-Cell Lymphoma and Organ Transplant Patients but Not of Healthy Adults

BACKGROUND

Three new parvoviruses of Protoparvovirus genus, bufavirus (BuV), tusavirus (TuV), and cutavirus (CuV), have recently been discovered in diarrheal stools. CuV was further detected in a proportion of cutaneous T-cell lymphoma (CTCL)/mycosis fungoides skin samples and in one melanoma.

PATIENTS AND METHODS

With novel multiplex quantitative polymerase chain reaction and antibody assays, we studied 3 patient groups for BuV, TuV, and CuV DNA and immunoglobulin G (IgG): CTCL patients, immunosuppressed solid-organ transplant recipients, and immunocompetent healthy adults.

RESULTS

CuV DNA was detected in skin biopsies of 4/25 (16.0%) CTCL and 4/136 (2.9%) transplant patients but not in any of 159 skin samples of 98 healthy adults. The dermal CuV-DNA prevalence was significantly higher in CTCL patients than in the other subjects. CuV DNA was further detected in healthy skin of 4 organ transplant recipients, 2 of whom also had CuV-positive skin carcinomas. One CTCL patient harbored CuV DNA in both malignant (CTCL, melanoma) and nonmalignant skin and sentinel lymph nodes but not in his prostate. The CuV IgG seroprevalences were among CTCL patients 9.5% (4/42), transplant recipients 6.5% (8/124), and healthy adults 3.8% (3/78). BuV and TuV DNAs were absent and antibodies infrequent in all cohorts. Parvoviral antibodies were shown to persist for ≥20 years and dermal CuV DNA for 4 years. All 3 CuV-DNA-positive patients, with both biopsies and sera available, were CuV-IgG positive.

CONCLUSION

Our results suggest that dermal CuV DNA carriage is associated with CTCL. Any putative roles of CuV in the carcinogenesis must be determined in forthcoming studies.

Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus Californianus) with Polyserositis and Steatitis

An emaciated subadult free-ranging California sea lion (Csl or Zalophus californianus) died following stranding with lesions similar to 11 other stranded animals characterized by chronic disseminated granulomatous inflammation with necrotizing steatitis and vasculitis, involving visceral adipose tissues in the thoracic and peritoneal cavities. Histologically, affected tissues had extensive accumulations of macrophages with perivascular lymphocytes, plasma cells, and fewer neutrophils. Using viral metagenomics on a mesenteric lymph node six mammalian viruses were identified consisting of novel parvovirus, polyomavirus, rotavirus, anellovirus, and previously described Csl adenovirus 1 and Csl bocavirus 4. The causal or contributory role of these viruses to the gross and histologic lesions of this sea lion remains to be determined.

Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology

Several members of the Protoparvovirus genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens.

Fatal canine parvovirus-2 (CPV-2) infection in a rescued free-ranging Taiwanese pangolin (Manis pentadactyla pentadactyla)

Carnivore protoparvovirus 1 includes feline parvovirus (FPV), variants of canine parvovirus-2 (CPV-2), mink enteritis virus, and raccoon parvovirus, important pathogens affecting both wild and domestic carnivores. In this report, we described a fatal CPV-2 infection in a rescued Taiwanese pangolin, which provides the first evidence of CPV-2 infection in a non-carnivore. Post-rescue, the Taiwanese pangolin died from complications resulting from a severe panleucocytopenia and bloody diarrhoea. A full autopsy was performed and microscopic examination of the tissues revealed ulcerative, necrotizing, and haemorrhagic glossitis, esophagitis and enteritis. The results of transmission electronic microscopy, polymerase chain reaction and in situ hybridization provided confirmatory evidence that the lesions in the tongue, oesophagus and intestine were associated with a protoparvovirus. Phylogenetic comparison of the whole VP2 gene from the current pangolin protoparvovirus strain showed close clustering with the CPV-2c strains from domestic dogs in Taiwan, China and Singapore. The amino acid sequence of the pangolin protoparvovirus showed 100% identity to the CPV-2c strains from domestic dogs in China, Italy, and Singapore. The current findings highlight that pangolins are susceptible to protoparvoviruses. The potential of cross-species transmission of protoparvoviruses between Carnivora and Pholidota should be considered when housing pangolins in close proximity to carnivores and adopting strict biosecurity measures to avoid cross-species transmission in rescue facilities and zoos.

Nearly full-length genome characterization of canine parvovirus strains circulating in Nigeria

Canine parvovirus type 2 (CPV‐2) emerged suddenly in the late 1970s as pathogen of dogs, causing a severe and often fatal gastroenteric disease. The original CPV‐2 was replaced by three antigenic variants, CPV‐2a, CPV‐2b and CPV‐2c, which to date have gained a worldwide distribution with different relative proportions. All previous studies conducted in Africa were based on partial VP2 gene sequences. The aim of this study was to provide a genome analysis to characterize the CPV strains collected in Nigeria, Africa. Rectal swab samples (n = 320) were collected in 2018 and tested by means of an immunochromatographic assay. Among the 144 positive samples, 59 were selected for further analyses using different molecular assays. The results revealed a high prevalence of CPV‐2c (91.5%) compared to the CPV‐2a variant (8.5%). The VP2 gene sequences showed a divergence from the strains analysed in 2010 in Nigeria and a closer connection with CPV strains of Asian origin. The non‐structural gene analysis evidenced amino acid changes never previously reported. The molecular analysis based on genomic sequences evidenced a geographical pattern of distribution of the analysed strains, suggesting a potential common evolutionary origin with CPV of Asian origin. This study represents the first CPV molecular characterization including all the encoding gene sequences conducted in the African continent and contributes to define the current geographical spread of the CPV variants worldwide.

Novel Parvovirus Related to Primate Bufaviruses in Dogs

A novel protoparvovirus species, related genetically to human bufaviruses, was identified in dogs with respiratory signs. The canine bufavirus was distantly related to the well-known canine protoparvovirus, canine parvovirus type 2, sharing low amino acid identities in the nonstructural protein 1 (40.6%) and in the capsid protein 1 (33.4%). By screening collections of fecal, nasal, and oropharyngeal samples obtained from juvenile dogs (<1 year of age), canine bufavirus DNA appeared as a common component of canine virome. The virus was common in the stool samples of dogs with or without enteric disease and in the nasal and oropharyngeal swab samples of dogs with respiratory signs. However, the virus was not detected in nasal and oropharyngeal swab samples from animals without clinical signs.

A SimpleProbe® real-time PCR assay for differentiating the canine parvovirus type 2 genotype

Background

Canine parvovirus type 2 (CPV‐2) causes an important canine viral disease worldwide. CPV‐2 belongs to the Protoparvovirus genus in the family Parvoviridae. An amino acid change at position 426 of the VP2 protein differentiate types of CPV‐2, designated as CPV‐2a (Asn), CPV‐2b (Asp), and CPV‐2c (Glu). In this study, we compared CPV‐2 genotyping results obtained by SimpleProbe^® real‐time PCR and DNA sequencing analysis to identify the accuracy and sensitivity of these methods.

Methods

One hundred rectal swabs were collected from CPV‐2 naturally infected dogs from 2015 to 2017 at the Animal Disease Diagnostic Center, National Pingtung University of Science and Technology. CPV‐2 genotyping was performed by SimpleProbe^® real‐time PCR and DNA sequencing to compare results.

Results

CPV‐2a (n = 23), 2b (n = 6) and 2c (n = 71) genotyping results obtained by both techniques were identical with specificity of 100% for SimpleProbe^® assay. In the SimpleProbe^® assay, amplifying the DNAs prepared from the clinical specimens showed three distinct melting curve peaks. CPV‐2b had the highest melting peak of 57.8°C (CI 95%: 57.7‐58.5°C) followed by CPV‐2c with a slightly lower melting peak of 52.3°C (CI 95%: 52.2‐53.2°C) and CPV‐2a with the lowest peak of 50.2°C (CI 95%: 50.1‐50.5°C).

Conclusion

This study developed a novel method for genotyping CPV‐2 strains using the SimpleProbe^® real‐time PCR assay. This assay is a reliable and sensitive tool for differentiating between the CPV‐2a, 2b and 2c and this technique can be used for molecular CPV‐2 epidemiology studies.

Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses

Amdoparvoviruses (family Parvoviridae: genus Amdoparvovirus) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify endogenous parvoviral elements (EPVs) disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived EPVs in the genome of the Transcaucasian mole vole (Ellobius lutescens). We also identify four EPVs in mammal and reptile genomes that are intermediate between amdoparvoviruses and their sister genus (Protoparvovirus) in terms of their phylogenetic placement and genomic features. In particular, we identify a genome-length EPV in the genome of a pit viper (Protobothrops mucrosquamatus) that is more similar to a protoparvovirus than an amdoparvovirus in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), yet exhibits characteristically amdoparvovirus-like genome features including: (1) a putative middle ORF gene; (2) a capsid gene that lacks a phospholipase A2 domain; (3) a genome structure consistent with an amdoparvovirus-like mechanism of capsid gene expression. Our findings indicate that amdoparvovirus host range extends to rodents, and that parvovirus lineages possessing a mixture of proto- and amdoparvovirus-like characteristics have circulated in the past. In addition, we show that EPV sequences in the mole vole and pit viper encode intact, expressible replicase genes that have potentially been co-opted or exapted in these host species.

Optimizing the Targeting of Mouse Parvovirus 1 to Murine Melanoma Selects for Recombinant Genomes and Novel Mutations in the Viral Capsid Gene

Combining virus-enhanced immunogenicity with direct delivery of immunomodulatory molecules would represent a novel treatment modality for melanoma, and would require development of new viral vectors capable of targeting melanoma cells preferentially. Here we explore the use of rodent protoparvoviruses targeting cells of the murine melanoma model B16F10. An uncloned stock of mouse parvovirus 1 (MPV1) showed some efficacy, which was substantially enhanced following serial passage in the target cell. Molecular cloning of the genes of both starter and selected virus pools revealed considerable sequence diversity. Chimera analysis mapped the majority of the improved infectivity to the product of the major coat protein gene, VP2, in which linked blocks of amino acid changes and one or other of two apparently spontaneous mutations were selected. Intragenic chimeras showed that these represented separable components, both contributing to enhanced infection. Comparison of biochemical parameters of infection by clonal viruses indicated that the enhancement due to changes in VP2 operates after the virus has bound to the cell surface and penetrated into the cell. Construction of an in silico homology model for MPV1 allowed placement of these changes within the capsid shell, and revealed aspects of the capsid involved in infection initiation that had not been previously recognized.

Protoparvovirus Knocking at the Nuclear Door

Protoparvoviruses target the nucleus due to their dependence on the cellular reproduction machinery during the replication and expression of their single-stranded DNA genome. In recent years, our understanding of the multistep process of the capsid nuclear import has improved, and led to the discovery of unique viral nuclear entry strategies. Preceded by endosomal transport, endosomal escape and microtubule-mediated movement to the vicinity of the nuclear envelope, the protoparvoviruses interact with the nuclear pore complexes. The capsids are transported actively across the nuclear pore complexes using nuclear import receptors. The nuclear import is sometimes accompanied by structural changes in the nuclear envelope, and is completed by intranuclear disassembly of capsids and chromatinization of the viral genome. This review discusses the nuclear import strategies of protoparvoviruses and describes its dynamics comprising active and passive movement, and directed and diffusive motion of capsids in the molecularly crowded environment of the cell.

The SAT Protein of Porcine Parvovirus Accelerates Viral Spreading through Induction of Irreversible Endoplasmic Reticulum Stress

The SAT protein (SATp) of porcine parvovirus (PPV) accumulates in the endoplasmic reticulum (ER), and SAT deletion induces the slow-spreading phenotype. The in vitro comparison of the wild-type Kresse strain and its SAT knockout (SAT^-) mutant revealed that prolonged cell integrity and late viral release are responsible for the slower spreading of the SAT^- virus. During PPV infection, regardless of the presence or absence of SATp, the expression of downstream ER stress response proteins (Xbp1 and CHOP) was induced. However, in the absence of SATp, significant differences in the quantity and the localization of CHOP were detected, suggesting a role of SATp in the induction of irreversible ER stress in infected cells. The involvement of the induction of irreversible ER stress in porcine testis (PT) cell necrosis and viral egress was confirmed by treatment of infected cells by ER stress-inducing chemicals (MG132, dithiothreitol, and thapsigargin), which accelerated the egress and spreading of both the wild-type and the SAT^- viruses. UV stress induction had no beneficial effect on PPV infection, underscoring the specificity of ER stress pathways in the process. However, induction of CHOP and its nuclear translocation cannot alone be responsible for the biological effect of SAT, since nuclear CHOP could not complement the lack of SAT in a coexpression experiment.IMPORTANCE SATp is encoded by an alternative open reading frame of the PPV genome. Earlier we showed that SATp of the attenuated PPV NADL-2 strain accumulates in the ER and accelerates virus release and spreading. Our present work revealed that slow spreading is a general feature of SAT^- PPVs and is the consequence of prolonged cell integrity. PPV infection induced ER stress in infected cells regardless of the presence of SATp, as demonstrated by the morphological changes of the ER and expression of the stress response proteins Xbp1 and CHOP. However, the presence of SATp made the ER stress more severe and accelerated cell death during infection, as shown by the higher rate of expression of CHOP and alteration of the localization of CHOP. The beneficial effect of irreversible ER stress on PPV spread was confirmed by treatment of infected cells with ER stress-inducing chemicals.

Cutavirus in Cutaneous Malignant Melanoma

A novel human protoparvovirus related to human bufavirus and preliminarily named cutavirus has been discovered. We detected cutavirus in a sample of cutaneous malignant melanoma by using viral enrichment and high-throughput sequencing. The role of cutaviruses in cutaneous cancers remains to be investigated.