Identification and characterization of two novel viruses in ocular infections in reindeer

Screening of Eurasian Tundra Reindeer for Viral Sequences by Next-Generation Sequencing

Reindeer husbandry is essential for the livelihood and culture of indigenous people in the Arctic. Parts of the herding areas are also used as pastures for farm animals, facilitating potential transmission of viruses between species. Following the Covid-19 pandemic, viruses circulating in the wild are receiving increased attention, since they might pose a potential threat to human health. Climate change will influence the prevalence of infectious diseases of both humans and animals. The aim of this study was to detect known and previously unknown viruses in Eurasian tundra reindeer. In total, 623 nasal and 477 rectal swab samples were collected from reindeer herds in Fennoscandia, Iceland, and Eastern Russia during 2016–2019. Next-generation sequencing analysis and BLAST-homology searches indicated the presence of viruses of domesticated and wild animals, such as bovine viral diarrhea virus, bovine papillomavirus, alcephaline herpesvirus 1 and 2, deer mastadenovirus B, bovine rotavirus, and roe deer picobirnavirus. Several viral species previously found in reindeer and some novel species were detected, although the clinical relevance of these viruses in reindeer is largely unknown. These results indicate that it should be possible to find emerging viruses of relevance for both human and animal health using reindeer as a sentinel species.

Gammaherpesvirus in Cervid Species from Norway: Characterization of a New Virus in Wild and Semi-Domesticated Eurasian Tundra Reindeer (Rangifer tarandus tarandus)

Gammaherpesvirus infections have been described in cervids worldwide, mainly the genera Macavirus or Rhadinovirus. However, little is known about the gammaherpesviruses species infecting cervids in Norway and Fennoscandia. Blood samples from semi-domesticated (n = 39) and wild (n = 35) Eurasian tundra reindeer (Rangifer tarandus tarandus), moose (Alces alces, n = 51), and red deer (Cervus elaphus, n = 41) were tested using a panherpesvirus DNA polymerase (DPOL) PCR. DPOL-PCR-positive samples were subsequently tested for the presence of glycoprotein B (gB) gene. The viral DPOL gene was amplified in 28.2% (11/39) of the semi-domesticated reindeer and in 48.6% (17/35) of the wild reindeer. All moose and red deer tested negative. Additionally, gB gene was amplified in 4 of 11 semi-domesticated and 15 of 17 wild Eurasian reindeer DPOL-PCR-positive samples. All the obtained DPOL and gB sequences were highly similar among them, and corresponded to a novel gammaherpesvirus species, tentatively named Rangiferine gammaherpesvirus 1, that seemed to belong to a genus different from Macavirus and Rhadinovirus. This is the first report of a likely host-specific gammaherpesvirus in semi-domesticated reindeer, an economic and cultural important animal, and in wild tundra reindeer, the lastpopulation in Europe. Future studies are required to clarify the potential impact of this gammaherpesvirus on reindeer health.

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.

Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples

The etiologic cause of encephalitis, meningitis or meningo-encephalitis is unknown in up to 70% of cases. Clinical shotgun metagenomics combined with host depletion is a promising technique to identify infectious etiologies of central nervous system (CNS) infections. We developed a straightforward eukaryotic host nucleic acid depletion method that preserves intact viruses and bacteria for subsequent shotgun metagenomics screening of clinical samples, focusing on cerebrospinal fluid (CSF). A surrogate CSF sample for a CNS infection paradigm was used to evaluate the proposed depletion method consisting of selective host cell lysis, followed by enzymatic degradation of the liberated genomic DNA for final depletion with paramagnetic beads. Extractives were subjected to reverse transcription, followed by whole genome amplification and next generation sequencing. The effectiveness of the host depletion method was demonstrated in surrogate CSF samples spiked with three 1:100 dilutions of Influenza A H3N2 virus (qPCR Ct-values 20.7, 28.8, >42/negative). Compared to the native samples, host depletion increased the amount of the virus subtype reads by factor 7127 and 132, respectively, while in the qPCR negative sample zero vs. 31 (1.4E-4 %) virus subtype reads were detected (native vs. depleted). The workflow was applied to thirteen CSF samples of patients with meningo-/encephalitis (two bacterial, eleven viral etiologies), a serum of an Andes virus infection and a nose swab of a common cold patient. Unlike surrogate samples, host depletion of the thirteen human CSF samples and the nose swab did not result in more reads indicating presence of damaged pathogens due to, e.g., host immune response. Nevertheless, previously diagnosed pathogens in the human CSF samples (six viruses, two bacteria), the serum, and the nose swab (Human rhinovirus A31) were detected in the depleted and/or the native samples. Unbiased evaluation of the taxonomic profiles supported the diagnosed pathogen in two native CSF samples and the native and depleted serum and nose swab, while detecting various contaminations that interfered with pathogen identification at low concentration levels. In summary, damaged pathogens and contaminations complicated analysis and interpretation of clinical shotgun metagenomics data. Still, proper consideration of these issues may enable future application of metagenomics for clinical diagnostics.

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.

Pestivirus infection in reindeer (Rangifer tarandus)

Reindeer species (Rangifer tarandus, Linnaeus, 1758) includes wild and semi-domesticated ruminants belonging to Capreaolinae subfamily of Cervidae family reared in Eurasia (reindeer subspecies) and North America (caribou subspecies). Herding of reindeer has a great historical, socio-economic and ecological importance, especially to indigenous ethnic minorities. Infectious disease threats may therefore impact not solely the animal population driving it to further extinction and irreversible alterations to the wild environments of northern hemisphere, but also add to cultural changes observed as negative impact of globalization. Introduction of new technologies to control of reindeer migration between dwindling pasture areas and intensification of reindeer husbandry may facilitate the intra- and interspecies transmission of pathogens. The role of the reindeer as a potential BVDV reservoir has been studied, however, the number of publications is rather limited. The observed seroprevalences of the virus varied significantly between different geographical regions with different epidemiological situation. Most frequently limited number of animals studied and the differences in the sensitivities and specificities of the diagnostic test used could have also influenced on the differences between the studies. No pestivirus has been ever detected in free-ranging reindeer, however, a putative pestivirus strain named V60-Krefeld has been isolated from reindeer kept at a German Zoo in the 1990’s. The virus was characterized as border disease virus type 2 (BDV-2) closely related to German ovine strains. The cross-neutralization studies of the semi-domesticated reindeer sera from Sweden suggested infection with a strain related to BDV-1 or BDV-2. The available data indicates that reindeer might be infected by a endemic species-specific BDV-like strain. However, the interspecies transmission of BVDV from domestic animals should not be excluded, since the susceptibility of reindeer to BVDV-1 has been confirmed under experimental conditions.

Molecular methods for identification and characterization of novel papillomaviruses

Papillomaviruses (PV) are a remarkably heterogeneous family of small DNA viruses that infect a wide variety of vertebrate species and are aetiologically linked with the development of various neoplastic changes of the skin and mucosal epithelia. Based on nucleotide similarity, PVs are hierarchically classified into genera, species and types. Novel human PV (HPV) types are given a unique number only after the whole genome has been cloned and deposited with the International HPV Reference Center. As of 9 March 2015, 200 different HPV types, belonging to 49 species, had been recognized by the International HPV Reference Center. In addition, 131 animal PV types identified from 66 different animal species exist. Recent advances in molecular techniques have resulted in an explosive increase in the identification of novel HPV types and novel subgenomic HPV sequences in the last few years. Among PV genera, the γ-PV genus has been growing most rapidly in recent years with 80 completely sequenced HPV types, followed by α-PV and β-PV genera that have 65 and 51 recognized HPV types, respectively. We reviewed in detail the contemporary molecular methods most often used for identification and characterization of novel PV types, including PCR, rolling circle amplification and next-generation sequencing. Furthermore, we present a short overview of 12 and 10 novel HPV types recently identified in Sweden and Slovenia, respectively. Finally, an update on the International Human Papillomavirus Reference Center is provided.

Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units

Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.