High pathogenic avian influenza A(H5) viruses of clade 2.3.4.4b in Europe-Why trends of virus evolution are more difficult to predict

Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020-2021 and 2021-2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations. This study used the complete genomes of 1,956 European HPAI A(H5Nx) viruses to investigate the virus evolution during this varying epidemiological outline. We investigated the spatiotemporal patterns of A(H5Nx) virus diffusion to/from and within Europe during the 2020-2021 and 2021-2022 epidemic waves, providing evidence of ongoing changes in transmission dynamics and disease epidemiology. We demonstrated the high genetic diversity of the circulating viruses, which have undergone frequent reassortment events, providing for the first time a complete overview and a proposed nomenclature of the multiple genotypes circulating in Europe in 2020-2022. We described the emergence of a new genotype with gull adapted genes, which offered the virus the opportunity to occupy new ecological niches, driving the disease endemicity in the European wild bird population. The high propensity of the virus for reassortment, its jumps to a progressively wider number of host species, including mammals, and the rapid acquisition of adaptive mutations make the trend of virus evolution and spread difficult to predict in this unfailing evolving scenario.

Frequent Occurrence of Simultaneous Infection with Multiple Rotaviruses in Swiss Pigs

Rotavirus (RV) infections are the most important viral cause of diarrhea in piglets in Switzerland and are thought to cause substantial economic losses to the pig industry. However, no data are available on the occurrence and dynamics of the main porcine RV species, namely RVA, RVB, and RVC, and the diversity of the circulating strains. We therefore tested fecal samples from a cross-sectional (n = 95) and a longitudinal (n = 48) study for RVA, RVB, and RVC by real-time RT-PCR and compared the results of the cross-sectional study to postmortem findings. In addition, eight samples were fully genotyped by using next-generation sequencing. In the cross-sectional study, triple RV infections significantly correlated with diarrhea and wasting and were most frequent in the weaned age group. In the longitudinal study, the shedding of RV peaked one week after weaning and decreased thereafter. Here, mainly double infections were seen, and only a few animals showed diarrhea. The full-genome sequencing revealed a genotype pattern similar to other European countries and, importantly, co-infection by up to four RVA strains. Our results imply that the weaning of piglets may trigger not only RV shedding but facilitate co-infection of multiple RV species and strains in the same host.

Management of Suspected Cases of Feline Immunodeficiency Virus Infection in Eurasian Lynx (Lynx lynx) During an International Translocation Program

The Eurasian lynx (Lynx lynx) population in Switzerland serves as a source for reintroductions in neighboring countries. In 2016–2017, three lynx from the same geographical area were found seropositive for feline immunodeficiency virus (FIV) in the framework of an international translocation program. This novel finding raised questions about the virus origin and pathogenicity to lynx, the emerging character of the infection, and the interpretation of serological results in other lynx caught for translocation. Archived serum samples from 84 lynx captured in 2001–2016 were retrospectively tested for FIV antibodies by Western blot. All archived samples were FIV-negative. The three seropositive lynx were monitored in quarantine enclosures prior to euthanasia and necropsy. They showed disease signs, pathological findings, and occurrence of co-infections reminding of those described in FIV-infected domestic cats. All attempts to isolate and characterize the virus failed but serological data and spatiotemporal proximity of the cases suggested emergence of a lentivirus with antigenic and pathogenic similarities to FIV in the Swiss lynx population. A decision scheme was developed to minimize potential health risks posed by FIV infection, both in the recipient and source lynx populations, considering conservation goals, animal welfare, and the limited action range resulting from local human conflicts. Development and implementation of a cautious decision scheme was particularly challenging because FIV pathogenic potential in lynx was unclear, negative FIV serological results obtained within the first weeks after infection are unpredictable, and neither euthanasia nor repatriation of multiple lynx was acceptable options. The proposed scheme distinguished between three scenarios: release at the capture site, translocation, or euthanasia. Until April 2021, none of the 40 lynx newly captured in Switzerland tested FIV-seropositive. Altogether, seropositivity to FIV was documented in none of 124 lynx tested at their first capture, but three of them seroconverted in 2016–2017. Diagnosis of FIV infection in the three seropositive lynx remains uncertain, but clinical observations and pathological findings confirmed that euthanasia was appropriate. Our experiences underline the necessity to include FIV in pathogen screenings of free-ranging European wild felids, the importance of lynx health monitoring, and the usefulness of health protocols in wildlife translocation.

Screening of Swiss Pig Herds for Hepatitis E Virus: A Pilot Study

Hepatitis E virus (HEV) is an important cause of acute hepatitis in humans worldwide. In industrialised countries, most infections are caused by the zoonotic genotype 3. The main reservoir was found in pigs, with fattening pigs as the main shedders. The aim of this study was to establish a screening tool to detect HEV in pig farms. HEV-positive samples were sequenced using Sanger sequencing. First, different sample materials, including floor swabs, slurry, dust swabs and faeces were tested for HEV. Floor swabs turned out to give the best results and, in the form of sock swabs, were used for the screening of Swiss pig herds. A total of 138 pig farms were tested, with a focus on fattening pigs. Overall, 81 farms (58.8%) were HEV positive. Most sequences belonged to subtype 3h, in which they formed a specific cluster (Swiss cluster). In addition, subtype 3l and two unassigned sequences were detected. As a conclusion, sock swabs were found to be a helpful tool to screen pig herds for HEV and establish a sequence collection that may enable molecular epidemiology and support outbreak investigation and prevention.

Benefit of Bovine Viral Diarrhoea (BVD) Eradication in Cattle on Pestivirus Seroprevalence in Sheep

Bovine viral diarrhoea virus (BVDV) and Border disease virus (BDV) are closely related pestiviruses of cattle and sheep, respectively. Both viruses may be transmitted between either species, but control programs are restricted to BVDV in cattle. In 2008, a program to eradicate bovine viral diarrhoea (BVD) in cattle was started in Switzerland. As vaccination is prohibited, the cattle population is now widely naïve to pestivirus infections. In a recent study, we determined that nearly 10% of cattle are positive for antibodies to BDV. Here, we show that despite this regular transmission of BDV from small ruminants to cattle, we could only identify 25 cattle that were persistently infected with BDV during the last 12 years of the eradication program. In addition, by determining the BVDV and BDV seroprevalence in sheep in Central Switzerland before and after the start of the eradication, we provide evidence that BVDV is transmitted from cattle to sheep, and that the BVDV seroprevalence in sheep significantly decreased after its eradication in cattle. While BDV remains endemic in sheep, the population thus profited at least partially from BVD eradication in cattle. Importantly, on a national level, BVD eradication does not appear to be generally derailed by the presence of pestiviruses in sheep. However, with every single virus-positive cow, it is necessary to consider small ruminants as a potential source of infection, resulting in costly but essential investigations in the final stages of the eradication program.

Development of a recombinant ELISA for ovine herpesvirus 2, suitable for use in sheep

The minor capsid protein of ovine herpesvirus 2, identified as a potential antigen for serological testing, was over-expressed and purified to allow its assessment in ELISA. The corresponding gene sequence (OvHV-2 orf65, Ov65) was modified to incorporate epitope tags and internal restriction enzyme sites in an E. coli codon-optimised version of the gene. This codon-optimised gene was then subject to internal deletions to identify regions of the protein that could be removed while maintaining protein solubility and antigenicity. It was found that a derivative with deletion of the conserved 5'-end of the gene (Ov65delB) expressed a polypeptide that was soluble when over-expressed in bacteria and was detected by OvHV-2 specific sera. Proteomic analysis of the affinity purified Ov65delB showed that it contained multiple predicted Ov65 tryptic peptides but also showed contamination by co-purifying E. coli proteins. An indirect ELISA, based on this affinity-purified OV65delB, was optimised for use with sheep and cattle samples and cut-off values were established based on known negative serum samples. Analysis of groups of samples that were either presumed infected (UK sheep) or tested OvHV-2 positive or negative by PCR (cattle MCF diagnostic samples) showed that the assay had 95 % sensitivity and 96 % specificity for sheep serum; and 80 % sensitivity and 95 % specificity for cattle serum. The lower sensitivity with cattle samples appeared to be due to a lack of serological response in some MCF-affected cattle. This recombinant antigen therefore shows promise as the basis of an inexpensive, simple and reliable test that can be used to detect OvHV-2-specific antibody responses in both MCF-affected animals and in OvHV-2 reservoir hosts.

Prevalence of Nasal Shedding of Equid Gammaherpesviruses in Healthy Swiss Horses

Equid Gamma herpesvirus (eGHV) infections have been reported worldwide and may be correlated with clinical signs, e.g., affecting the respiratory tract in young horses. eGHV are shed by healthy horses as well as horses with respiratory tract disease. The prevalence in healthy Swiss horses is unknown to date but this data would provide valuable information for causal diagnosis in clinical cases and formulation of biosecurity recommendations. Nasal swabs from 68 healthy horses from 12 Swiss stables and 2 stables near the Swiss border region in Germany were analyzed by panherpes nested PCR. Positive samples were sequenced. A multivariable model was used to determine if sex, age, breed, canton, or stable had a significant effect on the shedding status of each detected eGHV. Overall, the eGHV prevalence was 59% (n = 68); the prevalence for equid herpesvirus-2 (EHV-2), equid herpesvirus-5 (EHV-5) and asinine herpesvirus-5 (AHV-5) was 38%, 12% and 9%, respectively. Co-infections with multiple eGHVs were observed in 25% of the positive samples. The odds of shedding EHV-2 decreased with age (p = 0.01) whereas the odds of shedding AHV-5 increased with age (p = 0.04). Breed, sex, canton, or stable had no significant association with eGHV shedding. As EHV-2 shedding was common in healthy horses a positive PCR result must be interpreted with caution regarding the formulation of biosecurity recommendations and causal diagnosis. As EHV-5 and AHV-5 shedding was less common than EHV-2, a positive test result is more likely to be of clinical relevance. Shedding of multiple eGHV complicates the interpretation of positive test results in a horse.

Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

INTRODUCTION

Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.

METHODS

Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed.

RESULTS

Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection.

CONCLUSION

A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.

Viral infections shared between water buffaloes and small ruminants in Switzerland

Importation of exotic animals that may harbor infectious agents poses risks for native species with potentially severe impacts on animal health and animal production. Although the Asian water buffalo (Bubalus bubalis) population in Europe is steadily increasing, its susceptibility to viral infections and its role for interspecies transmission is largely unknown. To identify viral infections that are shared between exotic water buffaloes and native small ruminants, we collected blood samples from 3 Swiss farms on which water buffaloes were kept either without, or together with, sheep or goats. These samples were analyzed by next-generation sequencing (NGS) as well as by selected conventional tests, including PCR, ELISA, and in some cases a virus neutralization test. By NGS, a novel virus of the genus Gemykrogvirus (GyKV; Genomoviridae) was first detected in the buffaloes on one farm, and subsequently confirmed by PCR, and was also detected in the co-housed sheep. In contrast, this virus was not detected in buffaloes on the farms without sheep. Moreover, conventional methods identified a number of viral infections that were not shared between the exotic and the native animals, and provided evidence for potential roles of water buffaloes in the epidemiology of ruminant pestiviruses, especially bovine viral diarrhea virus, bluetongue virus, and possibly bovine alphaherpesvirus 2. Our results clearly indicate that water buffaloes are susceptible to interspecies viral transmission and may act as intermediate hosts, or even as reservoirs, for these viruses.

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

Active equine parvovirus-hepatitis infection is most frequently detected in Austrian horses of advanced age

BACKGROUND

Equine parvovirus-hepatitis (EqPV-H) research is in its infancy. Information regarding prevalence, geographical distribution, genetic diversity, pathogenesis and risk factors enhances understanding of this potentially fatal infection.

OBJECTIVES

Determining the prevalence of EqPV-H in Austrian equids. Investigating factors increasing probability of infection, liver-associated biochemistry parameters, concurrent equine hepacivirus (EqHV) infection and phylogenetic analysis of Austrian EqPV-H variants.

STUDY DESIGN

Cross-sectional study.

METHODS

Sera from 259 horses and 13 donkeys in Austria were analysed for anti-EqPV-H VP1-specific antibodies by luciferase immunoprecipitation system (LIPS) and EqPV-H DNA by nested polymerase chain reaction (PCR). Associations between infection status, sex and age were described. Glutamate dehydrogenase (GLDH), gamma-glutamyl transferase (GGT), bile acids and albumin concentrations were compared between horses with active infection and PCR-negative horses. PCR targeting partial EqPV-H NS1 was performed and phylogenetic analysis of Austrian EqPV-H variants was conducted. Complete coding sequences (CDS) of four Austrian variants were determined by next-generation sequencing (NGS) and compared with published sequences.

RESULTS

Horses' EqPV-H seroprevalence was 30.1% and DNA prevalence was 8.9%. One horse was co-infected with EqHV. Significantly, higher probability of active EqPV-H infection was identified in 16- to 31-year-old horses, compared with 1- to 8-year-old horses (P = 0.002; OR = 8.19; 95% CI = 1.79 to 37.50) and 9- to 15-year-old horses (P = 0.03; OR = 2.96; 95% CI = 1.08 to 8.17). Liver-associated plasma parameters were not significantly different between horses with active infection and controls. Austrian EqPV-H variants revealed high similarity to sequences worldwide. No evidence of EqPV-H was detected in donkeys.

MAIN LIMITATIONS

Equids' inclusion depended upon owner consent. There was only one sampling point per animal and the sample of donkeys was small.

CONCLUSIONS

EqPV-H antibodies and DNA are frequently detected in Austrian horses, without associated hepatitis in horses with active infection. The risk of active EqPV-H infection increases with increasing age. Phylogenetic evidence supports close relation of EqPV-H variants globally, including Austrian variants.

A case series highlighting the role of different gamma-herpesviruses in Equine Multinodular Pulmonary Fibrosis

INTRODUCTION

This case series describes three cases of equine multinodular pulmonary fibrosis (EMPF) diagnosed at the Clinic for Equine Internal Medicine at the University of Zurich between 2012 and 2017. Current information on etiology and treatment options are presented. Two horses showed mild signs of chronic lower respiratory tract disease and one horse was presented with acute signs of disease including recurrent fever spikes and tachypnea. Diagnosis was achieved by physical examination, radiographic findings, and PCR testing for equine herpesviruses (EHV) of bronchoalveolar lavage (BAL) fluid or lung tissue obtained by biopsy. All horses were euthanized due to continuing deterioration after attempted treatment. Post mortem histological examination of lung tissue showed severe multifocal diffuse to confluent fibrosis in two cases and in another horse a discrete nodular fibrosis pattern. Panherpes nested PCR revealed the presence of equine herpesvirus 5 (EHV-5) DNA in lung tissue of one horse whereas in two other horses, asinine herpes virus 5 (AHV-5) was detected. EMPF should be considered as a differential diagnosis in horses with acute and chronic respiratory disease, including horses non-responsive to treatment for equine asthma.

[Field trial for eradication of methicillin- resistant Staphylococcus aureus (MRSA) in a pig breeding farm by bacteriophages]

INTRODUCTION

In recent years, Livestock Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) are found frequently in pigs. The colonization of the care staff with LA-MRSA is strongly associated with the intensity and duration of animal contact and LA-MRSA herd prevalence. In human medicine, staphylococcal infections have been controlled successfully by topical or systemic administration of Staphylococcus - associated bacteriophages. Therefore, the present study investigated the effect of a bacteriophage cocktail on skin and mucosal colonization of pigs with MRSA in a pig farm with high MRSA prevalence. In a first experiment, the sows were washed with a bacteriophage cocktail and nose, mouth and vagina were rinsed before the sows were admitted to the farrowing house. Then, 10 ml of the bacteriophage cocktail was administered daily to the sows over the feed until weaning. The suckling piglets were sprayed and sampled twice a week during the suckling period and treated with the bacteriophage cocktail over the feed during the weaning period. In further experiments, the weaning room was nebulized three times a day with a bacteriophage cocktail and different concentrations of bacteriophages were added to the drinking water via Dosatron®. None of the experiments, however, showed an eradication of MRSA neither in nose nor in feces.

Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories

The value of next-generation sequencing (NGS)-based applications for testing purposes in human medicine is widely recognized. Although NGS-based metagenomic screening may be of interest in veterinary medicine, in particular for intensively farmed livestock species such as pigs, there is a lack of protocols tailored to veterinary requirements, likely because of the high diversity of species and samples. Therefore, we developed an NGS-based protocol for use in veterinary virology and present here different applications in porcine medicine. To develop the protocol, each step of sample preparation was optimized using porcine samples spiked with various RNA and DNA viruses. The resulting protocol was tested with clinical samples previously confirmed to be positive for specific viruses by a diagnostic laboratory. Additionally, we validated the protocol in an NGS viral metagenomics ring trial and tested the protocol on viral multiplex reference material (NIBSC, U.K.). We applied our ViroScreen protocol successfully for 1) virus identification, 2) virus characterization, and 3) herd screening. We identified torque teno sus virus and atypical porcine pestivirus in a neurologic case, determined the full-length genome sequence of swine influenza A virus in field samples, and screened pigs using pen floor fecal samples and chewing rope liquid.

Rapid and simple colorimetric loop-mediated isothermal amplification (LAMP) assay for the detection of Bovine alphaherpesvirus 1

As the causative agent of Infectious Bovine Rhinotracheitis (IBR) and Infectious Pustular Vulvovaginitis/Balanoposthitis (IPV/IPB), Bovine alphaherpesvirus 1 (BoHV-1) is responsible for high economic losses in the cattle industry worldwide. This study aimed to establish a fast, colorimetric loop-mediated isothermal amplification (LAMP) assay for the detection of viral DNA. Phenol red is used as pH-sensitive readout, relying on a distinct color change from pink to yellow in case of a positive reaction. LAMP reactions with different primers were compared and a newly designed set targeting the gene encoding the tegument protein V67 provided best results, enabling readout within 8-30 min. LAMP showed less cross-reactions with other ruminant alphaherpesviruses than qPCR but was 10-fold less sensitive. However, LAMP still detected down to 14 copies. The test performance was evaluated using 26 well-characterized nasal swabs from cattle with respiratory disease. All samples were correctly identified when using column-extracted DNA. Using a simple DNA precipitation method, only two weak-positive samples turned indeterminate. Combining this DNA precipitation with a makeshift water bath heated by a gastronomic immersion heater allowed successful application of the colorimetric LAMP assay under resource-limited conditions. This technique can therefore help in managing IBR/IPV outbreaks where sophisticated laboratory equipment is unavailable.

Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture

Bovine viral diarrhoea (BVD) is an important disease of cattle, with significant impacts on animal health and welfare. The wide host range of the causative pestiviruses may lead to formation of virus reservoirs in other ruminant or wildlife species, presenting a concern for the long-term success of BVD eradication campaigns. It is likely that the quasispecies nature of these RNA viruses contributes to their interspecies transmission by providing genetic plasticity. Understanding the spectrum of sequence variants present in persistently infected (PI) animals is, therefore, essential for studies of virus transmission. To analyse quasispecies diversity without amplification bias, we extracted viral RNA from the serum of a PI cow, and from cell culture fluid after three passages of the same virus in culture, to produce cDNA without amplification. Sequencing of this material using Illumina 250 bp paired-read technology produced full-length virus consensus sequences from both sources and demonstrated the quasispecies diversity of this pestivirus A genotype 1a field strain within serum and after culture. We report the distribution and diversity of over 800 SNPs and provide evidence for a loss of diversity after only three passages in cell culture, implying that cultured viruses cannot be used to understand quasispecies diversity and may not provide reliable molecular markers for source tracing or transmission studies. Additionally, both serum and cultured viruses could be sequenced as a set of 25 overlapping PCR amplicons that demonstrated the same consensus sequences and the presence of many of the same quasispecies variants. The observation that aspects of the quasispecies structure revealed by massively parallel sequencing are also detected after PCR and Sanger sequencing suggests that this approach may be useful for small or difficult to analyse samples.

A novel PCR protocol for detection and differentiation of neuropathogenic and non-neuropathogenic equid alphaherpesvirus 1

Equid alphaherpesvirus 1 (EHV-1) infections can have a major impact on the horse industry and equine welfare by causing abortion or respiratory or neurologic disease. A single nucleotide polymorphism (A₂₂₅₄→G₂₂₅₄) in open reading frame (ORF) 30, encoding the catalytic subunit of the DNA polymerase, has been shown to be a strong predictive marker for neuropathogenicity. Given that a previously established real-time PCR (rtPCR) protocol yielded unsatisfactory results concerning determination of the EHV-1 genotype, we developed and evaluated a new conventional PCR protocol enabling identification of the genotype by sequencing and restriction enzyme analysis (REA). Thirty samples from horses with signs typical for EHV-1 infection were tested by rtPCR and our new conventional PCR. The results showed that compared to rtPCR, the conventional PCR protocol combined with sequencing and REA was more reliable concerning unambiguous determination of the EHV-1 genotype. Results of our new assay confirmed previous findings, according to which the non-neuropathogenic genotype A₂₂₅₄ is predominantly found in animals with fever, respiratory signs, and abortions or perinatal mortality, whereas the neuropathogenic genotype G₂₂₅₄ is primarily detected in animals suffering from neurologic disease. In some samples, results pointed towards coinfection with both genotypes. Further studies are required in order to elucidate the significance of infections with genotype A₂₂₅₄ and G₂₂₅₄ in neurologic and non-neurologic cases, respectively.

[Confirmation of Tick-borne encephalitis virus in an European hedgehog (Erinaceus europaeus)]

INTRODUCTION

European hedgehogs (Erinaceus europaeus) have a high exposure to various ticks, which could transmit pathogens with direct health significance for the host and may have zoonotic potential. Tick-borne meningoencephalitis (FSME) is an important tick-borne disease in Switzerland, caused by the tick-borne encephalitis virus. About its occurrence in the European hedgehog population is little known. The present study examined various organs, blood and ticks of 65 European hedgehogs to obtain data of FSME virus presence in this species in Switzerland. Real-time RT-PCR from the lungs, liver, spleen and kidney of 56 hedgehogs and of 114 infesting ticks (Ixodes hexagonus or Ixodes ricinus) were used for the detection of viral RNA. In addition, 19 blood samples were tested for antibodies against FSME by ELISA. FSME virus antibodies were detected for the first time in the serum of a European hedgehog. Lung and spleen tissue samples of the same animal tested also weak virus positive on RT-PCR. Clinically, the hedgehog showed neurological symptoms, although these symptoms could have originated from an other diseases. No viral RNA was detected in any of the ticks. This study could not confirm if the meningoencephalitis in the hedgehog was triggered by the FSME viral infection. Nevertheless, the simultaneous detection of antibodies and virus RNA in the same animal makes the European hedgehog a competent host of the tick-borne encephalitis virus and leads to the assumption that this species can act as a reservoir.

Traces of history conserved over 600 years in the geographic distribution of genetic variants of an RNA virus: Bovine viral diarrhea virus in Switzerland

The first records of smallpox and rabies date back thousands of years and foot-and-mouth disease in cattle was described in the 16th century. These diseases stood out by their distinct signs, dramatic way of transmission from rabid dogs to humans, and sudden appearance in cattle herds. By contrast, infectious diseases that show variable signs and affect few individuals were identified only much later. Bovine viral diarrhea (BVD), endemic in cattle worldwide, was first described in 1946, together with the eponymous RNA virus as its cause. There is general agreement that BVD was not newly emerging at that time, but its history remains unknown. A search for associations between the nucleotide sequences of over 7,000 BVD viral strains obtained during a national campaign to eradicate BVD and features common to the hosts of these strains enabled us to trace back in time the presence of BVD in the Swiss cattle population. We found that animals of the two major traditional cattle breeds, Fleckvieh and Swiss Brown, were infected with strains of only four different subgenotypes of BVDV-1. The history of these cattle breeds and the events that determined the current distribution of the two populations are well documented. Specifically, Fleckvieh originates from the Bernese and Swiss Brown from the central Alps. The spread to their current geographic distribution was determined by historic events during a major expansion of the Swiss Confederation during the 15th and 16th centuries. The association of the two cattle populations with different BVD viral subgenotypes may have been preserved by a lack of cattle imports, trade barriers within the country, and unique virus-host interactions. The congruent traces of history in the distribution of the two cattle breeds and distinct viral subgenotypes suggests that BVD may have been endemic in Switzerland for at least 600 years.

Detection and Characterization of Okapi (Okapia johnstoni)-specific Papillomavirus type 1 (OjPV1)

Papillomavirus-specific DNA was detected in skin lesions collected from an okapi (Okapia johnstoni) in the Zoo Basel. According to the nucleotide sequence analysis, the virus belongs to the genus Deltapapillomavirus. Based on bioinformatics analysis, we propose to designate the newly identified virus as Okapia johnstoni Papillomavirus type 1 (OjPV1). OjPV1 is genetically most closely related to a recently described giraffe (Giraffa camelopardalis) -specific papillomavirus (GcPV1). Of note, the putative oncogenic E5 proteins from OjPV1 and GcPV1 are more conserved than the L1 proteins. This indicates, that the selection pressure on E5 may be more pronounced than that on the otherwise most conserved major capsid protein L1.

Selected Viruses Detected on and in our Food

PURPOSE OF REVIEW

The purpose of this review is to provide an update on recent literature and findings concerning selected foodborne viruses. Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health.

RECENT FINDINGS

Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually "only" contaminating food and are detected on the surface of foodstuffs. However, they are threats to human public health and make up for the majority of cases. In contrast, the meaning of viruses born from within the food such as natural animal and plant viruses is still in many cases unknown. An exception is Hepatitis E virus that is endemic in pigs, transmitted via pork meat and is recognised as an emerging zoonosis in industrialised countries.

SUMMARY

Even though the clinical meaning of "new" foodborne viruses, often detected by next generation sequencing, still needs clarification, the method has great potential to enhance surveillance and detection particularly in view of an increasingly globalised food trade.

Analysis of bovine viral diarrhoea virus: Biobank and sequence database to support eradication in Scotland

Samples from bovine viral diarrhoea virus (BVDV)-positive cattle were gathered by Scottish diagnostic laboratories and used to produce a Biobank of samples with associated location and identification data in support of the Scottish BVDV eradication scheme. The samples were subject to direct amplification and sequencing of the 5'-untranslated region (5'-UTR) to define the viral types and subtypes present. From 2693 samples collected prior to 2016, approximately 2300 sequences were obtained, representing 8 BVDV type 1 subtypes. No BVDV type 2 samples were detected. The samples came from all regions of the UK but 66 per cent were from Scotland. Analysis of the sequences showed great diversity in the 5'-UTR, with 1206 different sequences. Many samples carried virus with identical 5'-UTR sequences; often from single locations, but there were also examples of the same sequence being obtained from samples at several different locations. This work provides a resource that can be used to analyse the movement of BVDV strains both within Scotland and between Scotland and other nations, particularly in the latter stages of the Scottish eradication programme, and so inform the advice available to both livestock keepers and policymakers.

Assessment of the rabbit as a wildlife reservoir of bovine viral diarrhea virus: serological analysis and generation of trans-placentally infected offspring

Eradication of bovine viral diarrhea virus (BVDV) is ongoing in many European countries and is based on removal of persistently infected (PI) cattle. In this context, low-level risks, including alternative reservoirs of infection, may become more important as the number of BVDV-free herds increases. Alternative reservoirs include livestock, such as sheep and goats, as well as wildlife, including deer and rabbits. Due to the extensive nature of the beef industry in Scotland, where an eradication program started in 2010, contact between cattle and alternative reservoir hosts is common. Seroprevalence to BVDV in rabbit populations can be high. In addition, rabbits can be infected with BVDV by natural routes, indicating that they could be a wildlife reservoir of infection. We analyzed the potential risk to livestock from rabbit populations in the UK by two approaches. First, ∼260 serum samples from free-ranging wild rabbits in Scotland and northern England were tested for BVDV-specific antibodies by ELISA. Only three samples exhibited low level BVDV-specific reactivity, suggesting that BVDV infection of rabbits was not frequent. Second, rabbits were challenged with BVDV at day 7 or 12 of pregnancy. This did not lead to any clinical signs in the infected animals or obvious increases in abortion or stillbirth in the infected dams. Samples from the dams, placental material and ∼130 offspring were tested by BVDV-specific RT-PCR and antibody ELISA. Positive PCR results in the placentas and in the tissues and body fluids of rabbits up to 10 days old showed that trans-placental infection of rabbits with BVDV had occurred. Many of the offspring had BVDV-specific antibodies. These data support the view that a wildlife reservoir of BVDV in rabbit poses a small but non-zero risk of re-infection for BVDV-free cattle herds. Rabbits are susceptible to infection with BVDV but only a small proportion of free-living rabbits in the UK appear to have been infected.

Diagnostic gap in Bovine viral diarrhea virus serology during the periparturient period in cattle

Detection of antibodies against Bovine viral diarrhea virus (BVDV) in serum and milk by enzyme-linked immunosorbent assay (ELISA) is a crucial part of all ongoing national schemes to eradicate this important cattle pathogen. Serum and milk are regarded as equally suited for antibody measurement. However, when retesting a seropositive cow 1 day after calving, the serum was negative in 6 out of 9 different ELISAs. To further investigate this diagnostic gap around parturition, pre- and postcalving serum and milk samples of 5 cows were analyzed by BVDV antibody ELISA and serum neutralization test (SNT). By ELISA, 3 out of the 5 animals showed a diagnostic gap in the serum for up to 12 days around calving but all animals remained positive in SNT. In milk, the ELISA was strongly positive after birth but antibody levels decreased considerably within the next few days. Because of the immunoglobulin G (IgG)1-specific transport of serum antibodies into the mammary gland for colostrum production, the IgG subclass specificity of the total and the BVDV-specific antibodies were determined. Although all 5 animals showed a clear decrease in the total and BVDV-specific IgG1 antibody levels at parturition, the precalving IgG1-to-IgG2 ratios of the BVDV-specific antibodies were considerably lower in animals that showed the diagnostic gap. Results showed that BVDV seropositive cows may become "false" negative in several ELISAs in the periparturient period and suggest that the occurrence of this diagnostic gap is influenced by the BVDV-specific IgG subclass response of the individual animal.

Experimental infection of rabbits with bovine viral diarrhoea virus by a natural route of exposure

Bovine viral diarrhoea virus (BVDV) is an important pathogen of cattle that can naturally infect a wide range of even-toed ungulates. Non-bovine hosts may represent reservoirs for the virus that have the potential to hamper BVDV eradication programs usually focused on cattle. Rabbits are very abundant in countries such as the United Kingdom or Australia and are often living on or near livestock pastures. Earlier reports indicated that rabbits can propagate BVDV upon intravenous exposure and that natural infection of rabbits with BVDV may occur but experimental proof of infection of rabbits by a natural route is lacking. Therefore, New Zealand White rabbits were exposed to a Scottish BVDV field strain intravenously, oro-nasally and by contaminating their hay with virus. None of the animals showed any clinical signs. However, the lymphoid organs from animals sacrificed at day five after exposure showed histological changes typical of transient infection with pestivirus. Most organ samples and some buffy coat samples were virus positive at day five but saliva samples remained negative. Development of antibodies was observed in all intravenously challenged animals, in all of the nebulised group and in four of six animals exposed to contaminated hay. To our knowledge this is the first report of BVDV propagation in a species other than ruminants or pigs after exposure to the virus by a natural route. However, to assess the role of rabbits as a potential reservoir for BVDV it remains to be determined whether persistent infection caused by intra-uterine infection is possible and whether BVDV is circulating in wild rabbit populations.

Sheep persistently infected with Border disease readily transmit virus to calves seronegative to BVD virus

Bovine viral diarrhea- and Border disease viruses of sheep belong to the highly diverse genus pestivirus of the Flaviviridae. Ruminant pestiviruses may infect a wide range of domestic and wild cloven-hooved mammals (artiodactyla). Due to its economic importance, programs to eradicate bovine viral diarrhea are a high priority in the cattle industry. By contrast, Border disease is not a target of eradication, although the Border disease virus is known to be capable of also infecting cattle. In this work, we compared single dose experimental inoculation of calves with Border disease virus with co-mingling of calves with sheep persistently infected with this virus. As indicated by seroconversion, infection was achieved only in one out of seven calves with a dose of Border disease virus that was previously shown to be successful in calves inoculated with BVD virus. By contrast, all calves kept together with persistently infected sheep readily became infected with Border disease virus. The ease of viral transmission from sheep to cattle and the antigenic similarity of bovine and ovine pestiviruses may become a problem for demonstrating freedom of BVD by serology in the cattle population.

[Bovine viral diarrhea (BVD): from biology to control]

Bovine viral diarrhea virus (BVDV) is endemic worldwide. Together with classical swine fever and border disease viruses, it belongs to the genus Pestivirus of the family Flaviviridae. Most infections with BVDV take a transient, acute, course. Only rarely BVDV persists in its hosts. Due to the early time point of infection in utero, persistently infected (PI) animals are immunotolerant to the infecting non-cytopathic BVDV. In such animals the virus may mutate to a cytopathic biotype, causing lethal mucosal disease. In BVD-endemic regions, approximately 1% of the animals are PI. Removal of all PI animals leads to extinction of BVD. This approach to BVD eradication has been vindicated in Scandinavia. Following the same principles, regional and country-wide eradication programs are run in different parts of the world. These programs differ in the way PI animals are detected and in the role of vaccines. The Scandinavian two-step method of detecting PI animals is based on (i) the high level of seroprevalence in herds where PI animals are present and (ii) on testing all animals for virus in such herds. However, the high average herd seroprevalence in Switzerland made it impossible to define a reasonable threshold for virus testing. Therefore, all animals were directly tested for virus in the year 2008 and all newborn calves until the end of 2012, when the PI prevalence had dropped to 0.02%. Vaccination remains prohibited. Since 2013, surveillance for BVD is accomplished by serology. As a unique consequence of eradication, over 7500 viral strains are available to us for genetic studies.

Persistent infections after natural transmission of bovine viral diarrhoea virus from cattle to goats and among goats

Bovine viral diarrhoea virus (BVDV) is an economically important pathogen of cattle worldwide. Infection of a pregnant animal may lead to persistent infection of the foetus and birth of a persistently infected (PI) calf that sheds the virus throughout its life. However, BVD viruses are not strictly species specific. BVDV has been isolated from many domesticated and wild ruminants. This is of practical importance as virus reservoirs in non-bovine hosts may hamper BVDV control in cattle. A goat given as a social companion to a BVDV PI calf gave birth to a PI goat kid. In order to test if goat to goat infections were possible, seronegative pregnant goats were exposed to the PI goat. In parallel, seronegative pregnant goats were kept together with the PI calf. Only the goat to goat transmission resulted in the birth of a next generation of BVDV PI kids whereas all goats kept together with the PI calf aborted. To our knowledge, this is the first report which shows that a PI goat cannot only transmit BVD virus to other goats but that such transmission may indeed lead to the birth of a second generation of PI goats. Genetic analyses indicated that establishment in the new host species may be associated with step-wise adaptations in the viral genome. Thus, goats have the potential to be a reservoir for BVDV. However, the PI goats showed growth retardation and anaemia and their survival under natural conditions remains questionable.

Apoptosis in Bovine viral diarrhea virus (BVDV)-induced mucosal disease lesions: a histological, immunohistological, and virological investigation

Cattle persistently infected with a noncytopathic Bovine viral diarrhea virus (BVDV) are at risk of developing fatal "mucosal disease" (MD). The authors investigated the role of various apoptosis pathways in the pathogenesis of lesions in animals suffering from MD. Therefore, they compared the expression of caspase-3, caspase-8, caspase-9, and Bcl-2L1 (Bcl-x) in tissues of 6 BVDV-free control animals, 7 persistently infected (PI) animals that showed no signs of MD (non-MD PI animals), and 11 animals with MD and correlated the staining with the localization of mucosal lesions. Caspase-3 and -9 staining were markedly stronger in MD cases and were associated with mucosal lesions, even though non-MD PI animals and negative controls also expressed caspase-9. Conversely, caspase-8 was not elevated in any of the animals analyzed. Interestingly, Bcl-x also colocalized with mucosal lesions in the MD cases. However, Bcl-x was similarly expressed in tissues from all 3 groups, and thus, its role in apoptosis needs to be clarified. This study clearly illustrates ex vivo that the activation of the intrinsic, but not the extrinsic, apoptosis pathway is a key element in the pathogenesis of MD lesions observed in cattle persistently infected with BVDV. However, whether direct induction of apoptosis in infected cells or indirect effects induced by the virus are responsible for the lesions observed remains to be established.

Cytopathic bovine viral diarrhea viruses (BVDV): emerging pestiviruses doomed to extinction

Bovine viral diarrhea virus (BVDV), a Flaviviridae pestivirus, is arguably one of the most widespread cattle pathogens worldwide. Each of its two genotypes has two biotypes, non-cytopathic (ncp) and cytopathic (cp). Only the ncp biotype of BVDV may establish persistent infection in the fetus when infecting a dam early in gestation, a time point which predates maturity of the adaptive immune system. Such fetuses may develop and be born healthy but remain infected for life. Due to this early initiation of fetal infection and to the expression of interferon antagonistic proteins, persistently infected (PI) animals remain immunotolerant to the infecting viral strain. Although only accounting for some 1% of all animals in regions where BVDV is endemic, PI animals ensure the viral persistence in the host population. These animals may, however, develop the fatal mucosal disease, which is characterized by widespread lesions in the gastrointestinal tract. Cp BVD virus, in addition to the persisting ncp biotype, can be isolated from such animals. The cp viruses are characterized by unrestrained genome replication, and their emergence from the persisting ncp ones is due to mutations that are unique in each virus analyzed. They include recombinations with host cell mRNA, gene translocations and duplications, and point mutations. Cytopathic BVD viruses fail to establish chains of infection and are unable to cause persistent infection. Hence, these viruses illustrate a case of "viral emergence to extinction" - irrelevant for BVDV evolution, but fatal for the PI host.

Clinical appearance and pathology of cattle persistently infected with bovine viral diarrhoea virus of different genetic subgroups

Bovine viral diarrhoea (BVD) is an economically important cattle disease with a world-wide distribution that is caused by BVD virus, a pestivirus of the flaviviridae family. BVD viruses are genetically highly variable. They are classified into two genetic species (BVDV-1 and -2) that are further divided into numerous subgroups, particularly for BVDV-1. The complexity of these viruses is also reflected in their interaction with the host animals. Infections are either transient or persistent and can cause a wide spectrum of clinical signs, from no or very mild disease to severe forms, reminiscent of viral haemorrhagic fevers. In this work, we have analysed the clinical signs and the pathology of BVD viral infections in a cattle population where different subgroups of BVDV-1 genotype viruses are endemic. In addition, we have examined potential virulence properties of BVDV-1 subgroups during persistent infection by comparing the viral subgroups present in clinical cases with those detected in persistently infected (PI) animals sampled for epidemiological criteria, irrespective of their health condition. Furthermore, the clinical and postmortem findings were compared with respect to genetic characteristics of the viruses isolated from these animals. Our results indicate that the BVDV positive animals fall roughly into two categories, depending on the primary organ affected and the age, with lung-centred pathology occurring mainly in young animals and mucosal pathology predominantly in older animals. Furthermore, we found a markedly higher proportion of representatives of the BVDV-1e subgroup in stillborn calves and aborted foetuses originating from epidemically unrelated cattle herds, suggesting that BVDV-1e may play a special role in prenatal and perinatal losses.

Co-existence of genetically and antigenically diverse bovine viral diarrhoea viruses in an endemic situation

Bovine viral diarrhoea virus (BVDV) is an important cattle pathogen that causes acute or persistent infections. These are associated with immunotolerance to the viral strain persisting in animals that became infected early in their intrauterine development. To this date, the epidemiology of BVD in Switzerland runs virtually undisturbed by control measures such as restrictions on animal traffic or vaccination. Here, we analysed the viral genetics of 169 Swiss isolates and carried out crossed serum neutralisation tests to assess the antigenic spectrum of BVDV strains present in the cattle population. Besides confirming the presence of BVDV type 1 subgroups b, e, h and k, a single "orphan" BVDV-1 virus was detected that does not belong to any known BVDV-1 subgroup. No BVDV type 2 viruses were detected, suggesting that they are rare or not present in the cattle population. Antigenic comparison revealed significant differences between the different subgroups, with anti-1k immune serum having up to tenfold lower neutralising activity against 1b, 1e and 1h subgroup viruses, which however may still suffice to protect 1k-immune animals against superinfection by viruses of those other subgroups. Serum from routinely vaccinated animals revealed generally low titres but good cross-neutralisation. A geographic information system revealed that the viruses of the different subgroups are distributed in an apparently randomised fashion in the cattle population. This geographic distribution pattern may reflect peculiarities of the management practice in the Swiss cattle industry that, especially through annual transhumance of up to 25% of the entire population in the alpine region, tend to optimise the spread of BVDV.

Genetic heterogeneity of pestiviruses of ruminants in Switzerland

We have genetically analyzed ruminant pestiviruses. All >150 bovine viral diarrhea (BVD) viruses isolated from cattle in Switzerland belonged to genotype 1, with subgenogroups e, h, k and b found in decreasing frequency. To date, representatives of subgenogroup k have been detected in Switzerland only. Despite serological evidence of Border disease in sheep, only few Border disease viruses have been isolated, all of which belong to the novel group 3. Serological evidence suggested that pestivirus infections may occur also in wild ruminants in Switzerland but no isolates are available for analysis. In addition, we describe two pestiviruses, one a cell culture contaminant and the other isolated from a buffalo, that cluster with a recently proposed novel pestivirus species.

A transvaginal approach to repair of apical and other associated sites of pelvic organ prolapse with uterosacral ligaments

OBJECTIVE

The objectives of this study were (1) to describe a group of women with pelvic organ prolapse associated with apical loss of support through grading with the Baden-Walker halfway system before, during, and after the corrective operation, (2) to describe the operative repair of the support defects, (3) to report the morbidity associated with the operative repair, and (4) to assess the durability of the repair at each site.

STUDY DESIGN

Between January 1, 1994, and December 31, 1998, a total of 302 consecutive women with apical and associated other support defects were evaluated before, during, and after the corrective operation by the senior author (Bob L. Shull). All patients underwent transvaginal reconstructive surgery with native tissue. Two hundred eighty-nine patients (96%) returned for at least one postoperative visit, and they constitute the group used for the follow-up data. Perioperative morbidity was considered to include hemorrhage necessitating homologous blood transfusion, visceral injury, neurologic impairment, or death. Durability was assessed by means of life-table analysis for each of 5 sites in the vagina.

RESULTS

All patients had preoperative or intraoperative evidence of grade 1 or greater apical loss of support of and at least one other site of pelvic organ prolapse. Two hundred eighty-nine patients (96%) returned for at least one postoperative visit. Two hundred fifty-one patients (group 1, 87%) had optimal anatomic outcomes, with no persistent or recurrent support defects at any site. Thirty-eight patients (group 2, 13%) had one or more sites with at least grade 1 loss of support during the follow-up interval. Twenty-four of these 38 patients had grade 1 defects that were detectable only on careful pelvic examination. Fourteen of these patients (5%) had grade 2 or greater persistent or recurrent support defects. The anterior segment (bladder) was the site with the most persistent or recurrent support defects, which means that it was the site of the least durable repair. The urethra and cuff had the most durable repairs. Morbidity included a 1% transfusion rate, a 1% ureteral injury or ureteral kinking rate, and a 0.3% postoperative death rate.

CONCLUSION

Careful preoperative and intraoperative evaluation of pelvic support defects and the use of native connective tissue and uterosacral ligaments are associated with excellent anatomic outcomes. The durability of the surgical correction varies according to the individual site of repair and the duration of postoperative follow-up.