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.

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A metagenomic study was performed on 498 female and 40 male Aedes albopictus mosquitos collected in August and September 2019 in Ticino, a region in southern Switzerland, to address the question regarding the risk of the local transmission of zoonotic viruses. A total of 13 viruses from seven different virus families and several unclassified viral taxa were identified. Reads of insect-specific flaviviruses were present in all pools, and a complete genome of aedes flavivirus was assembled and phylogenetically analysed. The most abundant virus was Wenzhou sobemo-like virus, assembled from 1.3 × 105 to 3.6 × 106 reads in each pool. In a pool of male mosquitos, a complete genome of aedes Iflavi-like virus was detected and phylogenetically analysed. Most importantly, genomes of human pathogenic viruses were not found. This is the first study to determine the virome of Ae. albopictus from Switzerland and forms a baseline for future longitudinal investigations concerning the potential role of Ae. albopictus as a vector of clinically relevant viruses.

Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.

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.

We present here the full-length genome sequences of two hepatitis E virus genotype 3 (HEV-3) isolates from a human stool sample from a patient with acute hepatitis and a raw sausage containing pig liver. Sequence analysis implies that Swiss HEV isolates may form a novel subgroup of HEV-3 viruses.

Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in a research setting, it is now increasingly being used in the clinical realm as well, notably to support diagnosis of viral infections, thereby calling for quality control and the implementation of ring trials (RT) to benchmark pipelines and ensure comparable results. The Swiss NGS clinical virology community therefore decided to conduct a RT in 2018, in order to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and thereby contribute to the definition of common best practices. The RT consisted of two parts (increments), in order to disentangle the variability arising from the experimental compared to the bioinformatics parts of the laboratory pipeline. In addition, the RT was also designed to assess the impact of databases compared to bioinformatics algorithms on the final results, by asking participants to perform the bioinformatics analysis with a common database, in addition to using their own in-house database. Five laboratories participated in the RT (seven pipelines were tested). We observed that the algorithms had a stronger impact on the overall performance than the choice of the reference database. Our results also suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5–10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage. Performance was generally lower when increasing the number of viruses per sample. The lessons learned from this pilot study will be useful for the development of larger-scale RTs to serve as regular quality control tests for laboratories performing NGS analyses of viruses in a clinical setting.