Unusual "Asian-origin" 2c to 2b point mutant canine parvovirus (Parvoviridae) and canine astrovirus (Astroviridae) co-infection detected in vaccinated dogs with an outbreak of severe haemorrhagic gastroenteritis with high mortality rate in Hungary

Identification of a potential interspecies reassortant rotavirus G and avastrovirus 2 co-infection from black-headed gull (Chroicocephalus ridibundus) in Hungary

The black-headed gull is the most common nesting gull species in Hungary. Based on the lifestyle and feeding habits of the black-headed gull, which is highly adapted to the human environment, they can be carriers and spreaders of potential human and other animal pathogens. Between 2014 and 2018 within the framework of the "Life Bird Ringing program" a total of 7 faecal samples were collected from gulls and one sample (MR04) was randomly selected for viral metagenomics and mass sequencing. 95.4% and 4% of the reads were classified into family Seadornaviridae and Astroviridae, respectively, and then were verified by RT-PCR method. In this study, the complete genome of a potential interspecies reassortant rotavirus (RV) strain gull/MR04_RV/HUN/2014 (PP239049-PP239059) and the partial ORF1ab, complete ORF2 of a novel avian nephritis virus strain gull/MR04_AAstV/HUN/2014 (PP239060) was discussed. The strain gull/MR04_RV/HUN/2014 was closely related to rotavirus G (RVG) viruses based on the proteins VP1-VP3, VP6, NSP2, NSP3, and NSP5, but it was more related to the human rotavirus B (RVB) strain Bang373 based on the NSP1, NSP4 and VP7, VP4 proteins, which is assumed to be the result of reassortment between different RVG-RVB rotavirus species. The strain gull/MR04_AAstV/HUN/2014 belonged to the genus Avastrovirus species avastrovirus 2 (AAstV-2) and is related to members of group 6 of avian nephritis viruses (ANVs), but based on the genetic distances it may be the first representative of a separate group. Additional gull samples were found to be negative by RT-PCR. Gulls, which are well adapted to the human environment, could potentially spread enterically transmitted viral pathogens like interspecies reassortant rotaviruses (RVG/RVB), but further molecular surveillance is needed to explore more deeply the viral communities of gulls or other related species adapted to human environments.

Molecular characterization and lineage analysis of canine astrovirus strains from dogs with gastrointestinal disease in Ecuador based on ORF-2 gene analysis

Canine Astrovirus (CaAstV) part of the Astroviridae family and genus Mamastrovirus, is a linear RNA virus with a genome of approximately 6.6 kb with three open reading frames (ORF): ORF1a and ORF1b, which code for the most conserved non-structural proteins, and ORF2, which code for the capsid protein, the most variable region of the genome. This pathogen has been linked to gastrointestinal infections, primarily causing symptoms such as vomiting, diarrhea, lethargy and severe dehydration, mainly in co-infection with other enteric viruses. In the present study, the presence of CaAstV was identified in dogs with gastrointestinal disease in Ecuador using RT-qPCR with hydrolysis probes, these samples have also tested positive for canine parvovirus type 2 (CPV-2) and canine coronavirus (CCoV). Positive samples were used for end-point RT-PCR amplification and sequencing of ORF-2 using Sanger technology. The sequences were subjected to phylogenetic analysis to determine lineages and possible recombination events. Of the 502 samples tested, 336 were found to be positive for CaAstV, 49.4% in co-infection with CPV-2, 1% in co-infection with CCoV, and 4% in simultaneous infection with all three viruses. The presence of 4 of the 5 previously reported CaAstV lineages were identified, and three possible recombinant strains were identified. Given the high frequency of CaAstV infections in dogs with gastroenteritis and its high genetic variability, it emphasizes the need to implement routine diagnostic measures that include this pathogen as one of the main causes of the disease and a risk agent in case of multiple infections.

The first evidence of Asian-like CPV-2b in Slovakia in a vaccinated dog with an acute fatal course of parvovirus infection: a case report

This study provides a comprehensive description of the clinical course of a fatal parvovirus infection in a vaccinated dachshund puppy, along with the first identification of a new CPV-2 variant in Slovakia, elucidated through molecular amino acid analysis of the VP2 gene. The dog exhibited clinical signs such as apathy, vomiting, and bloody diarrhea. After confirming CPV-2 infection with a commercial snap test, intensive therapy was initiated. The dog succumbed within 48 h of admission. A rectal swab sample was collected, CPV-2 was examined using the PCR method, and sequenced. The virus detected in the patient was related to strains of CPV-2c of Asian origin and unrelated to European CPV-2b strains. The sequence had genetic signatures typical of Asian strains (VP2: 5Gly, 267Tyr, 324Ile, 370Arg, and 440Thr). Phylogenetic analysis classified this strain as similar to Asian strains of CPV-2c. It is believed to be derived from an Asian strain similar to CPV-2c that acquired the 426Asp mutation. With this finding, we present the first evidence of an Asian-like CPV-2b strain in the territory of Slovakia.

First Report on the Molecular Detection of Canine Astrovirus (CaAstV) in Dogs with Gastrointestinal Disease in Ecuador Using a Fast and Sensitive RT-qPCR Assay Based on SYBR Green®

Enteric viruses are responsible for a significant number of gastrointestinal illnesses in dogs globally. One of the main enteric viruses is the canine astrovirus (CaAstV), which causes diarrhea in dogs of various ages. It is linked to symptoms such as diarrhea, vomiting, depression and a significant mortality rate due to gastrointestinal disorders. It is a single-stranded positive RNA virus, with three open reading frames, ORF1a, ORF1b and ORF2, where the last one codes for the virus capsid protein and is the most variable and antigenic region of the virus. The aim of this work is to develop and standardize a quick detection method to enable the diagnosis of this etiological agent in dogs with gastroenteritis in Ecuador in order to provide prompt and suitable treatment. The assay was specific for amplification of the genome of CaAstV, as no amplification was shown for other canine enteric viruses (CPV-2, CCoV and CDV), sensitive by being able to detect up to one copy of viral genetic material, and repeatable with inter- and intra-assay coefficients of variation of less than 10% between assays. The standard curve showed an efficiency of 103.9%. For the validation of this method, 221 fecal samples from dogs affected with gastroenteritis of various ages from different provinces of Ecuador were used. From the RT-qPCR protocol, 119 samples were found positive for CaAstV, equivalent to 53.8% of the samples processed. CaAstV was detected in dogs where both the highest virus prevalence in the tested strains and the highest viral loads were seen in the younger canine groups up to 48 weeks; in addition, different strains of the virus were identified based on a sequenced fragment of ORF1b, demonstrating the first report of the presence of CaAstV circulating in the domestic canine population affected by gastroenteritis in Ecuador, which could be associated with the etiology and severity of enteric disease.

Co-infecting viruses of species Bovine rhinitis B virus (Picornaviridae) and Bovine nidovirus 1 (Tobaniviridae) identified for the first time from a post-mortem respiratory sample of a sheep (Ovis aries) in Hungary

In this study, a picornavirus and a nidovirus were identified from a single available nasopharyngeal swab (NPS) sample of a freshly deceased sheep, as the only vertebrate viruses found with viral metagenomics and next-generation sequencing methods. The sample was originated from a mixed feedlot farm in Hungary where sheep and cattle were held together but in separate stalls. Most of the sheep had respiratory signs (coughing and increased respiratory effort) at the time of sampling. Other NPS were not, but additional enteric samples were collected from sheep (n = 27) and cattle (n = 11) of the same farm at that time. The complete/nearly complete genomes of the identified viruses were determined using RT-PCR and Nanopore (MinION-Flonge) / Dye-terminator sequencing techniques. The results of detailed genomic and phylogenetic analyses indicate that the identified picornavirus most likely belongs to a type 4 genotype of species Bovine rhinitis B virus (BRBV-4, OR885914) of genus Aphthovirus, family Picornaviridae while the ovine nidovirus (OvNV, OR885915) - as a novel variant - could belong to the recently created Bovine nidovirus 1 (BoNV) species of genus Bostovirus, family Tobaniviridae. None of the identified viruses were detectable in the enteric samples using RT-PCR and generic screening primer pairs. Both viruses are well-known respiratory pathogens of cattle, but their presence was not demonstrated before in other animals, like sheep. Furthermore, neither BRBV-4 nor BoNVs were investigated in European cattle and/or sheep flocks, therefore it cannot be determined whether the presence of these viruses in sheep was a result of a single host species switch/spillover event or these viruses are circulating in not just cattle but sheep populations as well. Further studies required to investigate the spread of these viruses in Hungarian and European sheep and cattle populations and to identify their pathogenic potential in sheep.

Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals

Next-Generation Sequencing (NGS) techniques have revolutionized veterinary medicine for cats and dogs, offering insights across various domains. In veterinary parasitology, NGS enables comprehensive profiling of parasite populations, aiding in understanding transmission dynamics and drug resistance mechanisms. In infectious diseases, NGS facilitates rapid pathogen identification, characterization of virulence factors, and tracking of outbreaks. Moreover, NGS sheds light on metabolic processes by elucidating gene expression patterns and metabolic pathways, essential for diagnosing metabolic disorders and designing tailored treatments. In autoimmune diseases, NGS helps identify genetic predispositions and molecular mechanisms underlying immune dysregulation. Veterinary oncology benefits from NGS through personalized tumor profiling, mutation analysis, and identification of therapeutic targets, fostering precision medicine approaches. Additionally, NGS plays a pivotal role in veterinary genetics, unraveling the genetic basis of inherited diseases and facilitating breeding programs for healthier animals. Physiological investigations leverage NGS to explore complex biological systems, unraveling gene-environment interactions and molecular pathways governing health and disease. Application of NGS in treatment planning enhances precision and efficacy by enabling personalized therapeutic strategies tailored to individual animals and their diseases, ultimately advancing veterinary care for companion animals.

Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary

In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.

Molecular epidemiology of canine parvovirus type 2 in Sicily, southern Italy: A geographical island, an epidemiological continuum

Since it emerged as a major dog pathogen, canine parvovirus type 2 (CPV-2) has featured a remarkable genetic and phenotypic heterogeneity, whose biological, epidemiological, and clinical impact is still debated. The continuous monitoring of this pathogen is thus of pivotal importance. In the present study, the molecular epidemiology of CPV-2 in Sicily, southern Italy, has been updated by analysing 215 nearly complete sequences of the capsid protein VP2, obtained from rectal swabs/faeces or tissue samples collected between 2019 and 2022 from 346 dogs with suspected infectious gastrointestinal disease. The presence of the original CPV-2 type (4%) and CPV-2a (9%), CPV-2b (18%), or CPV-2c (69%) variants was documented. Over the years, we observed a decrease in the frequency of CPV-2a/-2b and a rapid increase of CPV-2c frequency, with a progressive replacement of the European lineage of CPV-2c by the Asian lineage. The observed scenario, besides confirming epidemiological relevance of CPV-2, highlights the occurrence of antigenic variant shifts over time, with a trend toward the replacement of CPV-2a, CPV-2b, and the European lineage of CPV-2c by the emerging Asian CPV-2c lineage. The comparison with other Italian and international sequences suggests the occurrence of viral exchange with other Italian regions and different countries, although the directionality of such viral flows could not be often established with confidence. In several instances, potential CPV-2 introductions led to epidemiological dead ends. However, major, long-lasting clades were also identified, supporting successful infection establishment, local spreading, and evolution. These results, besides demonstrating the need for implementing more effective control measures to prevent viral introductions and minimize circulation, stress the relevance of routine monitoring activities as the only tool to effectively understand CPV-2 epidemiology and evolution, and develop adequate countermeasures.

Investigation of circulating infectious agents in experimental Beagle dogs of a production colony and three research facilities in China from June 2021 to May 2022

To understand the epizootiologic characteristics of pathogens and opportunistic infections in one Beagle dog production colony and three research facilities, viruses and mycoplasma were detected in 1777 samples collected from Beagle dogs in China by polymerase chain reaction/reverse transcription polymerase chain reaction, and bacteria were isolated and identified by 16S rRNA sequence analysis. In addition, genotyping of the major circulating viruses was carried out by amplification of gene fragments and homology analysis. Canine coronavirus (CCoV), Escherichia coli, canine parvovirus (CPV), Bordetella bronchiseptica, Clostridium perfringens, Mycoplasma cynos, Klebsiella pneumoniae, Streptococcus canis, canine astrovirus (CaAstV), canine kobuvirus (CaKV), Pseudomonas aeruginosa, Proteus mirabilis, Macrococcus canis, Pasteurella canis, canine bocavirus (CBoV) and canine adenovirus (CAdV) were detected in the samples. Single, double, triple and quadruple infections accounted for 6.6%, 1.4%, 1.2% and 0.96% of samples, respectively. CCoV strains in 81 samples included three genotypes, CCoV-I, CCoV-IIa and CCoV-IIb, by analysis of S gene. The rate of single infection of CCoV-I, CCoV-IIa or CCoV-IIb was 19%, 38% or 7.4% respectively. The double and triple infection rates of CCoV were 32.8% and 2.5% respectively. All CPV strains in 36 samples belonged to CPV-2c. There were three amino acid differences in the Fiber protein of CAdV-positive sample QD2022, compared with the reference strain Toronto A26/61 and the vaccine strain YCA-18. These results suggest that CCoV and CPV are primary infectious agents, and that these two viruses were often identified in mixed infections, or coinfections alongside mycoplasma or other bacteria. These results will provide the basis for improvements in prevention and control of naturally occurring infectious diseases in Beagle dog production colonies and research facilities.

The genomic and epidemiological investigations of enteric viruses of domestic caprine (Capra hircus) revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species

IMPORTANCE

Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family Parvoviridae) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family Astroviridae), enteroviruses, or novel caripiviruses (named after the term caprine picornavirus) of family Picornaviridae found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.

Not Asian Anymore: Reconstruction of the History, Evolution, and Dispersal of the "Asian" Lineage of CPV-2c

Variability has been one of the hallmarks of canine parvovirus type 2 (CPV-2) since its discovery, and several lineages and antigenic variants have emerged. Among these, a group of viruses commonly called Asian CPV-2c has recently been reported with increasing frequency in different regions. Currently, its global epidemiology and evolution are essentially unknown. The present work deals with this information gap by evaluating, via sequence, phylodynamic, and phylogeographic analyses, all the complete coding sequences of strains classified as Asian CPV-2c based on a combination of amino acid markers and phylogenetic analysis. After its estimated origin around 2008, this lineage circulated undetected in Asia until approximately 2012, when an expansion in viral population size and geographical distribution occurred, involving Africa, Europe, and North America. Asia was predicted to be the main nucleus of viral dispersal, leading to multiple introduction events in other continents/countries, where infection establishment, persistence, and rapid evolution occurred. Although the dog is the main host, other non-canine species were also involved, demonstrating the host plasticity of this lineage. Finally, although most of the strains showed an amino acid motif considered characteristic of this lineage, several exceptions were observed, potentially due to convergent evolution or reversion phenomena.

Whole genome sequence analysis of CPV-2 isolates from 1998 to 2020

Canine parvovirus-2 (CPV-2) is a virus with worldwide spread causing canine gastroenteritis. New strains of this virus have unique characteristics and are resistant to some vaccine strains. Therefore, understanding the root causes of resistance has proven to be of increasing concern to many scientists. This study collected 126 whole genome sequences of CPV-2 subtypes with specific collection dates from the NCBI data bank. The whole genome sequences of CPV-2 collected from different countries were analyzed to detect the new substitutions and update these mutations. The result indicated 12, 7, and 10 mutations in NS1, VP1, and VP2, in that respective order. Moreover, the A5G and Q370R mutations of VP2 are the most common changes in the recent isolates of the CPV-2C subtype, and the new N93K residue of VP2 is speculated to be the cause of vaccine failure. To summarize, the observed mutations, which are increasing over time, causes several changes in viral characteristic. A comprehensive understanding of these mutations can lead us to control potential future epidemics associated with this virus more efficiently.

Canine Parvovirus in Turkey: First Whole-Genome Sequences, Strain Distribution, and Prevalence

Canine parvovirus (CPV) is a significant pathogenic virus with up to 100% morbidity and 91% mortality rates, especially in unvaccinated puppies. The emergence of new strains, interspecies transmission, and vaccine effectiveness can be enabled by just a few base changes in the CPV genome. Therefore, to cope with CPV disease, it is important to identify the viral agent and regularly monitor vaccine effectiveness against new strains. The present study has investigated CPV's genetic profile in Turkey by collecting 80 samples from dogs in Turkey between 2020 and 2022. These samples and all sequences previously studied for CPV in Turkey were analyzed for whole-genome sequences, nationwide strain distribution over the two years, and the central Turkey prevalence rate. Next-generation sequencing was used for the genome study, Sanger sequencing for strain detection, and PCR for the prevalence analyses. The CPV-2 variants circulating in Turkey form their own cluster while being closely related to Egypt variants. Substantial amino acid changes were detected in antigenically important regions of the VP2 gene. Moreover, CPV-2b has become the most frequent genotype in this region, while the incidence of CPV-2c is predicted to increase gradually over the coming years. The prevalence of CPV in central Turkey was 86.27%. This study thus provides powerful insights to further our understanding of CPV's genetic profile in Turkey and suggests that up-to-date vaccination efficacy studies are urgently needed.

Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris)

Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.