Porcine kobuvirus enhances porcine epidemic diarrhea virus pathogenicity and alters the number of intestinal lymphocytes in piglets

Recent epidemiological studies have discovered that a lot of cases of porcine epidemic diarrhea virus (PEDV) infection are frequently accompanied by porcine kobuvirus (PKV) infection, suggesting a potential relationship between the two viruses in the development of diarrhea. To investigate the impact of PKV on PEDV pathogenicity and the number of intestinal lymphocytes, piglets were infected with PKV or PEDV or co-infected with both viruses. Our findings demonstrate that co-infected piglets exhibit more severe symptoms, acute gastroenteritis, and higher PEDV replication compared to those infected with PEDV alone. Notably, PKV alone does not cause significant intestinal damage but enhances PEDV's pathogenicity and alters the number of intestinal lymphocytes. These results underscore the complexity of viral interactions in swine diseases and highlight the need for comprehensive diagnostic and treatment strategies addressing co-infections.

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.

HSP70 positively regulates translation by interacting with the IRES and stabilizes the viral structural proteins VP1 and VP3 to facilitate duck hepatitis A virus type 1 replication

The maintenance of viral protein homeostasis depends on the interaction between host cell proteins and viral proteins. As a molecular chaperone, heat shock protein 70 (HSP70) has been shown to play an important role in viral infection. Our results showed that HSP70 can affect translation, replication, assembly, and release during the life cycle of duck hepatitis A virus type 1 (DHAV-1). We demonstrated that HSP70 can regulate viral translation by interacting with the DHAV-1 internal ribosome entry site (IRES). In addition, HSP70 interacts with the viral capsid proteins VP1 and VP3 and promotes their stability by inhibiting proteasomal degradation, thereby facilitating the assembly of DHAV-1 virions. This study demonstrates the specific role of HSP70 in regulating DHAV-1 replication, which are helpful for understanding the pathogenesis of DHAV-1 infection and provide additional information about the role of HSP70 in infection by different kinds of picornaviruses, as well as the interaction between picornaviruses and host cells.

Whole-transcriptome sequencing revealed the role of noncoding RNAs in susceptibility and resistance of Pekin ducks to DHAV-3

As the most prevalent pathogen of duck viral hepatitis (DVH), duck hepatitis A virus genotype 3 (DHAV-3) has caused huge economic losses to the duck industry in China. Herein, we obtained whole-transcriptome sequencing data of susceptible (S) and resistant (R) Pekin duckling samples at 0 h, 12 h, and 24 h after DHAV-3 infection. We found that DHAV-3 infection induces 5,396 differentially expressed genes (DEGs), 85 differentially expressed miRNAs (DEMs), and 727 differentially expressed lncRNAs (DELs) at 24 hpi in S vs. R ducks, those upregulated genes were enriched in inflammation and cell communications pathways and downregulated genes were related to metabolic processes. Upregulated genes showed high connectivity with the miR-33, miR-193, and miR-11591, and downregulated genes were mainly regulated by miR-2954, miR-125, and miR-146b. With the construction of lncRNA-miRNA-mRNA axis, we further identified a few aberrantly expressed lncRNAs (e.g., MSTRG.36194.1, MSTRG.50601.1, MSTRG.34328.7, and MSTRG.29445.1) that regulate expression of hub genes (e.g., THBD, CLIC2, IL8, ACOX2, GPHN, SMLR1, and HAO1) by sponging those highly connected miRNAs. Altogether, our findings defined a dual role of ncRNAs in immune and metabolic regulation during DHAV-3 infection, suggesting potential new targets for treating DHAV-3 infected ducks.

2A2 protein of DHAV-1 induces duck embryo fibroblasts gasdermin E-mediated pyroptosis

The duck hepatitis A virus type 1 (DHAV-1) causes rapid death in ducklings by triggering a severe cytokine storm. Pyroptosis is an inflammatory form of programmed cell death that is directly related to an increase in pro-inflammatory cytokine levels. Only a few studies have explored the mechanisms underlying pyroptosis in virus-infected avian cells. In this study, we established an avian infection model in vitro by infecting duck embryo fibroblasts (DEFs) with the virulent DHAV-1 LY0801 strain. DHAV-1 infection induced pyroptosis in the DEFs by activating gasdermin E (GSDME) protein via caspase-3-mediated cleavage. The genes encoding the different structural and non-structural DHAV-1 proteins were cloned into eukaryotic expression plasmids, and the 2A2 protein was identified as the key protein involved in pyroptosis. The HPLC-tandem mass spectrometry (HPLC-MS/MS) and co-immunoprecipitation (Co-IP) analysis established that DHAV-1 2A2 directly interacted with the mitochondrial anti-viral signaling protein (MAVS) both intracellularly and in vitro. Furthermore, we got the results that N-terminal 1-130 aa of 2A2 was involved in the interaction with MAVS and the C-terminal TM domain of MAVS is necessary for the interaction with 2A2 by Co-IP analysis. To our knowledge, this is the first study to reveal that DHAV-1 protein interacts with host proteins to induce pyroptosis. Our findings provide new insights into the molecular pathogenesis of DHAV-1 infection, and a scientific basis for the prevention and treatment of duck viral hepatitis.

Duck hepatitis A virus type 1 infection induces hepatic metabolite and gut microbiota changes in ducklings

Duck hepatitis A virus type 1 (DHAV-1) can cause severe liver damage in infected ducklings and is a fatal and contagious pathogen that endangers the Chinese duck industry. The objective of this study was to explore the correlation mechanism of liver metabolism-gut microbiota in DHAV-1 infection. Briefly, liquid chromatography-mass spectrometry and 16S rDNA sequencing combined with multivariate statistical analysis were used to evaluate the effects of DHAV-1 infection on liver metabolism, gut microbiota regulation, and other potential mechanisms in ducklings. In DHAV-1-infected ducklings at 72 h postinfection, changes were found in metabolites associated with key metabolic pathways such as lipid metabolism, sugar metabolism, and nucleotide metabolism, which participated in signaling networks and ultimately affecting the function of the liver. The abundance and composition of gut microbiota were also changed, and gut microbiota is significantly involved in lipid metabolism in the liver. The evident correlation between gut microbiota and liver metabolites indicates that DHAV-host gut microbiome interactions play important roles in the development of duck viral hepatitis (DVH).

Experimental Seneca Valley virus infection in sows and their offspring

Neonatal mortality has been increasingly reported on swine breeding farms experiencing swine idiopathic vesicular disease (SIVD) outbreaks, which can be accompanied by lethargy, diarrhea, and neurologic signs in neonates. Seneca Valley Virus (SVV), or Senecavirus A, has been detected in clinical samples taken from pigs with SIVD. Experimental SVV inoculation has caused vesicular disease in pigs, particularly during the stages from weaning to finishing. However, it remains crucial to investigate whether SVV directly contributes to the increase in neonatal mortality rates. The following study was conducted to chronicle the pathogenesis of SVV infection in sows and their offspring. Ten sows were intranasally inoculated with 4.75 × 107 plaque-forming units of the virus per sow either late in gestation (n = 5) or within fourteen days of farrowing (n = 5). Each sow replicated SVV following intranasal inoculation, but only one out of ten sows developed a vesicular lesion on the snout. Evidence of transplacental infection was observed in two litters, and an additional two litters became infected following parturition out of five litters from sows inoculated in late gestation. No clinical signs were observed in the infected neonates. Likewise, no clinical signs were observed in the other five litters inoculated after farrowing, although each piglet did replicate the challenge virus. In this study, the experimental challenge of SVV did not result in neonatal mortality in contrast to observations in the field; however, it has shed light on the pathogenesis of the virus, the transmission of SVV between sows and their offspring, and host immune response that can help shape control measures in the field.

A meta-analysis for vaccine protection rate of duck hepatitis a virus in mainland China in 2009-2021

BACKGROUND

Duck hepatitis A virus (DHAV) is a single-stranded, positive-strand small RNA virus that causes a very high mortality rate in ducklings. The DHAV-3 subtype incidence rate has recently increased in China, causing great economic losses to the waterfowl breeding industry. We analyzed the protection rate of DHAV vaccines used in mainland China from 2009 to 2021 and evaluated the effectiveness of vaccine prevention and control to reduce the economic losses caused by DHAV to the waterfowl breeding industry. We screened five electronic research databases and obtained 14 studies and patents on the protection efficiency of DHAV-1 and DHAV-3 vaccines.

RESULTS

Meta-analysis demonstrated that immunized ducklings produced higher antibody levels and had a significantly higher survival rate than non-immunized ducklings [relative risk (RR) = 12, 95% confidence interval (CI) 6-26, P < 0.01]. The age of the ducks and vaccine valence did not affect protection efficiency. Data source analysis of the vaccine protection rate demonstrated that the vaccines conferred immune protection for ducklings in both small-scale experiments and large-scale clinical conditions. The analysis results revealed that although the vaccines conferred protection, the immune protective effect differed between small-scale experimental conditions and large-scale clinical conditions. This might have been due to non-standard vaccination and environmental factors.

CONCLUSIONS

Domestic DHAV vaccines can protect ducklings effectively. The subjects immunized (breeding ducks or ducklings) and vaccine valence had no effect on the protective effect. Both small-scale experiments and large-scale clinical conditions conferred immune protection on ducklings, but vaccine immunization under small-scale experimental conditions had slightly better protective effects than large-scale clinical immunization.

First report of Duck Hepatitis A virus genotype 2 in India

Sudden death of ducklings was reported in a duck farm located at Tiruvallur district in Tamil Nadu, India. Disease investigation began with post mortem findings of dead birds revealing enlarged pale-pink / pale-yellow liver with multifocal petechiae and ecchymosis. A positive amplification with duck hepatitis A virus specific primers by reverse transcription-polymerase chain reaction (RT-PCR) on the tissue samples collected from dead birds indicated infection by duck hepatitis A virus (DHAV), an avian picornavirus, known to cause acute and high-mortality in ducklings. The virus isolation was successful in 9-days old embryonated chicken eggs, in primary chicken embryo fibroblast (CEF) cells and from experimentally infected ducklings. The embryonic death on day 5 to 7 post inoculation in chicken embryos with signs of cutaneous hemorrhage, edema and greenish yellow liver together with histopathology of embryonic liver and kidney further confirmed DHAV infection. TEM analysis of the infected allantoic fluid and infected CEF cell culture supernatant showed the presence of spherical shaped, non-enveloped virion particles of ~ 20-38 nm diameter, typical for DHAV. Experimental infection of ducklings with RT-PCR positive tissue supernatant caused 40% to 50% mortality with typical petechial hemorrhages on the surface of liver. Further, histopathological analysis and RT-PCR of the inoculated duckling's tissues confirmed the presence of DHAV. Nucleotide sequencing of the 5'UTR region and VP1 region confirmed duck hepatitis A virus genotype 2 (DHAV-2). To the best of our knowledge, this is the first report of laboratory confirmation of DHAV-2 in India. This study warrants the need for the extensive epidemiological surveillance to understand the prevalence of DHAV-2 in India and to take appropriate control measures to curtail the disease spread.

Placenta-specific 8 facilitates the infection of duck hepatitis A virus type 1 by inhibiting the TLR7 MyD88-dependent signaling pathway

The placenta-specific 8 (PLAC8) gene, also known as ONZIN or C15, codes for a cysteine-rich peptide originally identified in mouse placental tissue and subsequently identified in a variety of epithelial tissues and immune cells. PLAC8 is also expressed in birds, such as ducks, where its functional roles remain unknown. Here, we aimed to determine the mRNA and protein expression profiles and the functional role of duck PLAC8 during the infection of duck hepatitis A virus type 1 (DHAV-1). We found that the duck PLAC8 is also a cysteine-rich polypeptide composed of 114 amino acid residues, with no signal peptide. Duck PLAC8 is highly expressed in the immune organs of young cherry valley ducks, including the thymus, bursa fabricius, and spleen. However, it has negligible expression level in liver, brain, kidney, and heart. Additionally, PLAC8 expression was considerably induced after DHAV-1 infection both in vitro and in vivo, especially in the immune organs of ducklings. This tissue expression distribution and induction upon infection suggest that PLAC8 might play a critical role in innate immunity. Our data showed that PLAC8 significantly suppressed the expression of Toll-like receptor 7 (TLR7), leading to decreased expression of downstream signaling molecules including myeloid differentiation primary response gene 88 (MyD88) and nuclear factor kappa-B (NF-κB). This ultimately resulted in low levels of type I interferon and interleukin 6 (IL-6). Additionally, PLAC8 positively regulated DHAV-1 replication levels. RNAi against PLAC8 in duck embryo fibroblasts considerably inhibited DHAV-1 propagation, while PLAC8 overexpression significantly facilitated DHAV-1 replication.

Duck hepatitis A virus type 1 transmission by exosomes establishes a productive infection in vivo and in vitro

Duck hepatitis A virus type 1 (DHAV-1) infection causes an acute and highly fatal disease in young ducklings. Exosomes are nano-sized small extracellular vesicles secreted by various cells, which participate in intercellular communication and play a key role in the physiological and pathological processes. However, the role of exosomes in DHAV-1 transmission remains unknown. In this study, through RT-PCR, WB analysis and TEM observation, the complete DHAV-1 genomic RNA, partial viral proteins, and virions were respectively identified in the exosomes derived from DHAV-1-infected duck embryo fibroblasts (DEFs). The productive DHAV-1 infection was transmitted by exosomes in DEFs, duck embryos, and ducklings, and high titers of neutralizing antibodies completely blocked DHAV-1 infection but did not significantly neutralize exosome-mediated DHAV-1 infection. To the best of our knowledge, this is the first report that exosome-mediated DHAV-1 infection was resistant to antibody neutralization in vivo and in vitro, which might be an immune evasion mechanism of DHAV-1.

Evolutionary Origin, Genetic Recombination, and Phylogeography of Porcine Kobuvirus

The newly identified porcine Kobuvirus (PKV) has raised concerns owing to its association with diarrheal symptom in pigs worldwide. The process involving the emergence and global spread of PKV remains largely unknown. Here, the origin, genetic diversity, and geographic distribution of PKV were determined based on the available PKV sequence information. PKV might be derived from the rabbit Kobuvirus and sheep were an important intermediate host. The most recent ancestor of PKV could be traced back to 1975. Two major clades are identified, PKVa and PKVb, and recombination events increase PKV genetic diversity. Cross-species transmission of PKV might be linked to interspecies conserved amino acids at 13-17 and 25-40 residue motifs of Kobuvirus VP1 proteins. Phylogeographic analysis showed that Spain was the most likely location of PKV origin, which then spread to pig-rearing countries in Asia, Africa, and Europe. Within China, the Hubei province was identified as a primary hub of PKV, transmitting to the east, southwest, and northeast regions of the country. Taken together, our findings have important implications for understanding the evolutionary origin, genetic recombination, and geographic distribution of PKV thereby facilitating the design of preventive and containment measures to combat PKV infection.

Complete genomic sequence analysis and intestinal tissue localization of a porcine Kobuvirus variant in China

Porcine kobuvirus (PKV) infection is very common in both healthy pigs and diarrhea pigs throughout the world. However, there is no proof that it causes diarrhea, and little is known about its role in diarrhea. There are only a few reports concerning porcine kobuvirus separation at present, which makes investigating its invasion and pathogenesis mechanisms difficult. This study sequenced the entire genome of a porcine kobuvirus strain termed "Wuhan2020" after it was isolated from intestinal tissue samples of healthy piglets. The analysis results revealed that it shared the most resemblance with the WUH1 strain (89.5%) and belonged to the same evolutionary branch as the Hungarian strain S-1-SUN. The PKV was located using the in situ hybridization (ISH) approach, which revealed that it was colonized in intestinal villus epithelial cells and lymphocytes in the Peyer's patch. In general, we analyzed the genetic evolution of PKV, discovered PKV susceptible cells and determined PKV localization in the intestine of infected pigs, providing a reference for future research.

Detection and genome characterization of bovine kobuvirus (BKV) in faecal samples from diarrhoeic calves in Quebec, Canada

Kobuviruses are known to infect the gastrointestinal tract of different animal species. Since its discovery in 2003, bovine kobuvirus (BKV) has been identified in faecal samples from diarrhoeic cattle in many countries, but only recently in North America. Although its possible role as an agent of calf diarrhoea remains to be determined, evidence is mounting. Our study reports for the first time the detection of BKV in faecal samples from diarrhoeic calves raised in Quebec, Canada. BKV was more commonly identified than eight known and common enteric calf pathogens. Further sequence analysis revealed that Canada BKV strain 1,043,507 was more closely correlated with the US BKV IL35164 strain than other BKV strains with complete genome. Continued surveillance and genomic characterization are needed to monitor BKV in the cattle around the world.

Evolutionary analysis of 3 isolates of Seneca Valley virus from a single pig farm

Vesicular disease caused by Seneca Valley virus (SVV) has recently emerged throughout China and caused certain industry losses. We used immunofluorescence and western blotting to confirm that 3 new SVV strains (CH-GDSG-2018-1, CH-GDSG-2018-2, and CH-GDSG-2018-3) were from 1 pig farm. Phylogenetic analysis revealed the following: i) all 3 strains belong to USA-GBI29-2015-like clades, ii) CH-GDSG-2018-3 might have diverged from CH-GDSG-2018-1 and CH-GDSG-2018-2, and iii) CH-GDSG-2018-3 is a recombinant of the CHhb17 and HeNKF-1 strains. Virus growth curves showed that CH-GDSG-2018-3 had stronger proliferation ability in vitro. Seneca Valley virus has evolved extensively within China and this study has furthered our understanding of SVV epidemiology.

Isolation, Characterization, and Molecular Detection of Porcine Sapelovirus

Porcine sapelovirus (PSV) is an important emerging pathogen associated with a wide variety of diseases in swine, including acute diarrhoea, respiratory distress, skin lesions, severe neurological disorders, and reproductive failure. Although PSV is widespread, serological assays for field-based epidemiological studies are not yet available. Here, four PSV strains were recovered from diarrheic piglets, and electron microscopy revealed virus particles with a diameter of ~32 nm. Analysis of the entire genome sequence revealed that the genomes of PSV isolates ranged 7569–7572 nucleotides in length. Phylogenetic analysis showed that the isolated viruses were classified together with strains from China. Additionally, monoclonal antibodies for the recombinant PSV-VP1 protein were developed to specifically detect PSV infection in cells, and we demonstrated that isolated PSVs could only replicate in cells of porcine origin. Using recombinant PSV-VP1 protein as the coating antigen, we developed an indirect ELISA for the first time for the detection of PSV antibodies in serum. A total of 516 swine serum samples were tested, and PSV positive rate was 79.3%. The virus isolates, monoclonal antibodies and indirect ELISA developed would be useful for further understanding the pathophysiology of PSV, developing new diagnostic assays, and investigating the epidemiology of the PSV.

Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia

The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as "Bopivirus C". Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8-15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species.

Differential metabolism-associated gene expression of duck pancreatic cells in response to two strains of duck hepatitis A virus type 1

Several outbreaks of duck hepatitis A virus type 1 (DHAV-1), which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. The causative agent is called pancreatitis-associated DHAV-1. The mechanisms involved in pancreatitis-associated DHAV-1 infection are still unclear. Transcriptome analysis of duck pancreas infected with classical-type DHAV-1 and pancreatitis-associated DHAV-1 was carried out. Deep sequencing with Illumina-Solexa resulted in a total of 53.9 Gb of clean data from the cDNA library of the pancreas, and a total of 29,597 unigenes with an average length of 993.43 bp were generated by de novo sequence assembly. The expression levels of D-3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which are involved in glycine, serine, and threonine metabolism pathways, were significantly downregulated in ducks infected with pancreatitis-associated DHAV-1 compared with those infected with classical-type DHAV-1. These findings provide information regarding differences in expression levels of metabolism-associated genes between ducks infected with pancreatitis-associated DHAV-1 and those infected with classical-type DHAV-1, indicating that intensive metabolism disorders may contribute to the different phenotypes of DHAV-1-infection.

No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity

Hospital-based and community-based 'high-risk cohort' studies investigating humans at risk of zoonotic infection due to occupational or residential exposure to animals were conducted in Vietnam, with diverse viruses identified from faecal samples collected from humans, domestic and wild animals. In this study, we focus on the positive-sense RNA virus family Picornaviridae, investigating the prevalence, diversity, and potential for cross-species transmission. Through metagenomic sequencing, we found picornavirus contigs in 23% of samples, belonging to 15 picornavirus genera. Prevalence was highest in bats (67%) while diversity was highest in rats (nine genera). In addition, 22% of the contigs were derived from novel viruses: Twelve phylogenetically distinct clusters were observed in rats of which seven belong to novel species or types in the genera Hunnivirus, Parechovirus, Cardiovirus, Mosavirus and Mupivirus; four distinct clusters were found in bats, belonging to one novel parechovirus species and one related to an unclassified picornavirus. There was no evidence for zoonotic transmission in our data. Our study provides an improved knowledge of the diversity and prevalence of picornaviruses, including a variety of novel picornaviruses in rats and bats. We highlight the importance of monitoring the human-animal interface for possible spill-over events.

Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary

In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5'UTR^IRES-?/P1(VP0-VP3-VP1)/P2(2A₁^NPG↓P-2A₂^H-box/NC-2B-2C)/P3(3A-3B^VPg-3C^Pro-3D^Pol)/3'UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.

Emergence of a novel recombinant USA/GBI29/2015-like strain of Seneca Valley virus in Guangdong Province, 2018

Since June 2017, several outbreaks of a Seneca Valley virus (SVV) USA/GBI29/2015-like strain have emerged in pigs in China. In our study, we successfully isolated the SVV strain CH-GDZQ-2018, confirmed by immunofluorescence and Western blot assays. Phylogenetic and recombinant analyses showed that the USA/GBI29/2015-like CH-GDZQ-2018 strain was the result of recombination between epidemic strains local to Guangdong, showing that SVV has undergone evolution in China.

Bovine kobuvirus-A comprehensive review

Bovine kobuvirus (BKV) is a single-stranded, positive sense, non-enveloped RNA virus in genus Kobuvirus of family Picornavirus. BKV was first identified in the culture media of HeLa cell containing calf serum in 2003. Since then, BKV has been detected in 13 countries of four different continents, suggesting widespread in the world. Herein, we review the detection and genomic characterization of BKV in 13 countries. All studies tested bovine faecal samples for BKV. These studies provide evidence that BKV might be a causative agent for neonatal calf diarrhoea. Therefore, further efforts including animal challenge study are urgently needed to unveil the pathogenicity of BKV.

Whole genome analysis of Aichivirus A, isolated from a child, suffering from gastroenteritis, in Pakistan

Viruses are the primary cause of acute gastroenteritis in children all over the world. Understanding the emergence and genetic variation of these viruses may help to prevent infections. Aichivirus (AiV) is a member of the Kobuvirus genus, which currently contains six officially recognized species: Aichivirus A-F. The species AiV A contains six types including Aichivirus 1 (AiV 1) and eventually, three genotypes have been identified in the human AiV 1 (named A to C). The present study describes the identification and sequencing of the polyprotein gene of a human AiV 1 strain PAK419 via NGS in Pakistani children with acute gastroenteritis. Our study strain PAK419 was classified as AiV 1 genotype A, most commonly found in Japan and Europe, and closely related to non-Japanese and European strains on the phylogenetic tree. PAK419 showed 95-98 % nucleotide sequence identity with strains isolated from Ethiopia (ETH/2016/P4), Australia (FSS693) and China (Chshc7). On phylogenetic observation PAK419 formed a distinct cluster in the AiV 1 genotype A with the above mentioned and other human AiV strains detected around the world (Germany, Brazil, Japan, Thailand, Korea and Vietnam). The data clearly showed that Pakistani AiV strains and human strains identified from all over the world are distinct from Aichivirus strains found in bovine, swine, canine, feline, caprine, ferret, bat, and environmental samples. The distinguishing characteristics of the AiV genome showed a lower probability of inter-genotypic recombination events, which may support the lack of AiV serotypes. PAK419 also had a high content of C nucleotide (37.4 %), as found in previous studies, which could also restrict the possible genetic variation of AiV. This study demonstrate the power of NGS in uncovering unknown gastroenteric etiological agents circulating in the population.

Characterization of a novel picornavirus isolated from moribund aquacultured clownfish

Over the last decade, a number of USA aquaculture facilities have experienced periodic mortality events of unknown aetiology in their clownfish (Amphiprion ocellaris). Clinical signs of affected individuals included lethargy, altered body coloration, reduced body condition, tachypnea, and abnormal positioning in the water column. Samples from outbreaks were processed for routine parasitological, bacteriological, and virological diagnostic testing, but no consistent parasitic or bacterial infections were observed. Histopathological evaluation revealed individual cell necrosis and mononuclear cell inflammation in the branchial cavity, pharynx, oesophagus and/or stomach of four examined clownfish, and large basophilic inclusions within the pharyngeal mucosal epithelium of one fish. Homogenates from pooled external and internal tissues from these outbreaks were inoculated onto striped snakehead (SSN-1) cells for virus isolation and cytopathic effects were observed, resulting in monolayer lysis in the initial inoculation and upon repassage. Transmission electron microscopy of infected SSN-1 cells revealed small round particles (mean diameter=20.0-21.7 nm) within the cytoplasm, consistent with the ultrastructure of a picornavirus. Full-genome sequencing of the purified virus revealed a novel picornavirus most closely related to the bluegill picornavirus and other members of the genus Limnipivirus. Additionally, pairwise protein alignments between the clownfish picornavirus (CFPV) and other known members of the genus Limnipivirus yielded results in accordance with the current International Committee on Taxonomy of Viruses criteria for members of the same genus. Thus, CFPV represents a proposed new limnipivirus species. Future experimental challenge studies are needed to determine the role of CFPV in disease.

Discovery of Lanama Virus, a Distinct Member of Species Kunsagivirus C (Picornavirales: Picornaviridae), in Wild Vervet Monkeys (Chlorocebus pygerythrus)

We report the discovery and sequence-based molecular characterization of a novel virus, lanama virus (LNMV), in blood samples obtained from two wild vervet monkeys (Chlorocebus pygerythrus), sampled near Lake Nabugabo, Masaka District, Uganda. Sequencing of the complete viral genomes and subsequent phylogenetic analysis identified LNMV as a distinct member of species Kunsagivirus C, in the undercharacterized picornavirid genus Kunsagivirus.

Comparison of historical and contemporary isolates of Senecavirus A

Senecavirus A (SVA) was discovered as a cell culture contaminant in 2002, and multiple attempts to experimentally reproduce disease were unsuccessful. Field reports of porcine idiopathic vesicular disease (PIVD) cases testing PCR positive for SVA in addition to outbreaks of PIVD in Brazil and the United States in 2015 suggested SVA was a causative agent, which has now been consistently demonstrated experimentally. Ease of experimental reproduction of disease with contemporary strains of SVA raised questions concerning the difficulty of reproducing vesicular disease with historical isolates. The following study was conducted to compare the pathogenicity of SVA between historical and contemporary isolates in growing pigs. Six groups of pigs (n = 8) were intranasally inoculated with the following SVA isolates: SVV001/2002, CAN/2011, HI/2012, IA/2015, NC/2015, SD/2015. All isolates induced vesicular disease in at least half of the inoculated pigs from each group. All pigs replicated virus as demonstrated by serum and/or swab samples positive for SVA by quantitative PCR. Pig sera tested by virus neutralization assay demonstrated cross-neutralizing antibodies against all viruses utilized in the study. Cross-neutralizing antibodies from pigs inoculated with historical isolates were lower than those pigs that were inoculated with contemporary isolates. Phylogenetic analysis revealed two clades with SVV001/2002 being in a separate clade compared to the other five isolates. Although differences in the infection kinetics and sequences of these six isolates were found, clinical presentation of vesicular disease was similar between both historical and contemporary isolates.

Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model

Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases.

The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales

Novel posa-like viral genomes were first identified in swine fecal samples using metagenomics and were designated as unclassified viruses in the order Picornavirales. In the present study, nine husavirus strains were identified in China. Their genomes share 94.1–99.9% similarity, and alignment of these nine husavirus strains identified 697 nucleotide polymorphism sites across their full-length genomes. These nine strains were directly clustered with the Husavirus 1 lineage, and their genomic arrangement showed similar characteristics. These posa-like viruses have undergone a complex evolutionary process, and have a wide geographic distribution, complex host spectrum, deep phylogenetic divergence, and diverse genomic organizations. The clade of posa-like viruses forms a single group, which is evolutionarily distinct from other known families and could represent a distinct family within the Picornavirales. The genomic arrangement of Picornavirales and the new posa-like viruses are different, whereas the posa-like viruses have genomic modules similar to the families Dicistroviridae and Marnaviridae. The present study provides valuable genetic evidence of husaviruses in China, and clarifies the phylogenetic dynamics and the evolutionary characteristics of Picornavirales.

Proteome Analysis Reveals Syndecan 1 Regulates Porcine Sapelovirus Replication

Porcine sapelovirus A (PSV) is a single stranded, positive-sense, non-enveloped RNA virus that causes enteritis, pneumonia, polioencephalomyelitis, and reproductive disorders in pigs. Research on PSV infection and interaction with host cells is unclear. In this study, we applied tandem mass tag proteomics analysis to investigate the differentially expressed proteins (DEPs) in PSV-infected pig kidney (PK)-15 cells and explored the interactions between PSV and host cells. Here we mapped 181 DEPs, including 59 up-regulated and 122 down-regulated DEPs. Among them, osteopontin (SPP1), induced protein with tetratricopeptide repeats 5 (IFIT5), ISG15 ubiquitin-like modifier (ISG15), vinculin (VCL), and syndecan-1 (SDC1) were verified significantly changed using RT-qPCR. Additionally, overexpression of SDC1 promoted PSV viral protein (VP)1 synthesis and virus titer, and silencing of SDC1 revealed the opposite results. Our findings show that SDC1 is a novel host protein and plays crucial roles in regulating PSV replication.

Identification and genome characterization of a novel picornavirus from ducks in China

A novel picornavirus, referred to as Duck/FC22/China/2017, was isolated from breeding ducks in China and genetically characterized by conducting metagenomics studies. The complete genome consists of a single-stranded, positive-sense RNA made up of 7448 nucleotides (nt) and follows the common picornavirus genome layout: 5' UTR-VP0-VP3-VP1-2A-2B-2C-3A-3B-3C-3D-3' UTR. A typical type-IV internal ribosomal entry site and a conserved 'barbell-like' structure were identified in the 5' UTR and 3' UTR, respectively. The unique 6423-nt open reading frame was predicted to encode a 2141-amino-acid (aa) polyprotein precursor. A pairwise aa sequence identity comparison and phylogenetic analysis revealed that Duck/FC22/China/2017 is closely related to duck aalivirus, duck hepatitis A virus, turkey avisivirus, and red-crowned crane picornavirus.

Emerging Infectious Diseases of Rabbits

Recently, multiple infectious organisms have been identified as the cause of emerging diseases in lagomorphs. The most important of these emerging diseases is rabbit hemorrhagic disease virus (RHDV) type 2, a new variant with differences in pathogenicity to classical RHDV. Hepatitis E is considered an emerging zoonotic infectious disease, with widespread prevalence in many different rabbit populations. Mycobacteriosis has been recently reported in other captive domestic rabbit populations. This article provides a recent review of the published literature on emerging infectious diseases in rabbits, including farmed, laboratory, and pet rabbits, some of which have zoonotic potential.

Emergence and phylogenetic analysis of a novel Seneca Valley virus strain in the Guangxi Province of China

Senecavirus A (SVA), also known as Seneca Valley virus (SVV), is an emerging infectious pathogen which have been detected in swine herds from the Brazil, USA, Colombia, Thailand, Canada and some provinces in China, suggesting an increasing geographic distribution of this novel virus. Here, we isolated and characterized a SVV, designated SVA CH-GX-01-2018, thought to be responsible for typical vesicular lesions on the snouts and hooves of finishing pigs from a swine herds in Guangxi province, China, in August 2018. Phylogenetic analysis and sequence alignment indicated that this SVA CH-GX-01-2018 strain was closely related to the strains isolated in 2017 in Guangdong province, a neighboring province of Guangxi, South China, with 98.6% identity at the genome nucleotide level. Our findings characterized a novel SVV infection in pigs from South China and emphasize the importance of surveillance, reinforcing biosecurity measures and developing vaccines to prevent the spread of this viral pathogen.

Genetic and Biological Diversity of Porcine Sapeloviruses Prevailing in Zambia

Porcine sapelovirus (PSV) has been detected worldwide in pig populations. Although PSV causes various symptoms such as encephalomyelitis, diarrhea, and pneumonia in pigs, the economic impact of PSV infection remains to be determined. However, information on the distribution and genetic diversity of PSV is quite limited, particularly in Africa. In this study, we investigated the prevalence of PSV infection in Zambia and characterized the isolated PSVs genetically and biologically. We screened 147 fecal samples collected in 2018 and found that the prevalences of PSV infection in suckling pigs and fattening pigs were high (36.2% and 94.0%, respectively). Phylogenetic analyses revealed that the Zambian PSVs were divided into three different lineages (Lineages 1–3) in the clade consisting of Chinese strains. The Zambian PSVs belonging to Lineages 2 and 3 replicated more efficiently than those belonging to Lineage 1 in Vero E6 and BHK cells. Bioinformatic analyses revealed that genetic recombination events had occurred and the recombination breakpoints were located in the L and 2A genes. Our results indicated that at least two biologically distinct PSVs could be circulating in the Zambian pig population and that genetic recombination played a role in the evolution of PSVs.

Bovine Kobuvirus in Calves with Diarrhea, United States

We detected bovine kobuvirus (BKV) in calves with diarrhea in the United States. The strain identified is related genetically to BKVs detected in other countries. Histopathologic findings also confirmed viral infection in 2 BKV cases. Our data show BKV is a potential causative agent for diarrhea in calves.

Bovine Astrovirus Surveillance in Uruguay Reveals High Detection Rate of a Novel Mamastrovirus Species

Viral infections affecting cattle lead to economic losses to the livestock industry worldwide, but little is known about the circulation, pathogenicity and genetic diversity of enteric bovine astrovirus (BoAstV) in America. The aim of this work was to describe the prevalence and genetic diversity of enteric BoAstV in dairy cattle in Uruguay. A total of 457 fecal and 43 intestinal contents from dairy calves were collected between July 2015 and May 2017 and tested by RT-PCR, followed by sequencing and phylogenetic analyses of the polymerase and capsid regions. Twenty-six percent (128/500) of the samples were positive. Three different species within the Mamastrovirus genus were identified, including Mamastrovirus 28, Mamastrovirus 33 (3 samples each) and an unclassified Mamastrovirus species (19 samples). The unclassified species was characterized as a novel Mamastrovirus species. BoAstV circulates in Uruguayan dairy cattle with a high genetic diversity. The eventual clinicopathological significance of enteric BoAstV infection in cattle needs further investigation.

Novel Picornavirus in Lambs with Severe Encephalomyelitis

Using metagenomic analysis, we identified a novel picornavirus in young preweaned lambs with neurologic signs associated with severe nonsuppurative encephalitis and sensory ganglionitis in 2016 and 2017 in the United Kingdom. In situ hybridization demonstrated intralesional neuronotropism of this virus, which was also detected in archived samples of similarly affected lambs (1998–2014).

Genetic diversity and evolution of the emerging picornavirus Senecavirus A

Senecavirus A (SVA) is an emerging picornavirus that causes vesicular disease (VD) in swine. The virus has been circulating in swine in the United Stated (USA) since at least 1988, however, since 2014 a marked increase in the number of SVA outbreaks has been observed in swine worldwide. The factors that led to the emergence of SVA remain unknown. Evolutionary changes that accumulated in the SVA genome over the years may have contributed to the recent increase in disease incidence. Here we compared full-genome sequences of historical SVA strains (identified before 2010) from the USA and global contemporary SVA strains (identified after 2011). The results from the genetic analysis revealed 6.32 % genetic divergence between historical and contemporary SVA isolates. Selection pressure analysis revealed that the SVA polyprotein is undergoing selection, with four amino acid (aa) residues located in the VP1 (aa 735), 2A (aa 941), 3C (aa 1547) and 3D (aa 1850) coding regions being under positive/diversifying selection. Several aa substitutions were observed in the structural proteins (VP1, VP2 and VP3) of contemporary SVA isolates when compared to historical SVA strains. Some of these aa substitutions led to changes in the surface electrostatic potential of the structural proteins. This work provides important insights into the molecular evolution and epidemiology of SVA.

Molecular-based investigation and genetic characterization of porcine stool-associated RNA virus (posavirus) lineages 1 to 3 in pigs in South Korea from 2017 to 2019

Recent results on the detection and genetic characterization of stool-associated RNA viruses from different species have increased the knowledge about the extreme genetic diversity of picornaviruses. This study aimed to investigate the presence of unclassified porcine stool-associated RNA viruses (posaviruses) in South Korea and to elucidate the molecular evolution of the viruses. By RT-PCR, posaviruses 1 and 3 were exclusively found in fecal samples and consistently detected in three consecutive years in six of eight provinces, with 148/697 (21.2%) and 33/84 (39.3%) positive samples and farms, respectively. Every age group but the older age groups (finisher, sow) had significantly higher positive rates of posavirus 1 than posavirus 3. An analysis of the RNA-dependent RNA polymerase sequences by likelihood mapping and maximum-likelihood-based phylogenetic analysis revealed that stool-associated RNA viruses formed four supergroups that were well separated from all recognized families of the order Picornavirales. Five genomes of Korean posaviruses generated in this study were phylogenetically grouped with posavirus 1 and posavirus 3 and were predicted to have the typical genome organization of picornaviruses.

Equine Rhinitis A Virus Infection in Thoroughbred Racehorses-A Putative Role in Poor Performance?

The aim of this study was to identify respiratory viruses circulating amongst elite racehorses in a training yard by serological testing of serial samples and to determine their impact on health status and ability to race. A six-month longitudinal study was conducted in 30 Thoroughbred racehorses (21 two-year-olds, five three-year-olds and four four-year-olds) during the Flat racing season. Sera were tested for the presence of antibodies against equine herpesvirus 1 and 4 (EHV-1 and EHV-4) and equine rhinitis viruses A and B (ERAV and ERBV) by complement fixation (CF) and equine arteritis virus (EAV) by ELISA. Antibodies against equine influenza (EI) were measured by haemagglutination inhibition (HI). Only ERAV was circulating in the yard throughout the six-month study period. Seroconversion to ERAV frequently correlated with clinical respiratory disease and was significantly associated with subsequent failure to race (p = 0.0009). Over 55% of the two-year-olds in the study seroconverted to ERAV in May and June. In contrast, only one seroconversion to ERAV was observed in the older horses. They remained free of any signs of respiratory disease and raced successfully throughout the study period. The importance of ERAV as a contributory factor in the interruption of training programmes for young horses may be underestimated.

Vesicular disease in pigs inoculated with a recent Canadian isolate of Senecavirus A

The objective of this study was to investigate whether a virulent Canadian isolate of Senecavirus A (SVA) causes idiopathic vesicular disease (IVD) in pigs. Senecavirus A, which was first isolated in the United States in 2002 as Seneca Valley Virus, was linked to cases of porcine idiopathic vesicular disease in Canada in 2007 and in the United States in 2010. Since 2014, SVA outbreaks in Brazil, the US, Canada, China, Thailand, and Colombia point to an expanding global distribution and the need to study the pathogenicity of the virus. Unlike the prototype virus, recent US isolates of SVA have been shown to cause vesicular disease in pigs. We report vesicular disease in pigs following experimental inoculation with a 2016 Canadian isolate of SVA. All inoculated pigs developed vesicular lesions regardless of route of inoculation. Virus was detected in blood and oral fluids as well as on oral and fecal swabs. In addition, all pigs seroconverted to SVA by 6 days post-inoculation (DPI). This study confirms that recent Canadian isolates of SVA cause vesicular disease in pigs and highlights the importance of monitoring SVA for increased virulence.

Bluegill Picornavirus isolated from a mortality event involving Bluegill (Lepomis macrochirus) in the upper Mississippi River

A mortality event involving an estimated 1,000 adult bluegills (Lepomis macrochirus) was observed in an ice-covered backwater lake of the upper Mississippi River near Alma, Wisconsin, in December of 2017. Macroscopic signs of disease included abdominal distension due to fluid accumulation within the internal organs as well as external and internal haemorrhaging. Histological evaluation revealed chronic peritonitis with peritoneal adhesions in all fish examined. Kidney, spleen and ascites fluid samples were collected from diseased bluegills and examined for the presence of pathogens. Bluegill picornavirus (BGPV) was isolated using tissue cell culture methods utilizing a recently developed, uncharacterized bluegill fry cell line (BF-4), and the presence of this virus was confirmed through molecular identification. The current geographic range, known susceptible hosts as well as historical epizootics associated with BPGV is discussed. The ability of BGPV to cause significant mortality in wild fish further emphasizes the importance of monitoring both wild and hatchery populations for this pathogen.

Pathogenicity of two Chinese Seneca Valley virus (SVV) strains in pigs

Seneca Valley virus (SVV) has been identified as the causative agent of SVV-associated vesicular disease (SAVD). To investigate the pathogenicity of two newly isolated SVV strains (GD-S5/2018 and GD04/2017) in China, experimental infections of pigs were performed. In pig experiments, both SVV strains successfully infected all animals, evidenced by presence of virus shedding and robust protective antibody responses. SVV GD-S5/2018 infection resulted in characteristic clinical signs, and ulcerative lesions on the tongue and gums. However, SVV GD04/2017 did not cause any clinical symptoms except depression in pigs during the experiment. Taken together, these results demonstrate that SVV GD-S5/2018 is a virulent strain for pigs, whereas SVV GD04/2017 is nearly avirulent. The established animal models for SVV infection will be utilized to dissect the immunity and pathogenesis, and develop vaccines and antivirals.

Improved one-tube RT-PCR method for simultaneous detection and genotyping of duck hepatitis A virus subtypes 1 and 3

Background

The cocirculation of duck hepatitis A virus subtypes 1 (DHAV-1) and 3 (DHAV-3) in ducklings has resulted in significant economic losses. Ducklings with DHAV-1 or DHAV-3 infection show similar clinical signs and gross lesions; hence, it is important to identify the viral subtypes in infected ducklings as early as possible for better clinical management.

Methods and results

Based on multiple 5’ noncoding region (5’-NCR) sequences of DHAV-1 and DHAV-3 strain alignments, universal and type-specific primers were designed and synthesized. With three primers in one-tube reverse transcription-PCR (RT-PCR), reference DHAV-1 and DHAV-3 isolates ranging over 60 years and across many different countries were successfully amplified, indicating that the primer sequences were completely conserved. The sequence results and the sizes of amplicons from reference DHAV-1 and DHAV-3 isolates are completely correlated with their subtypes. Moreover, with this one-tube RT-PCR system, amplicon sizes from liver samples of reference DHAV-1- or DHAV-3-infected birds fit closely with their subtypes, which was determined by virus isolation and neutralization testing. No other duck-origin RNA viruses were detected. The sensitivity of viral RNA detection was 10 pg. With this system, 20% subtype 1, 45% subtype 3, and 9% coinfection of two subtypes were detected in 55 clinical samples.

Conclusions and significance

This novel approach could be used for rapidly typing DHAV-1 or DHAV-3 infection in routine clinical surveillance or epidemiological screening.

Molecular detection and genomic characteristics of bovine kobuvirus from dairy calves in China

In this study, 96 diarrheic and 77 non-diarrheic fecal samples from dairy calves were collected from 14 dairy farms in 4 provinces to investigate the molecular prevalence and genomic characteristics of Bovine Kobuvirus (BKoV) in China. The results showed that the BKoV positive rate for the diarrheic feces (35.42%) was significantly higher than that for the non-diarrheic feces (11.69%, p < 0.001). Interestingly, three potential novel VP1 lineages were identified from 15 complete VP1 sequences, and a unique triple nucleotide insertion which can result in an aa insertion, was first observed in the 11/12 VP0 fragments with 660 bp long in this study, compared with known BKoV VP0 sequences. Moreover, the first Chinese BKoV genome was successfully obtained from a diarrheic fecal sample, named CHZ/CHINA. The open reading frame (ORF) of the genome from strain CHZ/China shares 87.4%–88.3% nucleotide (nt) and 93.7%–96.4% amino acid (aa) identity, compared with the three known genomes of BKoV. Interestingly, phylogenetic tree based on aa sequences of these genomes showed that CHZ/CHINA was clustered into an independent branch, suggesting the strain may represent a novel BKoV strain. The findings contribute to better understanding the molecular characteristics and evolution of BKoV.

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Three potential novel VP1 lineages in BKoV.

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A unique VP0 sequence type in BKoV.

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The first BKoV genome from China which may represent a novel BKoV strain.

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Contributing to better understanding the molecular characteristics of BKoV.

The role of Virus "X" (Tortoise Picornavirus) in kidney disease and shell weakness syndrome in European tortoise species determined by experimental infection

Tortoise Picornavirus (ToPV) commonly known as Virus "X" was recently discovered in juvenile European tortoises suffering from soft carapace and plastron as well as kidney disease. Therefore, this virus was a potential candidate to be a causative agent for these disease patterns. Spur thighed tortoises (Testudo graeca) seemed to be more susceptible to establish clinical symptoms than other European species like T. hermanni. Thus this trial investigated the role of ToPV in the described syndrome. Two groups of juvenile European tortoises (T. graeca and T.hermanni) each of 10 animals, were cloacally, oronasally and intracoelomically inoculated with an infectious dose (~ 2000 TICD) of a ToPV strain isolated from a diseased T. graeca. A control group of two animals of each species received non-infected cell culture supernatant. The tortoises were examined daily and pharyngeal and cloacal swabs for detection of ToPV-RNA by RT-PCR were taken from each animal every six days for a period of 6 months. At the end of the study the remaining animals were euthanised and dissected. Bacteriological and parasitological tests were performed and organ samples of all tortoises were investigated by RT-PCR for the presence of ToPV and histopathology. Animals that were euthanised at the end of the experiment, were examined for presence of specific anti-ToPV antibodies. Several animals in both inoculated groups showed retarded growth and a light shell weakness, in comparison to the control animals. Three animals were euthanised during the trial, showing reduced weight gain, retarded growth, severe shell weakness and apathy, in parallel to clinical observations in naturally infected animals. In all inoculated animals of both species an intermittent virus shedding, starting from 18 days post inoculation (d.p.i.), till 164 d.p.i. was detected, while the control animals remained negative. The virus was successfully reisolated in terrapene heart cell culture in 16 of 20 inoculated animals of both species. Histopathology of most inoculated animals revealed a lack of bone remodeling and vacuolisation in kidney tubuli which supports the described pathogenesis of nephropathy and osteodystrophy. Anti- ToPV antibody titres ranged from 1:2 to >1:256 in 13 of 20 animals, whereas all control animals were seronegative. The study proofed the Henle Koch`s postulates of ToPV as causative agent for shell dystrophy and kidney disease in both testudo species. The proposed species specific sensitivity towards clinical disease was not observed.

Molecular evolution and characterization of novel Seneca Valley virus (SVV) strains in South China

Seneca Valley virus (SVV) is an emerging swine virus associated with porcine vesicular disease. From June to the end of 2017, five SVV strains were isolated from the swine herds in Guangdong, China. Complete genomic sequences of these newly discovered SVV strains were analyzed by genomic and phylogenetic analysis. The results revealed that these SVV strains could be grouped into five genetic branches together with most of other Chinese strains. Interestingly, it is for the first time that a stretch of 11-nucleotide insertion was found in the 5' UTR region of SVV GD04/2017 strain. Additionally, phylogenetic analysis based on the ORF and VP1 genes showed that the SVV GD06/2017 strain is significantly distinct from all previous Chinese SVV strains. Furthermore, the five SVV strains displayed similar growth kinetics in the ST-R cell line, while the SVV GD04/2017 and GD06/2017 strains presented relatively slower rates than the GD01/2017 and GD03/2017 strains. The findings of this study indicate the emergence of novel SVV strains in China, which would increase the knowledge about SVV genetic diversity and reinforce the importance of SVV surveillance.

Lethal Respiratory Disease Associated with Human Rhinovirus C in Wild Chimpanzees, Uganda, 2013

We describe a lethal respiratory outbreak among wild chimpanzees in Uganda in 2013 for which molecular and epidemiologic analyses implicate human rhinovirus C as the cause. Postmortem samples from an infant chimpanzee yielded near-complete genome sequences throughout the respiratory tract; other pathogens were absent. Epidemiologic modeling estimated the basic reproductive number (R₀) for the epidemic as 1.83, consistent with the common cold in humans. Genotyping of 41 chimpanzees and examination of 24 published chimpanzee genomes from subspecies across Africa showed universal homozygosity for the cadherin-related family member 3 CDHR3-Y₅₂₉ allele, which increases risk for rhinovirus C infection and asthma in human children. These results indicate that chimpanzees exhibit a species-wide genetic susceptibility to rhinovirus C and that this virus, heretofore considered a uniquely human pathogen, can cross primate species barriers and threatens wild apes. We advocate engineering interventions and prevention strategies for rhinovirus infections for both humans and wild apes.

The development of two field-ready reverse transcription loop-mediated isothermal amplification assays for the rapid detection of Seneca Valley virus 1

Seneca Valley virus 1 (SVV-1) has been associated with vesicular disease in swine, with clinical signs indistinguishable from those of other notifiable vesicular diseases such as foot-and-mouth disease. Rapid and accurate detection of SVV-1 is central to confirm the disease causing agent, and to initiate the implementation of control processes. The development of rapid, cost-effective diagnostic assays that can be used at the point of sample collection has been identified as a gap in preparedness for the control of SVV-1. This study describes the development and bench validation of two reverse transcription loop-mediated amplification (RT-LAMP) assays targeting the 5'-untranslated region (5'-UTR) and the VP3-1 region for the detection of SVV-1 that may be performed at the point of sample collection. Both assays were able to demonstrate amplification of all neat samples diluted 1/100 in negative pig epithelium tissue suspension within 8 min, when RNA was extracted prior to the RT-LAMP assay, and no amplification was observed for the other viruses tested. Simple sample preparation methods using lyophilized reagents were investigated, to negate the requirement for RNA extraction. Only a small delay in the time to amplification was observed for these lyophilized reagents, with a time from sample receipt to amplification achieved within 12 min. Although diagnostic validation is recommended, these RT-LAMP assays are highly sensitive and specific, with the potential to be a useful tool in the rapid diagnosis of SVV-1 in the field.

Asian black bear (Ursus thibetanus) picornavirus related to seal aquamavirus A

The complete genome of a bear picornavirus 1 (BePV-1) in the viscera of an Asian black bear (Ursus thibetanus) from China was characterized using viral metagenomics and RT-PCR/Sanger sequencing. The genome of BePV1 is 6703 nt long, contains a type-IV IRES 5'UTR with the '8-like' motif, encodes a 2053-aa-long polyprotein showing a 3-4-4 organization pattern and two 2A genes. BePV-1 showed the highest overall genome nucleotide sequence identity of 71.7% to a picornavirus genome from an Arctic ringed seal (Phoca hispida) from Canada, classified as a member of the species Aquamavirus A, currently the only one in the genus Aquamavirus. Phylogenetic and genetic distance analyses of P1 and 3D indicated that Asian bear picornavirus (aquamavirus B) represents the second sequenced member of the genus Aquamavirus.

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet's microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (106.42-107.01 copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.