Sequential Variational Autoencoder with Adversarial Classifier for Video Disentanglement.

In this paper, we propose a sequential variational autoencoder for video disentanglement, which is a representation learning method that can be used to separately extract static and dynamic features from videos. Building sequential variational autoencoders with a two-stream architecture induces inductive bias for video disentanglement. However, our preliminary experiment demonstrated that the two-stream architecture is insufficient for video disentanglement because static features frequently contain dynamic features. Additionally, we found that dynamic features are not discriminative in the latent space. To address these problems, we introduced an adversarial classifier using supervised learning into the two-stream architecture. The strong inductive bias through supervision separates dynamic features from static features and yields discriminative representations of the dynamic features. Through a comparison with other sequential variational autoencoders, we qualitatively and quantitatively demonstrate the effectiveness of the proposed method on the Sprites and MUG datasets.

Involvement of Felis catus papillomavirus type 2 in the tumorigenesis of feline Merkel cell carcinoma.

Merkel cell carcinoma (MCC) is a cutaneous neuroendocrine tumor. We recently demonstrated that cats with MCC often have other proliferative cutaneous lesions, such as squamous cell carcinoma (SCC) and basal cell carcinoma (BCC). Based on this finding, we hypothesize that Felis catus papillomavirus (FcaPV) is involved in the development of MCC in cats, similar to SCC and BCC. To investigate this hypothesis, the presence of FcaPV nucleic acid and immunoreactivity for tumor suppressor proteins were examined in 21 feline MCC cases. Polymerase chain reaction using FcaPV type-specific primers detected FcaPV2 DNA in 20/21 samples of MCC. The complete FcaPV2 sequence was characterized in one case. In situ hybridization for FcaPV2 E7 revealed punctate nuclear signals within tumor cells in 19/21 MCC. Increased immunoreactivity for p16CDKN2A protein and decreased immunoreactivity for retinoblastoma (pRb) and p53 proteins were observed in 20/21 MCC. These results suggest that feline MCC cases are infected with FcaPV2 and the subsequent inhibition of pRb and p53 induced by integrated viral oncogenes is associated with feline MCC tumorigenesis, similar to other PV-induced proliferative cutaneous lesions. On the other hand, the single case of FcaPV2-negative MCC showed strong p53 immunoreactivity, suggesting mutations in p53 caused by cancer inducers other than FcaPV2 infection in this case. The present study suggests FcaPV2 as a cause of feline MCC.

Full-genome characterization of a novel Felis catus papillomavirus 4 subtype identified in a cutaneous squamous cell carcinoma of a domestic cat.

The present study describes two full-genome sequences of Felis catus papillomavirus type 4 (FcaPV4) identified in squamous cell carcinoma (SCC) of two domestic cats. Two full-genome sequences of FcaPV4 were detected and characterized by PCR and sequencing. The L1 nucleotide sequence homology of one case showed 95.70% sequence identity to the reference FcaPV4, suggesting that this isolate should be classified as a subtype. Reverse-transcriptase PCR (RT-PCR) of two oncogenes, E6 and E7 was performed to confirm mRNA expression. Expression of E6 and E7 mRNA was detected in both cases, suggesting that FcaPV4 contributes to the development of SCC. This is the first report of FcaPV4 subtype. The present study will update the genomic features of FcaPV4 and contribute to deepening our knowledge about the etiological roles of FcaPV4 in feline cutaneous SCC.

Genomic characterization of a novel bovine papillomavirus type 28.

Infection of bovine papillomavirus (BPV) has been associated with mucosal and/or cutaneous tumor development in bovids. To date, up to 27 genotypes of BPVs have been identified and classified based on the nucleotide sequence identity of L1 open reading frame. In the present study, the complete sequence of a novel BPV concurrently identified with BPV1 and BPV2 in the facial cutaneous papilloma lesion of a domestic cattle was characterized. The whole genome of the unclassified BPV was 7263 base pairs in full length with GC ratio of 42.9%. In comparison with published BPV sequences, L1 nucleotide sequence of the novel BPV shared 75% identity with BPV15, and was suggested to be classified in the genus, Xipapillomavirus. According to the criteria established by the International Committee on the Taxonomy of Viruses, the novel BPV was designated as BPV type 28.

Coinfection of a lingual lesion with bovine papular stomatitis virus and bovine papillomavirus.

To date, there have been no reports of coinfection with bovine papular stomatitis virus (BPSV) and bovine papillomavirus (BPV) in the same lesion. In the present study, one lingual papilloma-like sample was collected at an abattoir from the tongue of a 31-month-old Japanese black cow. Coinfection with BPSV and BPV was confirmed by histopathology, immunohistochemistry, PCR and RT-PCR. The evidence for coinfection with BPSV and BPV in the same lesion and an association of BPV with lingual papillomatosis will contribute to future epidemiological studies of these two viruses.

ICTV Virus Taxonomy Profile: Papillomaviridae.

The Papillomaviridae is a family of small, non-enveloped viruses with double-stranded DNA genomes of 5 748 to 8 607 bp. Their classification is based on pairwise nucleotide sequence identity across the L1 open reading frame. Members of the Papillomaviridae primarily infect mucosal and keratinised epithelia, and have been isolated from fish, reptiles, birds and mammals. Despite a long co-evolutionary history with their hosts, some papillomaviruses are pathogens of their natural host species. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Papillomaviridae, which is available at http://www.ictv.global/report/papillomaviridae.

Generation of a Recombinant Akabane Virus Expressing Enhanced Green Fluorescent Protein.

UNLABELLED: We generated a recombinant Akabane virus (AKAV) expressing enhanced green fluorescence protein (eGFP-AKAV) by using reverse genetics. We artificially constructed an ambisense AKAV S genome encoding N/NSs on the negative-sense strand, and eGFP on the positive-sense strand with an intergenic region (IGR) derived from the Rift Valley fever virus (RVFV) S genome. The recombinant virus exhibited eGFP fluorescence and had a cytopathic effect in cell cultures, even after several passages. These results indicate that the gene encoding eGFP in the ambisense RNA could be stably maintained. Transcription of N/NSs and eGFP mRNAs of eGFP-AKAV was terminated within the IGR. The mechanism responsible for this appears to be different from that in RVFV, where the termination sites for N and NSs are determined by a defined signal sequence. We inoculated suckling mice intraperitoneally with eGFP-AKAV, which resulted in neurological signs and lethality equivalent to those seen for the parent AKAV. Fluorescence from eGFP in frozen brain slices from the eGFP-AKAV-infected mice was localized to the cerebellum, pons, and medulla oblongata. Our approach to producing a fluorescent virus, using an ambisense genome, helped obtain eGFP-AKAV, a fluorescent bunyavirus whose viral genes are intact and which can be easily visualized. IMPORTANCE: AKAV is the etiological agent of arthrogryposis-hydranencephaly syndrome in ruminants, which causes considerable economic loss to the livestock industry. We successfully generated a recombinant enhanced green fluorescent protein-tagged AKAV containing an artificial ambisense S genome. This virus could become a useful tool for analyzing AKAV pathogenesis in host animals. In addition, our approach of using an ambisense genome to generate an orthobunyavirus stably expressing a foreign gene could contribute to establishing alternative vaccine strategies, such as bivalent vaccine virus constructs, for veterinary use against infectious diseases.

Comparative analysis of LTR and structural genes in an equine infectious anemia virus strain isolated from a feral horse in Japan.

Although equine infectious anemia virus (EIAV) poses a major threat to the equine industry worldwide, the molecular epidemiology of this virus is poorly understood. Recently, an EIAV strain (EIAVMiyazaki2011-A) representing a new monophyletic group was discovered in feral horses in southern Japan. In the present study, the EIAVMiyazaki2011-A proviral genome is compared with evolutionarily divergent EIAV isolates to investigate conservation of functional elements or motifs within the long terminal repeats (LTRs) and structural genes. This analysis represents a significant step forward in increasing understanding of the molecular conservation and variation between geographically distinct strains of this equine lentivirus.

Bos grunniens papillomavirus type 1: a novel deltapapillomavirus associated with fibropapilloma in yak.

Papillomaviruses (PVs) have been widely identified among vertebrates, but have not yet been reported to infect yaks. We report, for the first time, a novel deltapapillomavirus that was associated with fibropapilloma in yak herds on the Qinghai-Tibetan Plateau. Six skin papilloma samples were collected and examined using histopathology, immunohistochemistry and PCR assays. The samples were identified as fibropapilloma and were found to contain PV antigens. Sequencing of diagnostic PCR products and the full-length genome revealed that all samples were infected with the same PV type. The whole virus genome was 7946 bp in length and possessed the common PV genomic organization. The virus was identified as a novel PV type and designated Bos grunniens papillomavirus type 1 (BgPV-1) based on the nucleotide sequence alignment of the L1 ORF. It is classified in the Delta-4 species of the genus Deltapapillomavirus based on phylogenetic analysis of the L1 ORF. Identification of this novel PV type provides further information about the pathology, development of diagnostic methods and evolutionary studies of the family Papillomaviridae.

Identification of a novel equine infectious anemia virus field strain isolated from feral horses in southern Japan.

Although equine infectious anemia (EIA) was described more than 150 years ago, complete genomic sequences have only been obtained from two field strains of EIA virus (EIAV), EIAV(Wyoming) and EIAV(Liaoning). In 2011, EIA was detected within the distinctive feral Misaki horse population that inhabits the Toi-Cape area of southern Japan. Complete proviral sequences comprising a novel field strain were amplified directly from peripheral blood of one of these EIAV-infected horses and characterized by nucleotide sequencing. The complete provirus of Miyazaki2011-A strain is 8208 bp in length with an overall genomic organization typical of EIAV. However, this field isolate possesses just 77.2 and 78.7 % nucleotide sequence identity with the EIAV(Wyoming) and EIAV(Liaoning) strains, respectively, while similarity plot analysis suggested all three strains arose independently. Furthermore, phylogenetic studies using sequences obtained from all EIAV-infected Misaki horses against known viral strains strongly suggests these Japanese isolates comprise a separate monophyletic group.

Detection of bovine leukemia virus in beef cattle kept in the Central Coast Regions of Vietnam.

Bovine leukemia virus (BLV) is the etiologic agent of enzootic bovine leucosis. Our previous study showed the BLV existence in cattle kept in the Red River Delta Region of Vietnam. However, no positive samples were identified in beef cattle. Besides, information related to the BLV circulation in the remained parts of Vietnam is limited. Therefore, we tested the existence of BLV in 48 beef cattle kept in the Central Coast Regions. Nested PCR targeting the BLV-env-gp51 confirmed the prevalence of 14.6% in investigated regions. Phylogenetic analysis suggested the co-existence of genotypes 1 and 10. The close relationship between strains found in Vietnam, Thailand, Myanmar, and China was revealed suggesting the possibility of BLV transmission through the movement of live cattle.

Characterization of novel bovine papillomavirus type 12 (BPV-12) causing epithelial papilloma.

Bovine papillomavirus type 12 (BPV-12, putative type BAA1) was detected in epithelial papilloma located on the tongue of an infected cow. Then, the whole genome was sequenced, and phylogenetic analysis illustrated that it should be classified as a member of the genus Xipapillomavirus. The viral genome is 7197 base pairs in length and contains five early ORFs (E1, E2, E4, E7 and E8), three late ORFs (L1, L2 and L3), and a long control region that possesses replication regulatory elements. Meanwhile, mRNA of each gene was detected in the papilloma sample. The papilloma was identified as epithelial papilloma by histological and immunohistochemical examination. Based on the genome information and pathological properties, BAA1 was designated as BPV-12 in this study.

Development of a nested PCR assay to detect equine infectious anemia proviral DNA from peripheral blood of naturally infected horses.

Equine infectious anemia (EIA) has posed a major challenge and caused significant losses to the equine industry worldwide. PCR detection methods have considerable potential as an adjunct to conventional serological diagnostic techniques. However, most published PCR methods, including that recommended by the OIE, were designed using laboratory-adapted virus strains and do not function with field isolates of EIA virus (EIAV). In the present study, a nested PCR assay for detection of EIAV proviral DNA in peripheral blood cells of naturally infected horses was developed. Primer sets were designed based on conserved 5' regions of the viral genome extending from the LTR to the tat gene. Preliminary studies demonstrated that the method has a detection limit of 10 genomic copies and, when applied to a naturally EIAV-infected feral horse population, shows 100 % correlation with conventional serological diagnostic techniques. This assay provides a powerful new tool in the control of EIAV.

Identifying the factors that affect the willingness of pig farmers to participate in the electronic prescription system.

Electronic data collection systems are being developed in countries around the world to monitor antimicrobial use at farm level. We conducted a questionnaire survey that is destined for pig farmers who are then able to communicate what factors influence their willingness to participate in an electronic prescription system. A principal component analysis was performed on the variables that were associated with the willingness to participate in the system. Using the principal components obtained from the principal component analysis and the attributes of the farmers as explanatory variables, we performed a logistic regression analysis. The results revealed that farmers with a high level of information technology (IT) literacy and a certain degree of active business management and farmers who are not currently familiar with business management practices but who are willing to use data were more willing to participate in the electronic prescription system than those who do not have a high level of IT literacy and/or who are not willing to use data for business management. Contrarily, farmers' intention to manage drug usage does not contribute to the willingness to participate in the system. These results show that the farmers' understanding of the benefits and ease of participation in the electronic prescription system is important for establishing the system, thus promoting the convenience of the system is the most effective way to gain cooperation of farmers when establishing the system.

Calcium bicarbonate as an antimicrobial, antiviral, and prion-inhibiting agent (Review).

Calcium bicarbonate does not act as a disinfectant at neutral pH; however, it exerts strong antimicrobial activity after it is placed in a high-voltage electric field, whereby it assumes an alkaline pH (12.4). Moreover, the microbicidal activity of the resulting solution (named CAC-717) is not influenced by the presence of organic material or resistance of the agent to inactivation. When sprayed on the skin surface, the pH of CAC-717 decreases rapidly to 8.84. CAC-717 comprises fine particles of 50-500 nm. When these mesoscopic crystals are dissolved in water, they destroy the genomes of bacteria or viruses and neutralize the infectious properties of abnormal prion proteins produced in ScN2a cells. The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic has resulted in unprecedented international demand for disinfectants. A small titer of SARS-CoV-2 remains infectious even after 30 sec in growth medium at pH 12.4. CAC-717 has exhibited a strong virucidal effect (3.6 to 4.4 log10 decrease) against all examined SARS-CoV-2 isolates, including mutant forms. Similarly, human noroviruses also remain intact at pH 12.4; however, CAC-717 has been shown to cause a 3.25 log10 reduction in norovirus genomic RNA compared to untreated samples. Existing evidence suggests that an unidentified mechanism controls the virucidal activity of CAC-717.

Evaluating the antimicrobial use on dairy farms in Chiba Prefecture in Japan using the antimicrobial treatment incidence, an indicator based on Japanese defined daily doses from 2014-2016.

The use of antimicrobial agents in food-producing animals may lead to the emergence and spread of antimicrobial resistance in bacteria of animal origin. However, there is a paucity of data on the quantity of antimicrobials use on dairy farms in Japan. This study describes antimicrobial use on dairy farms from 1 January 2014 to 31 December 2016 in five administrative districts (central, eastern, western, southern and northern) of Chiba Prefecture. The use of antimicrobial agents in dairy cattle over these three years was evaluated in terms of the antimicrobial treatment incidence (ATI; theoretical number of animals per 1,000 animal-days subjected to antimicrobial treatment) using data collected from a total of 442 dairy farms in that prefecture. Our results revealed that the average ATI on these farms for these years ranged from 38.7 to 39.4 with no significant difference between years and that the average ATI for these administrative districts varied between 32.9 and 43.2 with a significant variation between some of the districts. Approximately 84% of antimicrobials were administered intramammarily, 13-14% by injection and 1-2% orally. Scenario analyses were performed to assess the effect of changes in some of the defined daily dose (DDDjp) values used to calculate the ATI. Our results revealed that the calculated ATI is considerably affected by the changes in the long-acting factor used for assigning the DDDjp values of intramammary products for dry cows and the way in which DDD values are assigned for combination products.

Antimicrobial use and its association with the presence of methicillin-resistant staphylococci (MRS) and extended-spectrum beta-lactamases (ESBL)-producing coliforms in mastitic milk on dairy farms in the Chiba Prefecture, Japan.

Food-producing animals, including dairy cattle, are potential reservoirs of antimicrobial resistance. However, there is limited data on antimicrobial use and the selection of resistant bacteria. Therefore, we investigated the association between antimicrobial use and resistance to mastitis pathogens using 2016 data from milk samples collected from cows with mastitis in 134 dairy farms in Chiba Prefecture, one of the principal dairy production prefectures in Japan. We recorded the antimicrobial use and isolation of methicillin-resistant staphylococci (MRS) and extended-spectrum beta-lactamase (ESBL)-producing coliforms (E. coli and Klebsiella spp.), and used the antimicrobial treatment incidence (ATI; the theoretical number of animals per 1000 animal-days subjected to antimicrobial treatment) to indicate antimicrobial use on each farm. The farms in which MRS or ESBL-producing coliforms were isolated from at least one mastitic milk sample were classified as antimicrobial resistance (AMR)-positive, and those in which neither MRS nor ESBL-producing coliforms were isolated were classified as AMR-negative. The AMR-positive farms showed a significantly higher ATI (median 45.17) than AMR-negative farms (median 38.40). The results indicate that high antimicrobial usage is associated with AMR in staphylococci and coliforms isolated from mastitic milk on dairy farms in Chiba Prefecture.

A reassortant G3P[12] rotavirus A strain associated with severe enteritis in donkeys (Equus asinus).

BACKGROUND: In contrast to horses, the only evidence suggesting gastrointestinal disease in neonatal donkeys is associated with Group A rotaviruses (RVAs) is the detection of viral antigens by ELISA in just 1 of 82 symptomatic donkey foals. No additional, more comprehensive investigations have been conducted, and RVAs if circulating in donkey populations have not been molecularly characterised. OBJECTIVES: To investigate if RVAs are associated with an outbreak of severe enteritis in neonatal donkeys and if associated determine the genotype(s) along with the phylogenetic relationship to RVA strains circulating in horses. STUDY DESIGN: Cross-sectional. METHODS: RT-PCR-based techniques were used for RVA diagnosis and gene amplification. Statistical significance was determined by Chi-square and Fisher's exact two-sided tests. Genotyping was performed by RotaC and phylogenetic analysis by neighbour joining. RESULTS: In 2019, acute enteritis occurred in 119 of 206 donkey foals (≤4 months) at two intensive donkey farms in the Shandong province of China. The highest morbidity (68.1%), mortality (29.5%) and fatality levels (45.5%) occurred in foals in the 30-89 day, 30-59 day and 0-29 day age groups respectively. RVA gene sequences were detected in 107 (89.9%) of the symptomatic individuals while further analysis demonstrated the outbreak was associated with the same G3P[12] RVA strain designated RVA/Donkey-wt/CHN/Don01/2019/G3P[12]. Although the VP4 gene of Don01 exhibited close phylogenetic relationships with equivalent RVA sequences commonly circulating in horses, encoding VP7 was more closely associated with sequences isolated from bats suggesting this new donkey strain arose via an intergenogroup reassortment event. MAIN LIMITATIONS: Actual prevalence not determined because <7% of asymptomatic donkey foals were included in this study. The complete genomic sequence of RVA/Donkey-wt/CHN/Don01/2019/G3P[12] remains to be determined. CONCLUSIONS: Valuable new information about the molecular epidemiology of rotaviruses in different equid species is provided by isolation and molecular characterisation of a novel RVA strain from neonatal donkeys.

Association between BoLA-DRB3 polymorphism and bovine leukemia virus proviral load in Vietnamese Holstein Friesian cattle.

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis. Polymorphism in bovine leukocyte antigen (BoLA)-DRB3 allele can influence the host immune response to pathogens, including BLV. However, association between specific BoLA-DRB3 alleles and BLV proviral load (PVL), which is a useful index for estimating disease progression and transmission risk, in Vietnamese cattle are unknown. Here, association study of BoLA-DRB3 allele frequency between cattle with high or low PVL demonstrated BoLA-DRB3*12:01 associates with high PVL in Vietnamese Holstein Friesian (HF) crossbred cattle. This is the first study to demonstrate that BoLA-DRB3 polymorphism confers susceptibility to BLV high PVL in HF crossbred kept in Vietnam. Our results may be useful in disease control and eradiation for BLV through genetic selection.

Rapid and sensitive detection of bovine coronavirus and group a bovine rotavirus from fecal samples by using one-step duplex RT-PCR assay.

Bovine coronavirus (BCoV) and group A bovine rotavirus (BRV) are two of major causes for neonatal calf diarrhea. In the present study, a one-step duplex RT-PCR was established to detect and differentiate BCoV and group A BRV from fecal samples. The sensitivity of this method for BCoV and group A BRV was 10 PFU/100 µl and 1 PFU/100 µl, respectively. Twenty-eight diarrhea fecal samples were detected with this method, the result showed that 2 samples were identified as co-infected with BCoV and group A BRV, 26 samples were group A BRV positive, and 2 samples were negative. It proved that this method is sensitive for clinical fecal samples and is worth applying to laboratory diagnosis for BCoV and group A BRV.