Prevalence study and genetic typing of bovine viral diarrhea virus (BVDV) in four bovine species in China

Bovine viral diarrhoea viruses from New Zealand belong predominantly to the BVDV-1a genotype

AIM

To determine which genotypes of bovine viral diarrhoea virus (BVDV) circulate among cattle in New Zealand.

METHODS

Samples comprised BVDV-1-positive sera sourced from submissions to veterinary diagnostic laboratories in 2019 (n = 25), 2020 (n = 59) and 2022 (n = 74) from both beef and dairy herds, as well as archival BVDV-1 isolates (n = 5). Fragments of the 5' untranslated region (5' UTR) and glycoprotein E2 coding sequence of the BVDV genome were amplified and sequenced. The sequences were aligned to each other and to international BVDV-1 sequences to determine their similarities and phylogenetic relationships. The 5' UTR sequences were also used to create genetic haplotype networks to determine if they were correlated with selected traits (location, type of farm, and year of collection).

RESULTS

The 5' UTR sequences from New Zealand BVDV were closely related to each other, with pairwise identities between 89% and 100%. All clustered together and were designated as BVDV-1a (n = 144) or BVDV-1c (n = 5). There was no evidence of a correlation between the 5' UTR sequence and the geographical origin within the country, year of collection or the type of farm. Partial E2 sequences from New Zealand BVDV (n = 76) showed 74-100% identity to each other and clustered in two main groups. The subtype assignment based on the E2 sequence was the same as based on the 5' UTR analysis. This is the first comprehensive analysis of genomic variability of contemporary New Zealand BVDV based on the analysis of the non-coding (5' UTR) and coding (E2) sequences.

CONCLUSIONS AND CLINICAL RELEVANCE

Knowledge of the diversity of the viruses circulating in the country is a prerequisite for the development of effective control strategies, including a selection of suitable vaccines. The data presented suggest that New Zealand BVDV are relatively homogeneous, which should facilitate eradication efforts including selection or development of the most suitable vaccines.

Detection of emerging HoBi-like Pestivirus (BVD-3) during an epidemiological investigation of bovine viral diarrhea virus in Xinjiang: a first-of-its-kind report

Xinjiang pastoral area is the second largest pastoral area in China, accounting for 26.8% of the available grassland area in the country, and the geographical advantage of cattle breeding industry is very obvious. Bovine viral diarrhea virus (BVDV) has always been one of the important viral diseases that have plagued the development of cattle farming industry in the world. As one of the main pastoral areas of China's cattle farming industry, the Xinjiang pastoral area has also been deeply affected. In this study, 6,153 bovine serum samples were collected from 18 large-scale cattle farms in 13 cities in Xinjiang. The antibodies and antigens of 6,153 and 588 serum samples were detected by serological detection methods, respectively. Ten serum samples, which were antigen-positive by ELISA, were randomly selected for RT-PCR detection, sequencing, and phylogenetic analysis of suspected HoBi-like Pestivirus (HoBiPeV) strains. The results showed that the positive rates of BVDV antibodies and antigens were 53.68% (3,303/6,153) and 6.12% (36/588), respectively. One of the 10 randomly selected seropositive samples was infected with the HoBiPeV strain. HoBiPeV, also referred to as BVDV-3, is an emerging atypical Pestivirus that occurs in cattle and small ruminants, and its clinical signs are similar to those of BVDV infection. Based on the whole genome of the BVDV-3 reference strain (JS12/01) on the GenBank, the homology of the detected strain was 96.02%. The whole genome nucleotide sequence was submitted to the GenBank database, and the gene accession number was obtained: OP210314. The whole genome of isolate OP210314 was 12.239 nucleotides and contained a 5'-UTR of 340 nucleotides, a 3'-UTR of 199 nucleotides, and a large open reading frame (ORF) encoding a polyprotein consisting of 3,899 amino acids. In conclusion, the prevalence rate of BVDV infection in Xinjiang dairy cows is high, and the genetic diversity is increasing. This study successfully identified and isolated HoBiPeV in Xinjiang for the first time, posing a potential threat to the cattle industry in Xinjiang.

Pestivirus A Bovine viral diarrhea virus type 1 species genotypes circulating in China and Turkey

Background

Pestivirus A Bovine viral diarrhea virus type 1 (BVDV-1) is a heterogeneous species within the genus, affecting cattle and other ruminants, with economic impact on livestock production.

Aim

The study aimed to update the taxonomy of the Pestivirus A, BVDV-1 species and to verify the clustering of the strains reported as genotype 1v, originating from different countries.

Methods

Recently deposited strains from China, Turkey, and Iran have been evaluated by the palindromic nucleotide substitutions (PNS) genotyping method.

Results

Based on secondary structure analysis of the 5'-UTR sequences, strains reported as 1v from China were clustered as sub genotype 1.7.3 (1o). Genotype 1.19 (1w) was restricted to China and genotype 1.21 (1v) was present only in Turkey and Iran.

Conclusion

The application of the PNS method clarified the taxonomical status of strains, revealing the homonymy of genetically different clusters. Furthermore, these observations indicated geographic segregation in the Pestivirus A species, and confirmed the occurrence of new atypical genetic variants, with potential implications on control and prophylaxis.

Biological activity of recombinant bovine IFN-α and inhibitory effect on BVDV in vitro

Type I interferon has great broad-spectrum antiviral ability and immunomodulatory function, and its receptors are expressed in almost all types of cells. Bovine viral diarrhea virus (BVDV) is an important pathogen causing significant economic losses in cattle. In this study, a recombinant expression plasmid carrying bovine interferon-α(BoIFN-α)gene was constructed and transformed into E. coli BL21 (DE3) competent cells. SDS-PAGE and Westernblotting analysis showed that the recombinant BoIFN-α protein (rBoIFN-α) was successfully expressed. It is about 36KD and exists in the form of inclusion body. When denatured, purified and renatured rBoIFN-α protein stimulated MDBK cells, the expression of interferon stimulating genes (ISGs) such as ISG15, OAS1, IFIT1, Mx1 and IFITM1 were significantly up-regulated, and reached the peak at 12 h (P< 0.001). MDBK cells were infected with BVDV with moi of 0.1 and 1.0, respectively. The virus proliferation was observed after pretreatment with rBoIFN-α protein and post-infection treatment. The results showed that the denatured, purified and renatured BoIFN-α protein had good biological activity and could inhibit the replication of BVDV in MDBK cells in vitro, which provided a basis for BoIFN-α as an antiviral drug, immune enhancer and clinical application of BVDV.

Characterization of a Highly Virulent Noncytopathic Bovine Viral Diarrhea Virus 2b Isolate Detected in Cattle in Inner Mongolia, China

Bovine viral diarrhea virus (BVDV) infection causes subclinical to severe acute disease in cattle all over the world. Two genotypes of BVDV are recognized, BVDV1 and BVDV2. Currently, the subtypes of BVDV1b and BVDV2a are mainly circulating in China. Here, a newly noncytopathic (ncp) BVDV strain named BVDVNM21 was isolated and identified from cattle. We determined the complete genome sequence of BVDVNM21, phylogenetic analysis of 5′ untranslated region (5′UTR), Npro, and E2 gene, and complete genome showed the virus belongs to BVDV2b subtype and formed an independent clade within BVDV2b. Genome-wide sequence analysis showed that BVDVNM21 had high homology with SD1301 (98.10%) isolated from China. In the experimental infection study of guinea pigs and calves, they all developed similar clinical signs, including a pronounced and prolonged febrile response lasting more than 3 days and pronounced reduction in white blood cells (WBC) and platelets of more than 40%. Moreover, guinea pigs showed more acute infection characteristics after infection, and WBC decreased by more than 50% at 1 day postinfection (dpi), and they recovered in less than 3 days. The results indicated that the BVDVNM21 strain showed high virulence in calves. It was the first confirmed isolation of a highly pathogenic ncpBVDV2b in cattle, as well as the establishment of the BVDV-guinea pig model. This study may provide a basis for further research and control of the prevalence of BVDV2b in China.

Development and application of an indirect ELISA for the serological detection of bovine viral diarrhea virus infection based on the protein E2 antigen

BACKGROUND

Bovine viral diarrhea virus (BVDV) causes continuous economic losses to the livestock industry. Monitoring antibodies with enzyme-linked immunosorbent assay (ELISA) is a valuable tool to ensure the purification of BVDV in cattle. However, currently available ELISA kits based on the whole BVDV virion are both costly and time-consuming. The E2 protein has good immunogenicity, induces the secretion of neutralizing antibodies and is an essential immunogen for serological detection.

METHODS AND RESULTS

We developed a novel recombinant E2 protein-based indirect ELISA (rE2-iELISA) and conducted a serological survey for BVDV antibodies in 2021-2022 in Beijing, China. The results showed that E2 protein was successfully expressed with high immunogenicity and the optimal rE2-iELISA displayed high sensitivity, reproducibility and specificity. Clinical testing of 566 serum specimens indicated that 318 BVDV positive samples and 194 BVDV negative samples were tested by rE2-iELISA and the IDEXX BVDV ELISA-Ab kit, with a positive coincidence rate of 93.3%, a negative coincidence rate of 86.3%, and an overall coincidence rate of 90.5%.

CONCLUSION

This study established an rE2-iELISA method, which is a highly sensitive, specific and robust ELISA-test validated to detect anti-BVDV antibodies. These findings indicate that the newly developed rE2-iELISA method has the potential to be used as a rapid, reliable and cost-effective screening tool for BVDV infection and provides technical support for the evaluation of vaccine efficacy in cattle herds in the future.

Different Types of Vaccines against Pestiviral Infections: "Barriers" for "Pestis"

The genus Pestivirus of the family Flaviviridae mainly comprises classical swine fever virus (CSFV), bovine viral diarrhea virus 1 (BVDV-1), BVDV-2, border disease virus (BDV), and multiple new pestivirus species such as atypical porcine pestivirus (APPV), giraffe pestivirus, and antelope pestivirus. Pestiviruses cause infectious diseases, resulting in tremendous economic losses to animal husbandry. Different types of pestivirus vaccines have been developed to control and prevent these important animal diseases. In recent years, pestiviruses have shown great potential as viral vectors for developing multivalent vaccines. This review analyzes the advantages and disadvantages of various pestivirus vaccines, including live attenuated pestivirus strains, genetically engineered marker pestiviruses, and pestivirus-based multivalent vaccines. This review provides new insights into the development of novel vaccines against emerging pestiviruses, such as APPV and ovine pestivirus.

Isolation of BVDV-1a, 1m, and 1v strains from diarrheal calf in china and identification of its genome sequence and cattle virulence

Bovine viral diarrhea virus (BVDV) is an important livestock viral pathogen responsible for causing significant economic losses. The emerging and novel BVDV isolates are clinically and biologically important, as there are highly antigenic diverse and pathogenic differences among BVDV genotypes. However, no study has yet compared the virulence of predominant genotype isolates (BVDV-1a, 1b, and 1m) in China and the emerging genotype isolate BVDV-1v. The serological relationship among these genotypes has not yet been described. In this study, we isolated three BVDV isolates from calves with severe diarrhea, characterized as BVDV-1a, 1m, and novel 1v, based on multiple genomic regions [including 5-untranslated region (5'-UTR), Npro, and E2] and the phylogenetic analysis of nearly complete genomes. For the novel genotype, genetic variation analysis of the E2 protein of the BVDV-1v HB-03 strain indicates multiple amino acid mutation sites, including potential host cell-binding sites and neutralizing epitopes. Recombination analysis of the BVDV-1v HB-03 strain hinted at the possible occurrence of cross-genotypes (among 1m, 1o, and 1q) and cross-geographical region transmission events. To compare the pathogenic characters and virulence among these BVDV-1 genotypes, newborn calves uninfected with common pathogens were infected intranasally with BVDV isolates. The calves infected with the three genotype isolates show different symptom severities (diarrhea, fever, slowing weight gain, virus shedding, leukopenia, viremia, and immune-related tissue damage). In addition, these infected calves also showed bovine respiratory disease complexes (BRDCs), such as nasal discharge, coughing, abnormal breathing, and lung damage. Based on assessing different parameters, BVDV-1m HB-01 is identified as a highly virulent strain, and BVDV-1a HN-03 and BVDV-1v HB-03 are both identified as moderately virulent strains. Furthermore, the cross-neutralization test demonstrated the antigenic diversity among these Chinese genotypes (1a, 1m, and 1v). Our findings illustrated the genetic evolution characteristics of the emerging genotype and the pathogenic mechanism and antigenic diversity of different genotype strains, These findings also provided an excellent vaccine candidate strain and a suitable BVDV challenge strain for the comprehensive prevention and control of BVDV.

Bovine viral diarrhea virus in China: A comparative genomic and phylogenetic analysis with complete genome sequences

Bovine viral diarrhea virus (BVDV), causing bovine viral diarrhea (BVD) in cattle, is one of the highly contagious and devastating diseases of cattle. Since 1980, BVDV has been identified all-over China in a variety of animal species including cattle, camels, yaks, sheep, water buffalo, goats, Sika deer and pigs. In this study, 31 BVDV complete genomes reported in China (from 2004 to 2020) with other 112 genomes reported around the world were comparatively analyzed. Phylogenetic analysis shows that BVDV genomes reported worldwide clustered in three major clades i.e., BVDV-1, BVDV-2, and BVDV-3. The BVDV-1 is genetically the most diverged genotype and phylogenetically classified into 7 sub-clades in our study based on full-length genomes. The China BVDV genomes fall into all three major clades, e.g., BVDV-1, BVDV-2 and BVDV-3. China BVDV-1 clustered into five sub-clades, e.g., 1, 2, 3, 6 and 7, where sub-clade 7 clustered as a separate sub-clade. Full-length genome recombination analysis reveals that the BVDV-1 reported in China appears to be mainly involved in recombination events. In addition, comparative analysis of E2 proteins between BVDV-1, BVDV-2, and BVDV-3 reveals that the amino acid variations could affect 12 potential linear B cell epitopes, demonstrating a dramatic antigen drift in the E2 protein. These results provide a thorough view of the information about the genetic and antigenic diversity of BVDVs circulating in China and therefore could benefit the development of suitable strategies for disease control.

Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages

Bovine viral diarrhea virus (BVDV), serving as an important pathogen for newborn calves, poses threat to reproductive and economic losses in the cattle industry. To survey the infection rate and genetic diversity of BVDV in newborn calves in northern China, a total of 676 sera samples of newborn calves were collected from four provinces between 2021 and 2022. All sera samples were individually detected for BVDV infection by RT-PCR and ELISA. Our results showed that the overall serological rate was 9.76% (66/676) and the average positive rate of BVDV RNA was 8.14% (55/676) in the newborn calves. Eight BVDV strains were successfully isolated from RT-PCR positive sera samples, and four isolates displayed the cytopathic effect (CPE). Based on phylogenetic tree at the genome level, the eight strains were classified into subgenotype 1c. Moreover, the BVDV isolates had a close genetic relationship with the GSTZ strain at either nucleotide or codon usage level. Interestingly, in comparison of synonymous codon usage patterns between the BVDV isolates with CPE and ones without CPE, there were four synonymous codons (UCG, CCC, GCA, and AAC) which displayed the significant differences (p < 0.05) at codon usage pattern, suggesting that synonymous codon usage bias might play a role in BVDV-1c biotypes. In addition, the usage of synonymous codons containing CpG dinucleotides was suppressed by the BVDV-1c isolates, reflecting one of strategies of immune evasion of BVDV to its host. Taken together, our study provided data for monitoring and vaccination strategies of BVDV for newborn calves in northern China.

Prevalence characteristic of BVDV in some large scale dairy farms in Western China

The aim of this study was to analyze the prevalence characteristic of Bovine viral diarrhea virus (BVDV) in some large scale dairy farms in Western China. BVDV was detected in 30 samples of bulk tank milk (BTM) collected from 30 large dairy farms in 7 provinces of western China, 93.33% (28/30) of the farms were infected with BVDV, and S/P ratio was over 0.3 in 28 positive farms. The individual status was further estimated in the dairy farm (No. 10) with the highest positive rate (S/P ratio = 1.37) and the dairy farm (No. 17) with the lowest positive rate (S/P ratio = 0.39). Two hundred cows were, respectively, selected from calf, young cows and lactating cows in farm No. 10 and farm No. 17 and the serum sample of each enrolled cow was collected. The individual positive rate of serum antibody (Ab) was 87.17% (523/600) in farm No. 10 and 31.33% (188/600) in farm No. 17. The individual positive ratio of serum antibody in calves, young cows and lactating cows were 41.75 % (167/400), 58.75% (235/400) and 77.25% (309/400), respectively. BTM Ab of farm No. 10 has an S/P ratio more than 1.0, which indicated there were emergent or persistent infection (PI) cases, and further test showed that PI cases were 0.51% in farm No. 10. Pathogens were positive in 42.34% (163/385) of nasal mucus samples collected from cows with respiratory symptom, and BVDV cases were 57 in 163 positive samples. Three strains of NCP BVDV-1, one strain of CP BVDV-1, one strain of NCP BVDV-2 and one strain of CP BVDV-2 were successfully isolated. Phylogenetic analysis revealed that the subtypes of BVDV currently prevalent in western China were BVDV-1a, BVDV-1m, BVDV-1q and BVDV-2. The findings suggested that the BVDV infection is serious in some Large Scale Dairy Farms in Western China.

Investigation into an outbreak of Border disease virus in pigs in England

Border disease (BD) was first reported in 1959 in lambs from the border region of England and Wales. The causative virus (BD virus; BDV) has since been identified in several other ruminant species and pigs. The virus is prevalent in sheep flocks of UK, Europe and USA and has potential to inflict substantial economic losses. Natural BDV infection of pigs was first reported in the UK in 1992 from pigs with haemorrhagic lesions and more recently from healthy pigs in Spain and Japan. Here, a persistent problem of poor growth and anaemia in a small proportion of growing pigs on a mixed pig and sheep holding was investigated and tissues were tested in a pan viral microarray. The microarray detected BDV RNA in several tissues which was further confirmed by sequencing, specific BDV PCR and immunohistochemistry. Phylogenetically, the virus clustered with other BDVs in the sub‐genotype 1b. This investigation highlights likely interspecies transmission of pestiviruses and their impact on pestivirus detection and eradication programs.

Effects of Short-Chain Fatty Acid Modulation on Potentially Diarrhea-Causing Pathogens in Yaks Through Metagenomic Sequencing

Short-chain fatty acids (SCFA) are principal nutrient substrates of intestinal epithelial cells that regulate the epithelial barrier in yaks. Until now, metagenomics sequencing has not been reported in diarrheal yaks. Scarce information is available regarding the levels of fecal SCFA and diarrhea in yaks. So, our study aims to identify the potential pathogens that cause the emerging diarrhea and explore the potential relationship of short-chain fatty acids in this issue. We estimated diarrhea rate in yaks after collecting an equal number of fecal samples from affected animals. Metagenomics sequencing and quantitative analysis of SCFA were performed, which revealed 15%–25% and 5%–10% prevalence of diarrhea in yak’s calves and adults, respectively. Violin box plot also showed a higher degree of dispersion in gene abundance distribution of diarrheal yaks, as compared to normal yaks. We found 366,163 significant differential abundance genes in diarrheal yaks, with 141,305 upregulated and 224,858 downregulated genes compared with normal yaks via DESeq analysis. Metagenomics binning analysis indicated the higher significance of bin 33 (Bacteroidales) (p < 0.05) in diarrheal animals, while bin 10 (p < 0.0001), bin 30 (Clostridiales) (p < 0.05), bin 51 (Lactobacillales) (p < 0.05), bin 8 (Lachnospiraceae) (p < 0.05), and bin 47 (Bacteria) (p < 0.05) were significantly higher in normal yaks. At different levels, a significant difference in phylum (n = 4), class (n = 8), oder (n = 8), family (n = 16), genus (n = 17), and species (n = 30) was noticed, respectively. Compared with healthy yaks, acetic acid (p < 0.01), propionic acid (p < 0.01), butyric acid (p < 0.01), isobutyric acid (p < 0.01), isovaleric acid (p < 0.05), and caproic acid (p < 0.01) were all observed significantly at a lower rate in diarrheal yaks. In conclusion, besides the increased Staphylococcus aureus, Babesia ovata, Anaplasma phagocytophilum, Bacteroides fluxus, viruses, Klebsiella pneumonia, and inflammation-related bacteria, the decrease of SCFA caused by the imbalance of intestinal microbiota was potentially observed in diarrheal yaks.

Genetic characterization and clinical characteristics of bovine viral diarrhea viruses in cattle herds of Heilongjiang province, China

BACKGROUND

Heilongjiang province is the main cattle-producing area in China, and molecular epidemiological studies of bovine viral diarrhea viruses (BVDV) in cattle have not been performed in the province.

AIMS

The objective of this research was to determine the genetic and clinical characteristics of BVDV in cattle.

METHODS

Fifty-three BVDV-positive clinical samples were collected from 22 cattle farms in Heilongjiang, and the 5´-untranslated region (5´-UTR) was used to carry out a phylogenetic analysis of the viruses.

RESULTS

The similarity of the 5´-UTR sequences among these BVDVs was 84.2%-100%, and the phylogenetic analysis showed that all viruses belong to the BVDV-1 species, which is classified into five subtypes: BVDV-1b (47.17%, n=25), 1c (15.09%, n=8), 1d (16.98%, n=9), 1 m (3.77%, n=2), and 1o (16.98%, n=9). The statistical results showed that the BVDV-1b subtype had a positive correlation with gastrointestinal disease (P<0.05; 95% CI: 1.19 to 3.34). There were up to three or four BVDV-1 subtypes in some dairy cattle farms, but farms with a single subtype were prevalent (5/10).

CONCLUSION

BVDV-1b is predominant in cattle herds of Heilongjiang province, China, and shows a positive correlation with gastrointestinal disease. BVDV-1o was found for the first time in Chinese cattle, which increased the complex distribution of BVDV-1 subtypes in cattle herds of China.

Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea

Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.

Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

BACKGROUND

As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5' untranslated region and the N^pro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation.

RESULTS

To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19-32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage.

CONCLUSIONS

Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.

Key issues affecting the current status of infectious diseases in Chinese cattle farms and their control through vaccination

Infectious diseases can have a major impact on the profitability of the cattle industry. To determine the occurrence of bovine infectious diseases in China and the adoption of vaccination to control them, a national-wide questionnaire and focus group meeting were performed. The questionnaire was administered to 189 farmers including 93 dairy farmers, 80 beef cattle farmers and 16 yak farmers. Since it is compulsory to vaccinate cattle against foot and mouth disease, the coverage of vaccination to this disease was the highest (100% of dairy and yak farms and 92.5% of beef farms). However, the implementation of vaccination against other diseases was vastly different between cattle types with less than 50% of farms adopting vaccination (except brucellosis vaccine in yak farms). In a focus group meeting of 36 cattle experts on the key issues affecting the frequency of infectious diseases in cattle and the vaccination practices adopted on Chinese cattle farms, the lack of effective vaccines against single or multiple pathogens, a lack of tools for the early and correct diagnosis of disease, difficulties in licensing novel vaccines and diagnostic agents, low efficiency in disseminating knowledge on diseases and control products to producers were identified as key issues. In conclusion, except for FMD, the control of most infectious diseases of cattle in China requires improving. Development of improved control measures and diagnostic tests along with the development and implementation of educational material for producers on cattle diseases should be given priority.

Epidemiology of Bovine Pestiviruses Circulating in Italy

Pestiviruses are widespread and economically important pathogens of cattle and other animals. Pestivirus A (formerly known as Bovine viral diarrhea virus 1, BVDV-1), Pestivirus B (Bovine viral diarrhea virus 2, BVDV-2), and Pestivirus H (HoBi-like pestivirus, HoBiPeV) species are infecting primarily cattle. Like other RNA viruses, pestiviruses are characterized by a high degree of genetic variability. This high rate of variability is revealed by the existence of a number of viral subgenotypes within each species. In cattle, the highest number of pestivirus subgenotypes has been documented in European countries, particularly in Italy. The aim of this review is to report an up-to-date overview about the genetic diversity of pestiviruses in Italian cattle herds. All three bovine pestiviruses species have been identified in cattle population with variable frequency and geographical distribution. The genetic diversity of Italian pestiviral strains may have diagnostic and immunological implications, affecting the performance of diagnostic tools and the full cross-protection elicited by commercially available vaccines. Implementation and strengthening of coordinated approaches for bovine pestivirus control in Italy are recommended. Therefore, it would be extremely important to increase control and restriction measures to the trade of cattle and biological products of bovine origin, including those containing fetal bovine serum.

Identification and genotyping of a new subtype of bovine viral diarrhea virus 1 isolated from cattle with diarrhea

In 2019, diarrhea cases occurred on cattle farms in Qionglai and Guang'an, Sichuan Province. Two out of 20 (10%) serum and nasal swab samples were positive when tested using a bovine viral diarrhea virus (BVDV) antigen-capture ELISA kit. Two non-cytopathic strains of BVDV were isolated and named QL1903 and GA190608, respectively. The nucleotide sequences of the genomes of the two isolates were 89.52% identical. Phylogenetic analysis based on the 5'-UTR sequence revealed that the BVDV isolate QL1903 belonged to BVDV subtype 1b, whereas isolate GA190608 clustered with strains HN1814, EN-19, and BJ09_26 in a separate branch, which has tentatively been classified as a new genetic subtype, "1v".

Molecular detection and genotyping of bovine viral diarrhea virus in Western China

BACKGROUND

Bovine viral diarrhea virus (BVDV) is an important global viral pathogen of cattle and other ruminants. To survey the infection rate and genetic diversity of BVDV in western China, a total of 1234 serum samples from 17 herds of dairy cattle, beef cattle and yak in 4 provinces were collected in 2019.

RESULTS

All the 1234 serum samples were screened individually for BVDV by RT-PCR. Our results demonstrated that the average positive rate of BVDV was 7.2% (89/1234) in animals and 82.4% (14/17) in herds. Thirteen BVDV strains were isolated from RT-PCR positive clinical samples and they were all NCP biotype. BVDV-1a and 1c subgenotypes were identified from 22 selected virus isolates in 14 BVDV-positive herds. These results confirmed that BVDV-1a and BVDV-1c were circulating in western China, similar to the BVDV epidemics in cattle in other regions of China.

CONCLUSIONS

This study provides data for monitoring and vaccination strategies of BVDV in western China.

Insights into the origin and diversification of bovine viral diarrhea virus 1 subtypes

In this study, we performed phylogenetic and evolutionary analysis on bovine viral diarrhea virus 1 (BVDV-1) sequences to investigate the origin and temporal diversification of different BVDV-1 subtypes. Dated phylogenies using the complete polyprotein sequence were reconstructed, and the time of the most recent common ancestor (tMRCA) was estimated. The results demonstrated that BVDV-1 subtypes clustered into two phylogenetic clades, where the predominant subtypes worldwide grouped together. In the temporal analysis, the tMRCA of BVDV-1 was 1336, and the diversification into different subtypes appears to have occurred around 363 years ago. The present results help to elucidate the origins of BVDV-1 subtypes and the dynamics of ruminant pestiviruses.

Comprehensive analysis of lncRNA expression profiles in cytopathic biotype BVDV-infected MDBK cells provides an insight into biological contexts of host-BVDV interactions

Bovine viral diarrhea virus (BVDV) is the causative agent of bovine viral diarrhea-mucosal disease, which significantly affects the production performance of cattle, causing serious economic losses to the cattle industries worldwide. Up to now, some mechanisms involved in host–BVDV interaction are still not fully understood. The discovery of long non-coding RNAs (lncRNAs) has provided a new perspective on gene regulation in diverse biological contexts, particularly in viral infection and host immune responses. However, little is known about the profiles and functions of lncRNAs in host cells in response to BVDV infection. Here, we utilized Illumina sequencing to explore lncRNAs profiles in cytopathic (CP) biotype BVDV-infected MDBK cells to further reveal the potential roles of lncRNAs in BVDV infection and host–BVDV interaction with integrated analysis of lncRNAs and mRNA expression profiles. A total of 1747 significantly differentially expressed genes, DEGs (156 lncRNAs and 1591 mRNAs) were obtained via RNA-seq in BVDV-infected MDBK cells compared to mock-infected cells. Next, these DE lncRNAs and mRNAs were subjected to construct lncRNAs-mRNAs co-expression network followed by the prediction of potential functions of the DE lncRNAs. Co-expression network analysis elucidated that DE lncRNAs were significant enrichment in NOD-like receptor, TNF, NF-ĸB, ErbB, Ras, apoptosis, and fatty acid biosynthesis pathways, indicating that DE lncRNAs play important roles in host–BVDV interactions. Our data give an overview of changes in transcriptome and potential roles of lncRNAs, providing molecular biology basis for further exploring the mechanisms of host–BVDV interaction.

Investigation of viral pathogens in cattle with bovine respiratory disease complex in Inner Mongolia, China

As a multifactor disease, the bovine respiratory disease complex (BRDC) causes high morbidity and mortality that is devastating to the cattle industry. To assess viral infections in beef cattle suffering from respiratory diseases in Inner Mongolia, 302 nasal swabs and serum samples were randomly collected from cattle with mild respiratory symptoms between March 2018 and May 2019. Our results showed that the rate of RT-PCR results positive for nucleic acids of viral pathogens in 6 cities was between 54 and 80%.The rates of bovine viral diarrhea virus (BVDV), bovine herpesvirus 1 (BHV-1), bovine parainfluenza virus type 3(BPIV3), and bovine respiratory syncytial virus(BRSV)infections were 44.70% (135/302), 24.83% (75/302), 5.63% (17/302), and 6.95% (21/302),respectively. There are also 8.94% (27/302) of samples were positive for BVDV and BHV-1, and 3.97% (12/302) of samples were positive for BPIV3 and BRSV. In addition, the RT-PCR products were sequenced, and phylogenetic analysis based on these sequences was performed. The results indicated that: a) all of the BVDV isolates were BVDV-1 and were classified as BVDV-1a (66.67%) and BVDV-1b (33.33%); b) all of the BHV-1 isolates were classified as subtype 1.1; 44.44% of the isolates were closely related to modified live viral vaccine strains, and 55.56% of the isolates were closer to epidemic strains; c) all of the BPIV3 isolates belonged to BPIV3c; d) all of the BRSV isolates were classified into subgroup III. It is suggested that an important cause of respiratory diseases for beef cattle is viral infection, and phylogenetic analysis can help us choose the proper strain to develop a vaccine.

First report and genetic characterization of bovine torovirus in diarrhoeic calves in China

Background

Coronaviruses are notorious pathogens that cause diarrheic and respiratory diseases in humans and animals. Although the epidemiology and pathogenicity of coronaviruses have gained substantial attention, little is known about bovine coronavirus in cattle, which possesses a close relationship with human coronavirus. Bovine torovirus (BToV) is a newly identified relevant pathogen associated with cattle diarrhoea and respiratory diseases, and its epidemiology in the Chinese cattle industry remains unknown.

Results

In this study, a total of 461 diarrhoeic faecal samples were collected from 38 different farms in three intensive cattle farming regions and analysed. Our results demonstrated that BToV is present in China, with a low prevalence rate of 1.74% (8/461). The full-length spike genes were further cloned from eight clinical samples (five farms in Henan Province). Phylogenetic analysis showed that two different subclades of BToV strains are circulating in China. Meanwhile, the three BToV strains identified from dairy calves, 18,307, 2YY and 5YY, all contained the amino acid variants R614Q, I801T, N841S and Q885E.

Conclusions

This is the first report to confirm the presence of BToV in beef and dairy calves in China with diarrhea, which extend our understanding of the epidemiology of BToVs worldwide.

Genomic characterization of pestiviruses isolated from bovine, ovine and caprine foetuses in Turkey: A potentially new genotype of Pestivirus I species

This study was carried out to investigate the frequency and genetic diversity of pestiviruses in abortion cases in cattle and small ruminants in Turkey. During January 2012 and December 2017, a total of 2029 aborted foetuses (553 bovine foetuses, 1,388 sheep foetuses and 88 goat foetuses) were collected from different regions of Turkey. Real-time RT-PCR (RRT-PCR) assays were used to detect pestiviral RNA in aborted foetuses. To confirm the cause of abortion, pestivirus-positive foetuses were also examined for the presence of Brucella spp., Campylobacter spp., Chlamydophila abortus (C. abortus), akabane virus, bluetongue virus and Schmallenberg virus by molecular detection methods. Pestiviral RNA was detected in 61 (11%) of the 553 bovine foetuses, 124 (8.9%) of the 1,388 sheep foetuses and 3 (3.4%) of the 88 goat foetuses. Furthermore, C. abortus DNA was detected in 3 pestivirus-positive sheep foetuses, whereas other infectious agents were not detected in pestivirus-positive foetuses. Genetic characterization of the pestivirus RRT-PCR positive samples was conducted by sequencing 5' untranslated (5' UTR) and non-structural autoprotease (N^pro ) genomic regions. A total of 68 sequences were obtained, and phylogenetic analyses revealed that all sequences belonged to BVDV-1, including 1b (8/68), 1f (2/68), 1l (4/68), 1r (10/68), Aydin-like pestivirus (20/68) and one unknown genotype (24/68). The 5' UTR and N^pro sequences of this unknown genotype differed from pestiviruses previously described, providing evidence for the presence of an emerging genotype within the species Pestivirus I, tentatively named as 'Konya-like' pestivirus. 'Konya-like' pestivirus was the dominant genotype in sheep foetuses, whereas Aydin-like pestivirus was found to be the predominant genotype in bovine foetuses. To the best my knowledge, this is the first report of Aydin-like pestivirus infection in cattle. The information provided in this study contributes to the understanding the dissemination and evolution of pestiviruses and could be beneficial for developing more effective vaccines.

Genetic Diversity of Bovine Pestiviruses Detected in Backyard Cattle Farms Between 2014 and 2019 in Henan Province, China

Bovine pestiviruses include Pestivirus A (BVDV-1), Pestivirus B (BVDV-2), and Pestivirus H, which was originally called HoBi-like pestivirus. We conducted an epidemiological investigation for pestiviruses circulating in backyard cattle farms in central China. RT-PCR assays and sequences analysis were conducted on 54 nasal swabs, 26 serum samples, and three lung samples from cattle with respiratory infections and identified 29 pestivirus strains, including 24 Pestivirus A and five Pestivirus H strains. Phylogenetic analysis based on partial 5'-UTR and Npro sequences showed that the genotypes of 24 Pestivirus A strains included Pestivirus A 1b (six isolates), Pestivirus A 1m (six isolates), Pestivirus A 1q (two isolates), Pestivirus A 1u (one isolates), and Pestivirus A 1o (nine isolates, a putative new sub-genotype). In addition, a single Pestivirus H agenotype included all five Pestivirus H strains. This study revealed extensive genetic variations within bovine pestivirus isolates derived from cattle in backyard farms in Central China, and this epidemiological information improves our understanding of the epidemics of bovine Pestiviruses, as well as will be useful in designing and evaluating diagnostic methods and developing more effective vaccines.

Prevalence and genetic diversity of bovine viral diarrhea virus in dairy herds of China

To determine the nationwide prevalence and genetic diversity of bovine viral diarrhea virus (BVDV) in China, 92 dairy farms with more than 500 animals in 19 provinces of China were surveyed in 2017. At each farm, ear notch samples from calves less than six months old and bulk tank milk (BTM) samples were collected. A total of 901 ear notch samples and 329 BTM samples from 183 tanks were sampled. A total of 20 (20/901, 2.22 %) ear notch samples from 10 (10/92, 10.86 %) farms tested positive for BVDV by IDEXX Antigen Point-of-Care (POC) Test kit and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). In addition, 80 of 183 (80/183, 43.7 %) BTM samples from 43 (43/92, 46.7 %) farms were identified as positive by qRT-PCR. The RNA of positive and suspect samples identified by qRT-PCR was subjected to 5'- untranslated region (UTR) amplification by nested RT-PCR and then sequenced. A total of 119 sequences were obtained and phylogenetic analysis of these 5'-UTR sequences revealed the presence of eight different subgenotypes of BVDV-1 including 1a (n = 37, 31.09 %), 1b (n = 5, 4.20 %), 1c (n = 34, 28.57 %), 1d (n = 2, 1.68 %), 1m (n = 25, 21.01 %), 1q (n = 6, 5.04 %), and two unknown subgenotypes which were tentatively typed as "BVDV-1v" (n = 8, 6.72 %) and "BVDV-1w" (n = 2, 1.68 %), respectively. BVDV-1a, 1c, and 1m were the dominant strains, collectively accounting for 80.67 % (96/119) of all sequences. Phylogenetic analysis based on selected N-terminal autoprotease (N^pro) sequences confirmed the classification of the 5'-UTR sequences. In conclusion, the prevalence of BVDV persistent infection in dairy cattle was high and genetic diversity was high and increasing, revealing a serious threat to the health of cattle in China and highlighting the need for BVDV control.

Diseases associated with bovine viral diarrhea virus subtypes 1a and 2b in beef and dairy cattle in Uruguay

Bovine viral diarrhea virus (BVDV, Pestivirus) causes significant economic losses to the livestock industry worldwide. Although serological surveys show that BVDV exposure is widespread in cattle in Uruguay, BVDV-associated diseases are greatly underreported. The aim of this work is to describe the epidemiological, clinical, pathological, and virological findings from spontaneous outbreaks of BVDV-associated diseases in cattle in Uruguay. Diagnostic investigations were performed during 6 spontaneous disease outbreaks on beef and dairy cattle farms in the departments of Colonia, Rio Negro, and Soriano between November 2016 and April 2018. Carcasses of 8 naturally deceased cattle from these outbreaks were necropsied and subjected to histological examination and immunohistochemistry to detect BVDV antigen in the tissues. Reverse transcription real-time PCR and genomic sequencing were also performed to identify BVDV at the species and subtype levels. Other ancillary diagnostic tests, including bacterial cultures, were performed on a case-by-case basis to rule in/out differential diagnoses based on initial clinicopathological presumptive diagnoses. BVDV-associated conditions that were diagnosed in the 8 cases included mucosal disease, transient postnatal BVDV infections associated with digestive/septicemic salmonellosis by Salmonella serovar typhimurium, Histophilus somni bronchopneumonia, urinary tract coinfections with Escherichia coli and Streptococcus sp., enteric coinfection with coccidia, and transplacental fetal infections and abortions with Neospora caninum coinfection. BVDV-1a and BVDV-2b were each identified in four of the eight cases. We conclude that BVDV-1a and BVDV-2b contribute significantly to disease and mortality in cattle in Uruguay. Future research should estimate the economic impact of BVDV in the Uruguayan livestock sector.

RNA-Seq based transcriptome analysis during bovine viral diarrhoea virus (BVDV) infection

Background

Bovine viral diarrhoea virus (BVDV) is the member of the genus Pestivirus within the Flaviviridae family and responsible for severe economic losses in the cattle industry. BVDV can employ ‘infect-and-persist’ strategy and ‘hit-and-run’ strategy to remain associated with hosts and thus contributes to BVDV circulation in cattle herds. BVDV have also evolved various strategies to evade the innate immunity of host. To further understand the mechanisms by which BVDV overcomes the host cell innate immune response and provide more clues for further understanding the BVDV-host interaction, in this descriptive study, we conducted a investigation of differentially expressed genes (DEGs) of the host during BVDV infection by RNA-Seq analysis.

Results

Our analysis identified 1297, 1732, 3072, and 1877 DEGs in the comparison groups mock vs. MDBK cells infected with BVDV post 2 h (MBV2h), mock vs. MBV6h, mock vs. MBV12h, and mock vs. MBV24h, respectively. The reproducibility and repeatability of the results were validated by RT-qPCR. Enrichment analyses of GO annotations and KEGG pathways revealed the host DEGs that are potentially induced by BVDV infection and may participate in BVDV-host interactions. Protein-protein interaction (PPI) network analyses identified the potential interactions among the DEGs. Our findings suggested that BVDV infection induced the upregulation of genes involved in lipid metabolism. The expression of genes that have antiviral roles, including ISG15, Mx1, OSA1Y, were found to be downregulated and are thus potentially associated with the inhibition of host innate immune system during BVDV infection. The expression levels of F3, C1R, KNG1, CLU, C3, FB, SERPINA5, SERPINE1, C1S, F2RL2, and C2, which belong to the complement and coagulation signalling cascades, were downregulated during BVDV infection, which suggested that the complement system might play a crucial role during BVDV infection.

Conclusion

In this descriptive study, our findings revealed the changes in the host transcriptome expression profile during BVDV infection and suggested that BVDV-infection induced altering the host’s metabolic network, the inhibition of the expression of antiviral proteins and genes within the complement system might be contributed to BVDV proliferation. The above findings provided unique insights for further studies on the mechanisms underlying BVDV-host interactions.

Genetic analysis of NS5B gene from bovine viral diarrhea virus-infected cattle in Central and East Java, Indonesia

Background and Aim:

A previous study divided Indonesian bovine viral diarrhea virus (BVDV)-1 into subgenotypes BVDV-1a to BVDV-1d based on the partial NS5B gene using strain Bega as reference for BVDV-1a. In fact, it is clustered into BVDV-1c with strain Bega-like Australia. BVDV genotyping has been done on isolates from Jakarta, West and Central Java, but East Java isolates have not been genotyped. This study aimed to analyze genetic variability and amino acid residues in the nucleotide-binding pocket of the NS5B gene from infected cattle.

Materials and Methods:

Samples were obtained from the Sera Bank originating from active and passive surveillance of cattle that had been tested for BVDV antigen from 2013 to 2017. Detection of the p80 antibody and BVDV genotyping was carried out using ELISA and nested-multiplex-polymerase chain reaction (PCR), respectively. We defined 15 nested PCR products for partial sequencing of NS5B. Those field samples were selected from each location and year using proportional calculation as a representative sample. Homological and phylogenetic analyses of the partial NS5B gene were performed using BLAST and MEGA version 6.

Results:

Based on the phylogenetic tree analysis using 360 nucleotides as the partial NS5B gene, Indonesian BVDV-1 isolates from Central and East Java were subdivided to BVDV-1a (n=9), BVDV-1b (n=1), and BVDV-1c (n=5). In the present study, the homology of BVDV subgenotype -1a, -1b, and -1c was compared to the BVDV GenBank data and found 90-93%, 93%, and 92-95% respectively with the average pairwise distance of 0.207. A point mutation was shown at R283K of all BVDV isolates based on the sequence of three amino acid residues R283, R285, and I287 in the nucleotide-binding pocket as a part of the encoded RNA-dependent RNA polymerase.

Conclusion:

This study revealed the genetic variability of BVDV infecting cattle in Central Java and East Java, Indonesia, the subtypes BVDV-1a, BVDV-1b, BVDV-1c, and a point mutation at the R283K residue.

Pathogen spread and globalization: The case of Pestivirus heterogeneity in southern Italy

Pestiviruses are responsible for widespread diseases affecting cattle, pigs and other ruminants, presenting a wide range of clinical manifestations, with significant impact on animal production. Given the recent various reports of a relatively high number of new strains and atypical genomic variants, in the present study, ninety-seven genomic sequences from southern Italy have been evaluated applying the palindromic nucleotide substitutions method, based on 5'-UTR secondary structure alignment and computing genetic distance among strains in the internal ribosome entry site. Sequence analysis revealed a highly heterogeneous virus population, indicating the introduction of virus variants of Bovine viral diarrhea virus and Border disease virus species from foreign countries. The application of different analytical procedures was useful to avoid interpretation difficulties. Circulation of heterogeneous virus populations showed the need for more accurate epidemiological investigations and stringent veterinary controls to protect animal health and welfare.

RNA-Seq-based transcriptomic profiling of primary interstitial cells of Cajal in response to bovine viral diarrhea virus infection

Infections with bovine viral diarrhea virus (BVDV) contribute significantly to health-related economic losses in the beef and dairy industries and are widespread throughout the world. Severe acute BVDV infection is characterized by a gastrointestinal (GI) inflammatory response. The mechanism of inflammatory lesions caused by BVDV remains unknown. The interstitial cells of Cajal (ICC) network plays a pivotal role as a pacemaker in the generation of electrical slow waves for GI motility, and it is crucial for the reception of regulatory inputs from the enteric nervous system. The present study investigated whether ICC were a good model for studying GI inflammatory lesions caused by BVDV infection. Primary ICC were isolated from the duodenum of Merino sheep. The presence of BVDV was detected in ICC grown for five passages after BVDV infection, indicating that BVDV successfully replicated in ICC. After infection with BVDV strain TC, the cell proliferation proceeded slowly or declined. Morphological changes, including swelling, dissolution, and formation of vacuoles in the ICC were observed, indicating quantitative, morphological and functional changes in the cells. RNA sequencing (RNA-Seq) was performed to investigate differentially expressed genes (DEGs) in BVDV-infected ICC and explore the molecular mechanism of underlying quantitative, morphological and functional changes of ICC. Eight hundred six genes were differentially expressed after BVDV infection, of which 538 genes were upregulated and 268 genes were downregulated. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the 806 DEGs were significantly enriched in 27 pathways, including cytokine-cytokine receptor interaction, interleukin (IL)-17 signaling and mitogen-activated protein kinase (MAPK) signaling pathways. The DEGs and raw files of high-throughput sequencing of this study were submitted to the NCBI Gene Expression Omnibus (GEO) database (accession number GSE122344). Finally, 21 DEGs were randomly selected, and the relative repression levels of these genes were tested using the quantitative real-time PCR (qRT-PCR) to validate the RNA-Seq results. The results showed that the related expression levels of 21 DEGs were similar to RNA-Seq. This study is the first to establish a new infection model for investigating GI inflammatory lesions induced by BVDV infection. RNA-Seq-based transcriptomic profiling can provide a basis for study on BVDV-associated inflammatory lesions.

Increased genetic diversity of BVDV strains circulating in Eastern Anatolia, Turkey: first detection of BVDV-3 in Turkey

Bovine viral diarrhea virus (BVDV) is a pathogen associated with loss of meat, milk, and reproductive performance in cattle across the world. There have been two types of BVDV identified worldwide: BVDV-1 and BVDV-2. However, a new type of BVDV, named HoBi-like pestivirus (BVDV-3), has been identified recently. BVDV presence in Turkey has been reported since the 1990s, but a mandatory vaccination program has not been implemented in Turkey so far. In serological studies conducted in Turkey for BVDV, reported seropositivity has been 50% on average. The aim of this study is to determine the genetic diversity of BVDV in blood and abortion materials from bovine in eastern Turkey. The presence of the virus was determined by antigen ELISA test. As a result of the phylogenetic analysis of 5'UTR, Npro and E2 genomic regions of the BVDV (n = 28), BVDV-1 (n = 25) was identified as the dominant type. In addition, BVDV-2 (n = 2) and BVDV-3 (n = 1) were determined which is the first report of HoBi-like pestivirus in Turkey. Although BVDV-1l (n = 19) was detected as the predominant sub-type of BVDV-1, 1a (n = 2), 1b (n = 1), 1c (n = 1), and 1d (n = 2) were also identified. In 2 samples, the BVDV-2 type detected was the 2a sub-type. In this study, it is emphasized that BVDV can be present in the abort materials as an agent and that it should be examined in the herd screening. In addition, it is understood that molecular epidemiological studies should continue for determining the genetic diversity of the viruses and that such studies should be carried out on the country basis. Necessary diagnostic programs should be developed for animals, which are imported or buying from other barns, and protection and control measures should be taken. The increase of reports on BVDV heterogeneity in Turkey and worldwide gets up related to the occurrence and spread of new BVDV types or variants, with potential implications for animal health and disease control.

Bovine viral diarrhea in captive Rocky Mountain bighorn sheep associated with administration of a contaminated modified-live bluetongue virus vaccine

In late summer 2017, we observed acute, fatal cases of bovine viral diarrhea in captive Rocky Mountain bighorn sheep ( Ovis canadensis canadensis) in Colorado following use of a contaminated modified-live bluetongue virus vaccine. Following vaccination, at least 14 of 28 (50%) vaccinated bighorn sheep developed hemorrhagic diarrhea, and 6 of 28 (21%) vaccinated bighorn sheep died. Autopsy findings were predominantly necroulcerative-to-necrohemorrhagic gastrointestinal lesions. Less frequent lesions included suffusive hemorrhages of serosal surfaces of abdominal viscera, and lymphoid necrosis in gut-associated lymphoid tissues. All of the 6 bighorn sheep that died were positive on real-time PCR (rtPCR) for bovine viral diarrhea virus (BVDV) in multiple tissues. Seroconversion to BVDV-1 and immunohistochemistry for BVDV in affected tissues confirmed rtPCR results. Next-generation sequencing confirmed a match between the infecting strain of BVDV-1b and the contaminated vaccine.

Pathological and virological features of skin lesions caused by BVDV in cattle

Dermatitis might occur in mucosal disease (MD) caused by bovine viral diarrhea virus (BVDV). This study describes the pathological and virological features of skin lesions associated with BVDV infection in four persistently infected (PI) cattle. Skin samples were reprocessed for histopathology and IHC. BVDV isolates were obtained and were genetically characterized. In addition to upper alimentary system ulcerative lesions, all cattle (one outbreak and three individual cases) presented focal crusty and ulcerative lesions affecting the mucocutaneous and skin-horn junctions, interdigital clefts, pastern, and areas surrounding the dewclaws and diffuse thickened skin within 7-20 days of infection. Microscopic analysis revealed parakeratotic hyperkeratosis and single-cell keratinocyte death, accompanied by ballooning degeneration and spongiosis in the epidermis, as well as intraepithelial and subcorneal pustules. IHC showed BVDV antigen in the cytoplasm of keratinocytes undergoing individual cell death. Phylogenetic analysis revealed that the isolates from cattle #1, #2, and #4 belonged to BVDV-1a, whereas that from cattle #3 belonged to BVDV-1d. Cytopathic BVDV was isolated from cattle #2 and #3 (MD), and non-cytopathic BVDV was isolated from cattle #1 and #4. Thus, BVDV infection might cause acute disease, characterized by skin and upper alimentary system ulcerative lesions, in both MD and PI cattle.

Prevalence of bovine viral diarrhea virus in dairy cattle herds in eastern China

Bovine viral diarrhea virus (BVDV) is a worldwide spreading pestivirus affecting cattle and other ruminants; however, there have been few reports on epidemiologic investigation of BVDV in eastern China. In this study, bulk tank milk from 36 herds of dairy cattle in eastern China was submitted to serological investigations, 77.8% of herds was BVDV antibody positive. Individual animal status in two herds was further investigated collecting blood samples, the positive ratio was 49.74% and 24.64%, and the average positive ratio of calves, heifers, and lactating cows was 15.94%, 40.16%, and 41.7%, respectively. Moreover, clinical survey was carried out among 8170 dairy cattle from 36 herds, for diarrhea syndrome, respiratory problems and reproductive failure, and pathogens of all clinical cattle were further investigated. The results showed that BVDV was one of the main pathogen, which infected animals combining with various other viruses. Then, nine BVDV strains were isolated; phylogenetic analysis showed that BVDV subtypes currently circulating in eastern China were BVDV 1a and BVDV 1c. In addition, out of 377 cows tested, the 1.86% detected positive to the BVDV antigen. This study provided the foundation of further study on vaccination and control strategies of BVDV in eastern China.

Genetic Diversity of Bovine Viral Diarrhea Virus Infection in Goats in Southwestern China

Bovine viral diarrhea virus (BVDV) affects cows, pigs, sheep, goats, and other ruminants, as well as some wild animals. BVDV causes considerable economic losses every year and many countries have developed programs aimed at the eradication of this disease. The genetic diversity of BVDV in diseased goats has never been described in southwestern China. Thus, in this study, we applied antigen-capture ELISA and RT-PCR to survey the infection rate of BVDV in diseased goats in this region. Our results demonstrated that the average BVDV infection rate in goats was 17.51%, with all positive samples indicating infection by BVDV-1 and not BVDV-2, BVDV-3, or Border disease virus. The molecular characteristics of the 5′-untranslated region (5′-UTR) of BVDV-1 were recognized as belonging predominantly to the BVDV-1a, 1b, 1c, 1m, and 1p subtypes. BVDV-1b and 1m were the most abundant subtypes identified in this region, similar to the BVDV epidemics in cattle in other regions of China. This is the first study that describes the genetic characterization of BVDV in sick goats from southwestern China and is important for future studies and control programs.

Evaluation of the serum virome in calves persistently infected with Pestivirus A, presenting or not presenting mucosal disease

Bovine viral diarrhea virus 1, reclassified as Pestivirus A, causes an economically important cattle disease that is distributed worldwide. Pestivirus A may cause persistent infection in that calves excrete the virus throughout their lives, spreading the infection in the herd. Many persistently infected (PI) calves die in the first 2 years of life from mucosal disease (MD) or secondary infections, probably as a consequence of virus-induced immune depression. Here, high-throughput sequencing (HTS) was applied for evaluation of the total virome in sera of (i) PI calves displaying clinically apparent MD (n = 8); (ii) PI calves with no signs of MD (n = 8); and (iii) control, Pestivirus A-free calves (n = 8). All the groups were collected at the same time and from the same herd. Serum samples from calves in each of the groups were pooled, submitted to viral RNA/DNA enrichment, and sequenced by HTS. Viral genomes of Pestivirus A, Ungulate erythroparvovirus 1, bosavirus (BosV), and hypothetical circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses were identified. Specific real-time PCR assays were developed to determine the frequency of occurrence of such viruses in each of the groups. The absolute number of distinct viral genomes detected in both PI calf groups was higher than in the control group, as revealed by higher number of reads, contigs, and genomes, representing a wider range of taxons. Genomes representing members of the family Parvoviridae, such as U. erythroparvovirus 1 and BosV, were most frequently detected in all the three groups of calves. Only in MD-affected PI calves, we found two previously unreported Hypothetical single-stranded DNA genomes clustered along with CRESS-DNA viruses. These findings reveal that parvoviruses were the most frequently detected viral genomes in cattle serum; its frequency of detection bears no statistical correlation with the status of calves in relation to Pestivirus A infection, since clinically normal or MD-affected/non-affected PI calves were infected with similar U. erythroparvovirus 1 genome loads. Moreover, MD-affected PI calves were shown to support viremia of CRESS-DNA viral genomes; however, the meaning of such correlation remains to be established.

Who's who in the Bovine viral diarrhea virus type 1 species: Genotypes L and R

The bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, with relevant impact on animal production. The species presents high genomic heterogeneity, with implications on control and prophylactic programs. Genomic traits of different genetic groups are often related to geographic origin. Atypical sequences have been reported from Pestivirus isolates originated from cattle in Turkey. Based on phylogenetic analysis of 5' untranslated region and Npro and secondary structure analysis of the 5'-UTR RNA, Turkish isolates have been segregated in two distinct genotypes. Out of the twenty-three identified BVDV-1 genotypes, the Turkish clusters, named L and R or 1.16 and 1.14, according to palindromic nucleotide substitution genotyping method, represent genomic clusters so far, not described elsewhere, suggesting geographic segregation. In order to avoid confusion in the current taxonomy of the species, nomenclature of described homonymous genotypes, referred to different genomic clusters, should be corrected.

Characterization of fungus microbial diversity in healthy and diarrheal yaks in Gannan region of Tibet Autonomous Prefecture

Diarrhea is a serious epidemic in yaks on Qinghai Tibet plateau, but the exact pathogen is not confirmed. Diarrhea is related to the changes in diversity of intestinal flora. The current study herein is performed for high-throughput sequencing of fungus microbial diversity in healthy adult yaks, diarrheal adult yaks and diarrheal yak calves in Gannan Tibetan Autonomous Prefecture. A total 446726 optimized sequences were achieved. Over 250 OTUs in species level have been indentified for each sample. The Shannon and Simpson index revealed that there was no visible difference in the flora between different yak groups (p > 0.05). However, obvious difference was watched in the principal component of microbial community structure in different yak groups by PCA analysis, especially between healthy adult yak group and diarrheal adult yak groups. There were 248 fungus species shared in three groups. Interestingly, there were 97 fungus species shared in the diarrheal groups (calves and adult yaks), which were not found in the healthy yaks, while there were 212 fungus species only found in the healthy yaks. In the Phylum level, 1 phylum (Neocallimastigomycota) was discovered to have significant difference between healthy yaks and diarrheal yak calves (p < 0.05). In the genus level, 23 genus were found obvious difference between healthy adult yaks and diarrheal adults yaks (p < 0.05); 28 genus were found significant difference between healthy adult yaks and diarrheal yak calves (p < 0.05); 23 genus were found obvious difference between diarrheal adult yaks and diarrheal yak calves (p < 0.05). The present study herein first reported an insight of the change of microbial diversity of fungus in diarrhea yaks at altitude regions, which contributed towards the solid prevention of diarrhea in yaks.

Control of Bovine Viral Diarrhea

Bovine viral diarrhea (BVD) is one of the most important infectious diseases of cattle with respect to animal health and economic impact. Its stealthy nature, prolonged transient infections, and the presence of persistently infected (PI) animals as efficient reservoirs were responsible for its ubiquitous presence in cattle populations worldwide. Whereas it was initially thought that the infection was impossible to control, effective systematic control strategies have emerged over the last 25 years. The common denominators of all successful control programs were systematic control, removal of PI animals, movement controls for infected herds, strict biosecurity, and surveillance. Scandinavian countries, Austria, and Switzerland successfully implemented these control programs without using vaccination. Vaccination as an optional and additional control tool was used by e.g., Germany, Belgium, Ireland, and Scotland. The economic benefits of BVD control programs had been assessed in different studies.

Bovine viral diarrhea virus type 1 current taxonomy according to palindromic nucleotide substitutions method

Pestivirus bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, presenting a wide range of clinical manifestations, with relevant impact on zootechnic production. Understanding genomic characteristic and virus taxonomy is fundamental in order to sustain control and prophylactic programs. Given the recent various studies reporting a relatively high number of new strains, in particular from Asian countries, in the present study, four hundred-eighty-two genomic sequences have been evaluated applying the palindromic nucleotide substitutions method for genotyping. Based on the secondary structure alignment and computing genetic distance among strains in the 5' untranslated region of Pestivirus RNA, the current taxonomy of the species was reviewed. Twenty-two genotypes have been identified, applying a nomenclature based on divergence in the genus.

Seroprevalence and risk factors for selected respiratory and reproductive tract pathogen exposure in European bison (Bison bonasus) in Poland

After the complete extinction from the wild of European bison (Bison bonasus) at the beginning of the twentieth century, the worldwide species population was restored to approximately 5500 individuals, with the species however remaining endangered. Despite numerous studies on the ecology and genetics of European bison, the threats of infectious diseases have been largely unexamined. The aim of this study was to screen the exposure of the world's largest population of European bison to the pathogens, which may influence the condition and development of the endangered species. A total of 240 free-ranging and captive European bison from eight main Polish populations sampled were tested for the presence of specific antibodies against ten different viruses, bacteria or protozoan. The samples were collected from chemically immobilized, selectively culled or found dead animals. Based on serology, the exposure to bovine viral diarrhea virus (BVDV), bovine herpesvirus type 1 (BoHV-1), Mycoplasma and Brucella spp. was determined as rather accidental. Using gamma-interferon assay followed by Mycobacterium tuberculosis subs. caprae detection in tissues, diagnosis of bovine tuberculosis was made for 6 out of 78 (7.7%) bison from one captive herd. The highest seroprevalence was found for bovine adenovirus type 3 (BAdV-3) -60.2% and bovine parainfluenza type 3 (PIV-3) -34.0%, while the antibodies against bovine respiratory syncytial virus (BRSV), Toxoplasma gondii and Leptospira spp. were found in 10.4%, 10.4% and 8.7% of samples, respectively. In the multivariable statistical analysis using generalized linear mixed models (GLMMS), the risk factors for PIV-3 seropositivity included population type (free-living/captive), age and health status (apparently healthy/eliminated due to the poor condition). Higher risk of BAdV-3 seropositive result was observed in free-living female European bison. The high BAdV-3 and PIV-3 seroprevalences may suggest involvement of these pathogens in the most frequently observed respiratory disorders in European bison. Moreover, this is the first study demonstrating BAdV-3 exposure in the species.

ANTIVIRAL COMPOUNDS AND PREPARATIONS EFFECTIVE AGAINST BOVINE VIRAL DIARRHEA

Bovine viral diarrhea virus (BVDV) belongs to the genus Pestivirus, family Flaviviridae. It causes various clinical forms of infection leading to significant economic losses in beef and dairy industry worldwide. Furthermore, the virus is a contaminant of biological preparations (bovine fetal serum, continuous cell cultures, vaccines for human and veterinary medicine, interferons, trypsin, biotechnological preparations, embryos, stem cells, etc.). It is used as a test object when developing methods of decontamination. In some countries, a tool for monitoring the infection caused by the virus is vaccination based on the use of live and inactivated vaccines with varying efficiency. The antiviral compounds are a potential means of control in case of insufficient efficacy of vaccines. Their advantage for BVDV control is the ability to provide immediate protection for animals at risk in the case of an outbreak of the disease. This review summarizes the current state of knowledge about antiviral compounds against BVDV. It was noted that due to the use of advanced biomedical technologies there is a tendency to search for drugs that might be effective for antiviral therapy of BVDV, as indicated by numerous studies of new compounds and the antiviral efficacy of known drugs used in medical practice. In addition to the well-known antiviral targets for the virus, such as the RdRp, IMPDH, NS3, new targets were discovered, such as protein p7. Its mechanism of action remains to be explored. It can be concluded that there is a great potential for BVDV control through the use of antiviral drugs which has not yet implemented. The biggest obstacle for commercial implementation of identified compounds is the lack of demonstration of their efficacy in vivo. Further studies should be performed to develop a method for administering effective drugs to groups of animals.

Characterization of Two Bovine viral diarrhea virus Strains Originating from Cattle in Tibet, China

Here, we report two strains of Bovine viral diarrhea virus (BVDV), named XZ01 and XZ02, that were isolated from cattle in Tibet, China. They belong to subgenotype 1b. This report will help in understanding the molecular characteristics of BVDV in Tibetan cattle.

Variability and Global Distribution of Subgenotypes of Bovine Viral Diarrhea Virus

Bovine viral diarrhea virus (BVDV) is a globally-distributed agent responsible for numerous clinical syndromes that lead to major economic losses. Two species, BVDV-1 and BVDV-2, discriminated on the basis of genetic and antigenic differences, are classified in the genus Pestivirus within the Flaviviridae family and distributed on all of the continents. BVDV-1 can be segregated into at least twenty-one subgenotypes (1a–1u), while four subgenotypes have been described for BVDV-2 (2a–2d). With respect to published sequences, the number of virus isolates described for BVDV-1 (88.2%) is considerably higher than for BVDV-2 (11.8%). The most frequently-reported BVDV-1 subgenotype are 1b, followed by 1a and 1c. The highest number of various BVDV subgenotypes has been documented in European countries, indicating greater genetic diversity of the virus on this continent. Current segregation of BVDV field isolates and the designation of subgenotypes are not harmonized. While the species BVDV-1 and BVDV-2 can be clearly differentiated independently from the portion of the genome being compared, analysis of different genomic regions can result in inconsistent assignment of some BVDV isolates to defined subgenotypes. To avoid non-conformities the authors recommend the development of a harmonized system for subdivision of BVDV isolates into defined subgenotypes.

Complete Genome Sequence of a Bovine Viral Diarrhea Virus Subgenotype 1h Strain Isolated in Italy

We sequenced the complete genome of bovine viral diarrhea virus (BVDV) strain UM/126/07. It belongs to subgenotype 1h. The complete genome is composed of 12,196 nucleotides organized as one open reading frame encoding 3,898 amino acids. This is the first report of a full-length sequence of BVDV-1h.

Genome Sequence of a Subgenotype 1a Bovine Viral Diarrhea Virus in China

A bovine viral diarrhea virus (BVDV), GS5, of the BVDV-1a subgenotype was isolated from dairy cattle in Gansu Province, northwest China. Its near-full-length genome was determined to be closely related to an early Belgian BVDV-1a strain, WAX-N, but the relatedness to domestic strains is relatively low, indicating that different genetic evolution occurred between the viral strains in cattle in China.