Integrative Transcriptomics and Proteomics Analysis Provide a Deep Insight Into Bovine Viral Diarrhea Virus-Host Interactions During BVDV Infection

Development and validation of a 5K low-density SNP chip for Hainan cattle

BACKGROUND

This study aimed to design and develop a 5K low-density liquid chip for Hainan cattle utilizing targeted capture sequencing technology. The chip incorporates a substantial number of functional single nucleotide polymorphism (SNP) loci derived from public literature, including SNP loci significantly associated with immunity, heat stress, meat quality, reproduction, and other traits. Additionally, SNPs located in the coding regions of immune-related genes from the Bovine Genome Variation Database (BGVD) and Hainan cattle-specific SNP loci were included.

RESULTS

A total of 5,293 SNPs were selected, resulting in 9,837 DNA probes with a coverage rate of 85.69%, thereby creating a Hainan cattle-specific 5K Genotyping by Target Sequencing (GBTS) liquid chip. Evaluation with 152 cattle samples demonstrated excellent clustering performance and a detection rate ranging from 96.60 to 99.07%, with 94.5% of SNP sites exhibiting polymorphism. The chip achieved 100% gender coverage and displayed a heterozygosity rate between 14.20% and 29.65%, with a repeatability rate of 99.65-99.85%. Analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed the potential regulatory roles of exonic SNPs in immune response pathways.

CONCLUSION

The development and validation of the 5K GBTS liquid chip for Hainan cattle represent a valuable tool for genome analysis and genetic diversity assessment. Furthermore, it facilitates breed identification, gender determination, and kinship analysis, providing a foundation for the efficient utilization and development of local cattle genetic resources.

Construction of an IFNAR1 knockout MDBK cell line using CRISPR/Cas9 and its effect on bovine virus replication

The type I interferon (IFN) pathway is important for eukaryotic cells to resist viral infection, as well as an impediment to efficient virus replication. Therefore, this study aims to create an IFNAR1 knockout (KO) Madin-Darby bovine kidney (MDBK) cell line using CRISPR/Cas9 and investigate its application and potential mechanism in increasing viral replication of bovines. The IFNAR1 KO cells showed increased titers of bovine viral diarrhea virus (BVDV) (1.5 log10), with bovine enterovirus and bovine parainfluenza virus type 3 (0.5-0.8 log10). RNA-seq revealed reduced expression of the genes related IFN-I pathways including IFNAR1, STAT3, IRF9, and SOCS3 in IFNAR1 KO cells compared with WT cells. In WT cells, 306 differentially expressed genes (DEGs) were identified between BVDV-infected and -uninfected cells. Of these, 128 up- and 178 down-regulated genes were mainly associated with growth cycle and biosynthesis, respectively. In IFNAR1 KO cells, 286 DEGs were identified, with 82 up-regulated genes were associated with signaling pathways, and 204 down-regulated genes. Further, 92 DEGs were overlapped between WT and IFNAR1 KO cells including ESM1, IL13RA2, and SLC25A34. Unique DEGs in WT cells were related to inflammation and immune regulation, whereas those unique in IFNAR1 KO cells involved in cell cycle regulation through pathways such as MAPK. Knocking down SLC25A34 and IL13RA2 in IFNAR1 KO cells increased BVDV replication by 0.3 log10 and 0.4 log10, respectively. Additionally, we constructed an IFNAR1/IFNAR2 double-knockout MDBK cell line, which further increased BVDV viral titers compared with IFNAR1 KO cells (0.6 log10). Overall, the IFNAR1 KO MDBK cell line can support better replication of bovine viruses and therefore provides a valuable tool for bovine virus research on viral pathogenesis and host innate immune response.

Genetic analyses of the structural protein E2 bovine viral diarrhea virus isolated from dairy cattle in Yogyakarta, Indonesia

Background and Aim

Bovine viral diarrhea (BVD), a highly pathogenic ribonucleic acid (RNA) virus, causes devastating financial losses and reproductive deaths among dairy cattle in Yogyakarta and globally. This study aimed to identify point mutations within the E2 structural protein of the acquired BVD virus (BVDV) isolates using genetic analysis.

Materials and Methods

The study period shows that we performed the research in 2023. We collected 118 serum samples from 2019 to 2023, among which only 10 BVDV positive were used and 108 were negative lacking the BVDV antigen. An anti-Erns monoclonal antibody-coated protein was used in indirect antigen capture enzyme-linked immunosorbent assay (I-ACE) to detect the BVD antigen present in positive BVDV serum specimens. In the initial step of the two-step reverse transcription polymerase chain reaction, the enzyme (superscript III reverse transcriptase) and the primer (random hexamer) were used to convert the RNA of the BVDV into complementary deoxyribonucleic acid (cDNA) during the process of reverse transcription. The final step involved the amplification of the E2 gene of the resultant BVDV cDNA through gene-specific primers (E2_fwd: 5'-TGGTGGCCTTATGAGAC-3' and P7_rev: 5'-CCCATCATCACTATTTCACC-3') and enzyme (platinum taq DNA polymerase high fidelity). For conducting Sanger sequencing, those 3 BVDV-1-positive isolates (about 2.6% of all isolates) were selected as a typical specimen for each site and year between 2019 and 2023 using a proportional computation. Therefore, only two BVDV isolates with complete genomes were chosen to perform their homological and genetic analysis based on the E2 gene by means of Blast and MEGA Version 11 in addition to the Bioedit 7.2.5 program.

Results

By applying phylogenetic analysis relying on the E2 gene, a sum of 1011 nucleotides of the BVDV-1 isolates derived from each of the two BVDV-1 Indonesian isolates (n = 2) and its 23 reference BVDV strains were acquired from the National Center for Biotechnology Information (NCBI) database. The findings of the genetic analysis inside the phylogenetic tree revealed that the two BVDV Indonesian isolates were clustered into BVDV-1a subgenotype, while the reference BVDV strains were clustered into the five BVDV subgenotype, BVDV-1a (n = 6), BVDV-1b (n = 3), BVDV-1c (n = 11), BVDV-1m (n = 1), and BVDV-1n (n = 2). The branch exists in phylogenetic tree located before the division of our two BVDV isolates was divided into two branches with the same maximum bootstrap values of 99%, indicating a high degree of confidence, was seen. Next, we observed the branch near our study samples, which displayed the bootstrap value of 100, indicating that our 02 isolates were identical. In both isolates, V11 BVDV1/Indonesia/Yogyakarta/2023 and V16 BVDV1/Indonesia/Yogyakarta/2023 with GenBank accession numbers PP836388 and PP836389, respectively, conserved D7E residues were mutated as well as cysteine changed/altered into serine (S) was identified at amino acid position 201.

Conclusion

We identified two isolates of BVDV belonging to the BVDV-1a subgenotype. Our findings indicate that the conserved D7E residues of isolates V11 BVDV1/Indonesia/Yogyakarta/2023 and V16 BVDV1/Indonesia/Yogyakarta/2023 were altered. The Indonesian BVDV isolates exhibited a cysteine to serine mutation at amino acid position 201, leads to vaccination failure, range of animal's host will increase, and diagnostic kit will not be effective.

Integrated multi-omics analysis reveals liver metabolic reprogramming by fish iridovirus and antiviral function of alpha-linolenic acid

Iridovirus poses a substantial threat to global aquaculture due to its high mortality rate; however, the molecular mechanisms underpinning its pathogenesis are not well elucidated. Here, a multi-omics approach was applied to groupers infected with Singapore grouper iridovirus (SGIV), focusing on the roles of key metabolites. Results showed that SGIV induced obvious histopathological damage and changes in metabolic enzymes within the liver. Furthermore, SGIV significantly reduced the contents of lipid droplets, triglycerides, cholesterol, and lipoproteins. Metabolomic analysis indicated that the altered metabolites were enriched in 19 pathways, with a notable down-regulation of lipid metabolites such as glycerophosphates and alpha-linolenic acid (ALA), consistent with disturbed lipid homeostasis in the liver. Integration of transcriptomic and metabolomic data revealed that the top enriched pathways were related to cell growth and death and nucleotide, carbohydrate, amino acid, and lipid metabolism, supporting the conclusion that SGIV infection induced liver metabolic reprogramming. Further integrative transcriptomic and proteomic analysis indicated that SGIV infection activated crucial molecular events in a phagosome-immune depression-metabolism dysregulation-necrosis signaling cascade. Of note, integrative multi-omics analysis demonstrated the consumption of ALA and linoleic acid (LA) metabolites, and the accumulation of L-glutamic acid (GA), accompanied by alterations in immune, inflammation, and cell death-related genes. Further experimental data showed that ALA, but not GA, suppressed SGIV replication by activating antioxidant and anti-inflammatory responses in the host. Collectively, these findings provide a comprehensive resource for understanding host response dynamics during fish iridovirus infection and highlight the antiviral potential of ALA in the prevention and treatment of iridoviral diseases.

Integrative Transcriptomics and Proteomics Analysis Reveals Immune Response Process in Bovine Viral Diarrhea Virus-1-Infected Peripheral Blood Mononuclear Cells

Bovine viral diarrhea virus (BVDV) causes bovine viral diarrhea-mucosal disease, inflicting substantial economic losses upon the global cattle industry. Peripheral blood mononuclear cells (PBMCs) are the central hub for immune responses during host-virus infection and have been recognized as crucial targets for BVDV infection. In order to elucidate the dynamics of host-BVDV-1 interaction, this study harnessed RNA-seq and iTRAQ methods to acquire an extensive dataset of transcriptomics and proteomics data from samples of BVDV-1-infected PBMCs at the 12-h post-infection mark. When compared to mock-infected PBMCs, we identified 344 differentially expressed genes (DEGs: a total of 234 genes with downregulated expression and 110 genes with upregulated expression) and 446 differentially expressed proteins (DEPs: a total of 224 proteins with downregulated expression and 222 proteins with upregulated expression). Selected DEGs and DEPs were validated through quantitative reverse transcriptase-polymerase chain reaction and parallel reaction monitoring. Gene ontology annotation and KEGG enrichment analysis underscored the significant enrichment of DEGs and DEPs in various immunity-related signaling pathways, including antigen processing and presentation, complement and coagulation cascades, cytokine-cytokine receptor interaction, and the NOD-like receptor signaling pathway, among others. Further analysis unveiled that those DEGs and DEPs with downregulated expression were predominantly associated with pathways such as complement and coagulation cascades, the interleukin-17 signaling pathway, cytokine-cytokine receptor interaction, the PI3K-Akt signaling pathway, the tumor necrosis factor signaling pathway, and the NOD-like receptor signaling pathway. Conversely, upregulated DEGs and DEPs were chiefly linked to metabolic pathways, oxidative phosphorylation, complement and coagulation cascades, and the RIG-I-like receptor signaling pathway. These altered genes and proteins shed light on the intense host-virus conflict within the immune realm. Our transcriptomics and proteomics data constitute a significant foundation for delving further into the interaction mechanism between BVDV and its host.

Pestiviruses infection: Interferon-virus mutual regulation

Pestiviruses are a class of viruses that in some cases can cause persistent infection of the host, thus posing a threat to the livestock industry. Interferons (IFNs) are a group of secreted proteins that play a crucial role in antiviral defense. In this review, on the one hand, we elaborate on how pestiviruses are recognized by the host retinoic acid-inducible gene-I (RIG-I), melanoma-differentiation-associated protein 5 (MDA5), and Toll-like receptor 3 (TLR3) proteins to induce the synthesis of IFNs. On the other hand, we focus on reviewing how pestiviruses antagonize the production of IFNs utilizing various strategies mediated by self-encoded proteins, such as the structural envelope protein (E^rns) and non-structural protein (N^pro). Hence, the IFN signal transduction pathway induced by pestiviruses infection and the process of pestiviruses blockade on the production of IFNs intertwines into an intricate regulatory network. By reviewing the interaction between IFN and pestiviruses (based on studies on BVDV and CSFV), we expect to provide a theoretical basis and reference for a better understanding of the mechanisms of induction and evasion of the innate immune response during infection with these viruses.

Augmentation of 3β-hydroxysteroid-Δ24 Reductase (DHCR24) Expression Induced by Bovine Viral Diarrhea Virus Infection Facilitates Viral Replication via Promoting Cholesterol Synthesis

Bovine viral diarrhea virus (BVDV) is the etiologic agent of bovine viral diarrhea-mucosal disease, one of the most important viral diseases of cattle, leading to numerous losses to the cattle rearing industry worldwide. The pathogenicity of BVDV is extremely complex, and many underlying mechanisms involved in BVDV-host interactions are poorly understood, especially how BVDV utilizes host metabolism pathway for efficient viral replication and spread. In our previous study, using an integrative analysis of transcriptomics and proteomics, we found that DHCR24 (3β-hydroxysteroid-Δ24 reductase), a key enzyme in regulating cholesterol synthesis, was significantly upregulated at both gene and protein levels in the BVDV-infected bovine cells, indicating that cholesterol is important for BVDV replication. In the present study, the effects of DHCR24-mediated cholesterol synthesis on BVDV replication was explored. Our results showed that overexpression of the DHCR24 effectively promoted cholesterol synthesis, as well as BVDV replication, while acute cholesterol depletion in the bovine cells by treating cells with methyl-β-cyclodextrin (MβCD) obviously inhibited BVDV replication. In addition, knockdown of DHCR24 (gene silencing with siRNA targeting DHCR24, siDHCR24) or chemical inhibition (treating bovine cells with U18666A, an inhibitor of DHCR24 activity and cholesterol synthesis) significantly suppressed BVDV replication, whereas supplementation with exogenous cholesterol to the siDHCR24-transfected or U18666A-treated bovine cells remarkably restored viral replication. We further confirmed that BVDV nonstructural protein NS5A contributed to the augmentation of DHCR24 expression. Conclusively, augmentation of the DHCR24 induced by BVDV infection plays an important role in BVDV replication via promoting cholesterol production. IMPORTANCE Bovine viral diarrhea virus (BVDV), an important pathogen of cattle, is the causative agent of bovine viral diarrhea-mucosal disease, which causes extensive economic losses in both cow- and beef-rearing industry worldwide. The molecular interactions between BVDV and its host are extremely complex. In our previous study, we found that an essential host factor 3β-hydroxysteroid-δ24 reductase (DHCR24), a key enzyme involved in cholesterol synthesis, was significantly upregulated at both gene and protein levels in BVDV-infected bovine cells. Here, we experimentally explored the function of the DHCR24-mediated cholesterol synthesis in regulating BVDV replication. We elucidated that the augmentation of the DHCR24 induced by BVDV infection played a significant role in viral replication via promoting cholesterol synthesis. Our data provide evidence that BVDV utilizes a host metabolism pathway to facilitate its replication and spread.

Identification of key proteins of cytopathic biotype bovine viral diarrhoea virus involved in activating NF-κB pathway in BVDV-induced inflammatory response

Bovine viral diarrhoea virus (BVDV) is the etiologic agent of bovine viral diarrhea-mucosal disease, one of the most important viral diseases in cattle, with inflammatory diarrhea, enteritis, and mucosa necrosis as the major clinical manifestations. NF-κB is an important transcription complex that regulates the expression of genes involved in inflammation and immune responses. NLRP3 inflammasome plays a key role in the development of inflammatory diseases. However, whether the activation of NF-κB is crucial for BVDV infection-induced inflammatory responses remains unclear. The results of our present study showed that BVDV infection significantly activated the NF-κB pathway and promoted the expression of NLRP3 inflammasome components (NLRP3, ASC, pro-caspase 1) as well inflammatory cytokine pro-IL-1β in BVDV-infected bovine cells, resulting in the cleavage of pro-caspase 1 and pro-IL-1β into active form caspase 1 and IL-1β. However, the levels of the NLRP3 inflammasome components and inflammatory cytokines were obviously inhibited, as well the cleavage of pro-caspase 1 and pro-IL-1β in the pre-treated bovine cells with NF-κB-specific inhibitors after BVDV infection. Further, cytopathic biotype BVDV (cpBVDV) Erns and NS5A proteins with their key functional domains contributed to BVDV-induced inflammatory responses via activating the NF-κB pathway were confirmed experimentally. Especially, the NS5A can promote cholesterol synthesis and accelerate its augmentation, further activating the NF-κB signalling pathway. Conclusively, our data elucidate that the activation of NF-κB signaling pathway plays a crucial role in cpBVDV infection-induced inflammatory responses.

Downregulation of the Long Noncoding RNA IALNCR Targeting MAPK8/JNK1 Promotes Apoptosis and Antagonizes Bovine Viral Diarrhea Virus Replication in Host Cells

Bovine viral diarrhea virus (BVDV) is the causative agent of the bovine viral diarrhea-mucosal disease, which is a leading cause of economic losses in the cattle industry worldwide. To date, many underlying mechanisms involved in BVDV-host interactions remain unclear, especially the functions of long noncoding RNAs (lncRNAs). In our previous study, the lncRNA expression profiles of BVDV-infected Madin-Darby bovine kidney (MDBK) cells were obtained by RNA-seq, and a significantly downregulated lncRNA IALNCR targeting MAPK8/JNK1 (a key regulatory factor of apoptosis) was identified through the lncRNA-mRNA coexpression network analysis. In this study, the function of IALNCR in regulating apoptosis to affect BVDV replication was further explored. Our results showed that BVDV infection-induced downregulation of the lncRNA IALNCR in the host cells could suppress the expression of MAPK8/JNK1 at both the mRNA and protein levels, thereby indirectly promoting the activation of caspase-3, leading to cell-autonomous apoptosis to antagonize BVDV replication. This was further confirmed by the small interfering RNA (siRNA)-mediated knockdown of the lncRNA IALNCR. However, the overexpression of the lncRNA IALNCR inhibited apoptosis and promoted BVDV replication. In conclusion, our findings demonstrated that the lncRNA IALNCR plays an important role in regulating host antiviral innate immunity against BVDV infection. IMPORTANCE Bovine viral diarrhea-mucosal disease caused by BVDV is an important viral disease in cattle, causing severe economic losses to the cattle industry worldwide. The molecular mechanisms of BVDV-host interactions are complex. To date, most studies focused only on how BVDV escapes host innate immunity. By contrast, how the host cell regulates anti-BVDV innate immune responses is rarely reported. In this study, a significantly downregulated lncRNA, with a potential function of inhibiting apoptosis (inhibiting apoptosis long noncoding RNA, IALNCR), was obtained from the lncRNA expression profiles of BVDV-infected cells and was experimentally evaluated for its function in regulating apoptosis and affecting BVDV replication. We demonstrated that downregulation of BVDV infection-induced lncRNA IALNCR displayed antiviral function by positively regulating the MAPK8/JNK1 pathway to promote cell apoptosis. Our data provided evidence that host lncRNAs regulate the innate immune response to BVDV infection.

Non-structural proteins of bovine viral diarrhea virus

Bovine viral diarrhea virus (BVDV) belongs to the family Flaviviridae genus pestivirus. The viral genome is a single-stranded, positive-sense RNA that encodes four structural proteins (i.e., C, Erns, E1, and E2) and eight non-structural proteins (NSPs) (i.e., Npro, p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B). Cattle infected with BVDV exhibit a number of different clinical signs including diarrhea, abortion, and other reproductive disorders which have a serious impact on the cattle industry worldwide. Research on BVDV mainly focuses on its structural protein, however, progress in understanding the functions of the NSPs of BVDV has also been made in recent decades. The knowledge gained on the BVDV non-structural proteins is helpful to more fully understand the viral replication process and the molecular mechanism of viral persistent infection. This review focuses on the functions of BVDV NSPs and provides references for the identification of BVDV, the diagnosis and prevention of Bovine viral diarrhea mucosal disease (BVD-MD), and the development of vaccines.