Viruses in Bovine Respiratory Disease in North America: Knowledge Advances Using Genomic Testing

IDV Typer: An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution

Influenza D virus (IDV) is the most recent addition to the Orthomyxoviridae family and cattle serve as the primary reservoir. IDV has been implicated in Bovine Respiratory Disease Complex (BRDC), and there is serological evidence of human infection of IDV. Evolutionary changes in the IDV genome have resulted in the expansion of genetic diversity and the emergence of multiple lineages that might expand the host tropism and potentially increase the pathogenicity to animals and humans. Therefore, there is an urgent need for automated, accurate and rapid typing tools for IDV lineage typing. Currently, IDV lineage typing is carried out using BLAST-based searches and alignment-based molecular phylogeny of the hemagglutinin-esterase fusion (HEF) gene sequences, and lineage is assigned to query sequences based on sequence similarity (BLAST search) and proximity to the reference lineages in the tree topology, respectively. To minimize human intervention and lineage typing time, we developed IDV Typer server, implementing alignment-free method based on return time distribution (RTD) of k-mers. Lineages are assigned using HEF gene sequences. The server performs with 100% sensitivity and specificity. The IDV Typer server is the first application of an RTD-based alignment-free method for typing animal viruses.

Proteomic and Lipidomic Profiling of Calves Experimentally Co-Infected with Influenza D Virus and Mycoplasma bovis: Insights into the Host-Pathogen Interactions

The role of Influenza D virus (IDV) in bovine respiratory disease remains unclear. An in vivo experiment resulted in increased clinical signs, lesions, and pathogen replication in calves co-infected with IDV and Mycoplasma bovis (M. bovis), compared to single-infected calves. The present study aimed to elucidate the host-pathogen interactions and profile the kinetics of lipid mediators in the airways of these calves. Bronchoalveolar lavage (BAL) samples collected at 2 days post-infection (dpi) were used for proteomic analyses by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Additionally, lipidomic analyses were performed by LC-MS/MS on BAL samples collected at 2, 7 and 14 dpi. Whereas M. bovis induced the expression of proteins involved in fibrin formation, IDV co-infection counteracted this coagulation mechanism and downregulated other acute-phase response proteins, such as complement component 4 (C4) and plasminogen (PLG). The reduced inflammatory response against M. bovis likely resulted in increased M. bovis replication and delayed M. bovis clearance, which led to a significantly increased abundance of oxylipids in co-infected calves. The identified induced oxylipids mainly derived from arachidonic acid; were likely oxidized by COX-1, COX-2, and LOX-5; and peaked at 7 dpi. This paper presents the first characterization of BAL proteome and lipid mediator kinetics in response to IDV and M. bovis infection in cattle and raises hypotheses regarding how IDV acts as a co-pathogen in bovine respiratory disease.

Immune Responses to Influenza D Virus in Calves Previously Infected with Bovine Viral Diarrhea Virus 2

Bovine viral diarrhea virus (BVDV) induces immunosuppression and thymus depletion in calves. This study explores the impact of prior BVDV-2 exposure on the subsequent immune response to influenza D virus (IDV). Twenty 3-week-old calves were divided into four groups. Calves in G1 and G3 were mock-treated on day 0, while calves in G2 and G4 received BVDV. Calves in G1 (mock) and G2 (BVDV) were necropsied on day 13 post-infection. IDV was inoculated on day 21 in G3 calves (mock + IDV) and G4 (BVDV + IDV) and necropsy was conducted on day 42. Pre-exposed BVDV calves exhibited prolonged and increased IDV shedding in nasal secretions. An approximate 50% reduction in the thymus was observed in acutely infected BVDV calves (G2) compared to controls (G1). On day 42, thymus depletion was observed in two calves in G4, while three had normal weight. BVDV-2-exposed calves had impaired CD8 T cell proliferation after IDV recall stimulation, and the α/β T cell impairment was particularly evident in those with persistent thymic atrophy. Conversely, no difference in antibody levels against IDV was noted. BVDV-induced thymus depletion varied from transient to persistent. Persistent thymus atrophy was correlated with weaker T cell proliferation, suggesting correlation between persistent thymus atrophy and impaired T cell immune response to subsequent infections.

Total and pathogen-specific serum Immunoglobulin G concentrations in neonatal beef calves, Part 1: Risk factors

Maternal antibodies, delivered to the calf via colostrum, are crucial to prevent calfhood diseases and death. However, knowledge regarding the factors influencing this transfer of total and specific Immunoglobulin G (IgG) against common enteric and respiratory disease pathogens under current production conditions is sparse. The objectives of this study were to determine risk factors influencing total and pathogen-specific immunoglobulin G (IgG) concentrations against Escherichia coli (E. coli), bovine Rotavirus (BRoV), Cryptosporidium parvum (C. parvum), Bovine Viral Diarrhea Virus type 1 and 2 (BVDV), Parainfluenza Virus Type 3 (PI-3), Bovine Respiratory Syncytial Virus (BRSV), and Bovine Herpesvirus type 1 (BHV-1) in the serum of newborn beef calves. A total of 420 serum samples were collected from 1- to 7-day-old beef calves born on 6 farms in Alberta, Canada. Samples were analyzed by radial immunodiffusion for total IgG concentration and by enzyme-linked immunosorbent assays for pathogen-specific IgG concentrations against E. coli, BRoV, C. parvum, BVDV, PI-3, BRSV, and BHV-1. Multivariable multilevel linear and logistic regression models were built to evaluate dam- and calf-level risk factors associated with total and pathogen-specific IgG concentrations, failed transfer of passive immunity (FTPI; serum IgG < 10 g/L), and inadequate transfer of passive immunity (ITPI; serum IgG < 24 g/L). Farm was included as a random effect in all models to account for clustering at the herd level. Of the 420 calves included in this study, 5% (n = 20) and 18% (n = 75) of calves had FTPI and ITPI, respectively. Receiving colostrum intervention (i.e., being fed colostrum or colostrum product by either bottle or tube) was the most consistent risk factor for low total IgG concentration and significantly increased the odds of FTPI (Odds ratio (OR): 6.1, 95% CI: 2.0-18.9) and ITPI (OR: 4.8, 95% CI: 2.1-10.8). Calves born to cows consistently had higher pathogen-specific IgG concentrations (P < 0.0001), compared to calves born from heifers, and calves born to vaccinated dams had significantly higher BRoV, BVDV, and BHV-1-specific IgG concentrations. Interestingly, E.coli-specific IgG concentrations were associated with dam vaccination only in cows but not in heifers, which was likely due to differing vaccination strategies used. This study highlights the need to review and refine protocols with respect to dam vaccination and colostrum intervention on cow-calf operations.

Detection of Influenza D-Specific Antibodies in Bulk Tank Milk from Swedish Dairy Farms

Influenza D virus (IDV) has been detected in bovine respiratory disease (BRD) outbreaks, and experimental studies demonstrated this virus's capacity to cause lesions in the respiratory tract. In addition, IDV-specific antibodies were detected in human sera, which indicated that this virus plays a potential zoonotic role. The present study aimed to extend our knowledge about the epidemiologic situation of IDV in Swedish dairy farms, using bulk tank milk (BTM) samples for the detection of IDV antibodies. A total of 461 and 338 BTM samples collected during 2019 and 2020, respectively, were analyzed with an in-house indirect ELISA. In total, 147 (32%) and 135 (40%) samples were IDV-antibody-positive in 2019 and 2020, respectively. Overall, 2/125 (2%), 11/157 (7%) and 269/517 (52%) of the samples were IDV-antibody-positive in the northern, middle and southern regions of Sweden. The highest proportion of positive samples was repeatedly detected in the south, in the county of Halland, which is one of the counties with the highest cattle density in the country. In order to understand the epidemiology of IDV, further research in different cattle populations and in humans is required.

Multiplex RT-qPCR Application in Early Detection of Bovine Respiratory Disease in Healthy Calves

Bovine respiratory diseases (BRD) are associated with various predisposing factors, such as physical and physiological stress factors, and bacterial and viral pathogens. These stressors and viruses suppress immune defenses, leading to bacterial growth in the upper respiratory tract and invasion of pathogens into the lower respiratory tract. Therefore, continuous monitoring of the causative pathogens would contribute to the early detection of BRD. Nasal swabs and sera from 63 clinically healthy calves were continuously collected from seven farms in Iwate prefecture from 2019 to 2021. We attempted to monitor dynamics of BRD-associated pathogens by multiplex real-time RT-PCR (RT-qPCR) using their nasal swab samples. In addition, we attempted to monitor fluctuation of antibody titers against each BRD-associated pathogen by virus neutralization test (VNT) using their sera. In contrast, nasal swabs from 89 calves infected with BRD were collected from 28 farms in Iwate prefecture from 2019 to 2021. We attempted to analyze their nasal swab samples by multiplex RT-qPCR aim to detect BRD-associated pathogens that are dominant in this region. As a result, our analyses using samples from clinically healthy calves showed that positive results by multiplex RT-qPCR were closely related to a significant increase of antibody titers by VNT in bovine coronavirus (BCoV), bovine torovirus (BToV), and bovine respiratory syncytial virus (BRSV). In addition, our data exhibited that BCoV, BToV, BRSV, bovine parainfluenza virus 3, and Mycoplasma bovis have been more frequently detected in calves infected with BRD compared to those detected in clinically healthy calves. Moreover, the data presented herein revealed co-infections by combination multiple viral pathogens with bacterial pathogens are closely involved in the onset of BRD. Taken together, our study demonstrates multiplex RT-qPCR which can simultaneously analyze multiple pathogens, including viruses and bacteria, and is useful for the early detection of BRD.

Cluster analysis of bovine respiratory disease (BRD)-associated pathogens shows the existence of two epidemiological patterns in BRD outbreaks

A hierarchical cluster analysis was used to classify outbreaks of bovine respiratory disease (BRD; n = 156) in natural groups according to the detection of nine pathogens (parainfluenza 3 virus (PI-3), bovine respiratory syncytial virus (BRSV), bovine coronavirus (BCV), bovine viral diarrhea virus (BVDV), and bovine herpesvirus 1 (BHV-1), Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Pathogens were detected by individual q-PCRs. Two clusters were identified. Cluster 1 was characterized by a relatively high frequency (40-72%) of four BRD-associated viruses, supporting their primary involvement in BRD. Cluster 2 was characterized by frequencies of PI-3, BRSV, or BVDV below 10% each. P. multocida and M. haemolytica were detected with high frequencies in both clusters (P > 0.05), while M. bovis and H. somni showed a significantly higher frequency in cluster 1and 2, respectively. Outbreaks in cluster 1 were associated with preweaning calves younger than 5 months (OR 2.2; 95% CI 1.1-4.5) and with cold months, whereas cluster 2 was associated with fattening calves older than 5 months after arrival to feedlots and without any seasonality. Thus, in addition to the classic epidemiological BRD pattern characterized by the primary involvement of viruses occurring preferably during winter and affecting young calves, there is a second pattern in which viruses would be less relevant, affecting mainly calves older than 5 months at any time of the year. This study allows a better understanding of the BRD epidemiology, which can be useful when implementing management and prophylaxis measures for a better control of this disease.

Whole blood transcriptome analysis in dairy calves experimentally challenged with bovine herpesvirus 1 (BoHV-1) and comparison to a bovine respiratory syncytial virus (BRSV) challenge

Bovine herpesvirus 1 (BoHV-1), is associated with several clinical syndromes in cattle, among which bovine respiratory disease (BRD) is of particular significance. Despite the importance of the disease, there is a lack of information on the molecular response to infection via experimental challenge with BoHV-1. The objective of this study was to investigate the whole-blood transcriptome of dairy calves experimentally challenged with BoHV-1. A secondary objective was to compare the gene expression results between two separate BRD pathogens using data from a similar challenge study with BRSV. Holstein-Friesian calves (mean age (SD) = 149.2 (23.8) days; mean weight (SD) = 174.6 (21.3) kg) were either administered BoHV-1 inoculate (1 × 10⁷/mL × 8.5 mL) (n = 12) or were mock challenged with sterile phosphate buffered saline (n = 6). Clinical signs were recorded daily from day (d) -1 to d 6 (post-challenge), and whole blood was collected in Tempus RNA tubes on d six post-challenge for RNA-sequencing. There were 488 differentially expressed (DE) genes (p < 0.05, False Discovery rate (FDR) < 0.10, fold change ≥2) between the two treatments. Enriched KEGG pathways (p < 0.05, FDR <0.05); included Influenza A, Cytokine-cytokine receptor interaction and NOD-like receptor signalling. Significant gene ontology terms (p < 0.05, FDR <0.05) included defence response to virus and inflammatory response. Genes that are highly DE in key pathways are potential therapeutic targets for the treatment of BoHV-1 infection. A comparison to data from a similar study with BRSV identified both similarities and differences in the immune response to differing BRD pathogens.

Molecular Epidemiology of Pasteurella multocida Associated with Bovine Respiratory Disease Outbreaks

Studies that characterize bovine respiratory disease (BRD)-associated Pasteurella multocida isolates are scarce compared with research on isolates from other hosts and clinical backgrounds. In the present study, 170 P. multocida isolates from 125 BRD outbreaks were characterized by capsular and LPS typing as well as by virulotyping. Three capsular types (A, B, F) and three LPS genotypes (L2, L3, L6) were identified. Capsular and LPS typing revealed a very low genetic diversity (GD = 0.02) among P. multocida, with most isolates belonging to genotype A:L3 (97.6%). Virulotyping identified seven virulence-associated gene profiles, with two profiles including 95.9% of the isolates. A subset of isolates was further characterized by MLST and PFGE. The sequence types ST79 and ST13 were the most frequently identified and were grouped into the same clonal complex (CC13), a result that supports the clonal population structure of BRD-associated P. multocida isolates. PFGE typing also revealed a low genetic diversity (GD = 0.18), detecting a single pattern in 62.5% of the outbreaks in which multiple isolates were analyzed. Overall, 85.2% of the isolates belonged to pulsotypes with at least 80% genetic similarity, consistent with a clonal population structure observed by MLST analysis and corroborating the genetic relatedness of most P. multocida isolates associated with BRD in cattle.

Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1

Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.

Review of Associated Health Benefits of Algal Supplementation in Cattle with Reference to Bovine Respiratory Disease Complex in Feedlot Systems

Within the Australian beef industry bovine respiratory disease is considered one of the most common disease and costs the industry an average net loss of $1647.53 Australian dollars per animal death to bovine respiratory disease complex (BRD). This is due to the disease overwhelming the animal’s immune system during a period where they experience multiple stressors that consequently increase the animal’s susceptivity to disease. Research into the bioactive compounds commonly found in marine algae is rapidly increasing due to its positive health benefits and potential immune modulating properties. Algal supplementation within previous studies has resulted in improved reproduction potential, growth performance, increases antioxidant activity and decreased proinflammatory cytokine concentrations. Additional research is required to further understand the aetiology of BRD and complete analysis of the bioavailability of these bioactive compounds within marine algae to fully explore the potential of marine algae supplementation.

Bovine Respiratory Disease Considerations in Young Dairy Calves

Raising young dairy calves presents many challenges for producers and veterinarians including losses attributable to BRD. This article will discuss several key concepts for practitioners to consider when applying evidence-based medicine for the control and treatment of BRD in young dairy calves. The authors review BRD complex, provide considerations for diagnostic approaches, and discuss research associated with the control and treatment of BRD.

Use of nCounter mRNA profiling to identify at-arrival gene expression patterns for predicting bovine respiratory disease in beef cattle

Background

Transcriptomics has identified at-arrival differentially expressed genes associated with bovine respiratory disease (BRD) development; however, their use as prediction molecules necessitates further evaluation. Therefore, we aimed to selectively analyze and corroborate at-arrival mRNA expression from multiple independent populations of beef cattle. In a nested case-control study, we evaluated the expression of 56 mRNA molecules from at-arrival blood samples of 234 cattle across seven populations via NanoString nCounter gene expression profiling. Analysis of mRNA was performed with nSolver Advanced Analysis software (p < 0.05), comparing cattle groups based on the diagnosis of clinical BRD within 28 days of facility arrival (n = 115 Healthy; n = 119 BRD); BRD was further stratified for severity based on frequency of treatment and/or mortality (Treated_1, n = 89; Treated_2+, n = 30). Gene expression homogeneity of variance, receiver operator characteristic (ROC) curve, and decision tree analyses were performed between severity cohorts.

Results

Increased expression of mRNAs involved in specialized pro-resolving mediator synthesis (ALOX15, HPGD), leukocyte differentiation (LOC100297044, GCSAML, KLF17), and antimicrobial peptide production (CATHL3, GZMB, LTF) were identified in Healthy cattle. BRD cattle possessed increased expression of CFB, and mRNA related to granulocytic processes (DSG1, LRG1, MCF2L) and type-I interferon activity (HERC6, IFI6, ISG15, MX1). Healthy and Treated_1 cattle were similar in terms of gene expression, while Treated_2+ cattle were the most distinct. ROC cutoffs were used to generate an at-arrival treatment decision tree, which classified 90% of Treated_2+ individuals.

Conclusions

Increased expression of complement factor B, pro-inflammatory, and type I interferon-associated mRNA hallmark the at-arrival expression patterns of cattle that develop severe clinical BRD. Here, we corroborate at-arrival mRNA markers identified in previous transcriptome studies and generate a prediction model to be evaluated in future studies. Further research is necessary to evaluate these expression patterns in a prospective manner.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03178-8.

High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance

Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.