Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease

Abstract

Bovine respiratory disease (BRD) causes considerable economic losses in North America. The pathogenesis involves interactions between bacteria, viruses, environment and management factors. Primary viral infection can increase the risk of secondary fatal bacterial infection. The objective of this study was to use metagenomic sequencing to characterize the respiratory viromes of paired nasal swabs and tracheal washes from western Canadian feedlot cattle, with or without BRD. A total of 116 cattle (116 nasal swabs and 116 tracheal washes) were analysed. The presence of influenza D virus (IDV), bovine rhinitis A virus (BRAV), bovine rhinitis B virus (BRBV), bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) was associated with BRD. Agreement between identification of viruses in nasal swabs and tracheal washes was generally weak, indicating that sampling location may affect detection of infection. This study reported several viruses for the first time in Canada and provides a basis for further studies investigating candidate viruses important to the prevention of BRD.

The pulmonary virome, bacteriological and histopathological findings in bovine respiratory disease from western Canada

“…Secondly, some viruses, such as IDV (Ferguson et al, ), preferentially infect the upper respiratory tract, not the lung. In the current study, IDV was detected in the lung of only 1/130 cattle, compared with 16/116 upper respiratory tract samples in our previous study (Zhang et al, ). Similarly, UTPV1 was only detected in 8.5% (11/130) of pneumonic lungs, but was the most prevalent virus in nasal swabs and tracheal washes (36.2%, 42/116) (Zhang et al, ).…”

“…Most recently, application of advanced technologies for virus identification has resulted in further insight into the relationships between well‐recognized pathogens and BRD (Booker et al, ; Mehinagic et al, ; Oliveira et al, ). Previously, we detected 21 viruses in bovine nasal swabs and tracheal washes from western Canadian beef cattle, among which IDV, BRBV, BRSV and BCV were significantly associated with BRD (Zhang et al, ). In dairy calves, metagenomic sequencing showed a significant association between the presence of BRAV, IDV and bovine adenovirus 3 (BAdV3) in nasopharyngeal and pharyngeal samples with BRD (Ng et al, ).…”

“…After centrifugation at 13,000 g for 5 min, the supernatant was filtered (Filtropur S 0.2 µm, Sarstedt). Library preparation for metagenomic sequencing was performed as previously described (Zhang et al, ). Briefly, filtered supernatants were incubated with 24 units of DNase (Life Technologies) and 20 units of RNase ONE Ribonuclease (Promega) at 37°C for 90 min.…”

“…Bioinformatic analysis was performed as previously described (Zhang et al, ). In brief, quality trimming was performed using Trimmomatic‐0.32 (Bolger, Lohse, & Usadel, ) with minimum length of 50 and Phred score of 20.…”

“…Metagenomic sequencing has been shown to be a powerful tool for the detection of viruses (Buermans & den Dunnen, ), and previous studies have applied metagenomic sequencing to identify unconventional viruses associated with BRD (Mitra, Cernicchiaro, Torres, Li, & Hause, ; Ng et al, ; Zhang et al, ). As a result of these work, several unconventional viruses associated with BRD in dairy and beef cattle, such as influenza D virus (IDV) and bovine rhinitis virus A and B (BRAV and BRBV), have been identified (Mitra et al, ; Ng et al, ; Zhang et al, ). These studies have focused on the virome of ante‐mortem samples from the upper respiratory tract (nasal cavity and trachea).…”