Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease

Abstract

Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case–control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.

Can the Revolution in mRNA-Based Vaccine Technologies Solve the Intractable Health Issues of Current Ruminant Production Systems?

“…Similarly, with appropriate monitoring systems, it may be feasible to formulate vaccines in an informed manner, similar to the use of autologous vaccines in some livestock industries. Underpinning the application of vaccines in this manner could be the emergence of next-generation sequencing technologies to rapidly inform the most appropriate pathogen repertoire for the feedlot of interest [ 166 , 167 , 168 ]. When combined with other types of genetic testing, pathogen detection via these emerging technologies has the potential to inform vaccine coverage in a highly cost-effective manner [ 169 ].…”

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

“…In large production animals, Boros et al collected swine feces, sera, rectal, or nasal swab samples for studying the prevalence and genetic diversity of a picornavirus in farms and Létourneau (2023), utilized a broader metagenomics approach to identify viruses of the Herelleviridae, Microviridae, Myoviridae, Podoviridae, and Siphoviridae families [ 47 , 48 ]. In cattle, researchers have employed RNA-seq to study bovine reproductive, gastric, and respiratory diseases [ 49 , 50 , 51 , 52 , 53 ]. For cats, Fried et al (2021) utilized a combination of random metagenomic and transcriptomic analyses to investigate the association between feline calicivirus and feline chronic gingivostomatitis [ 54 ].…”