ArticleFrontiers in veterinary science2025
Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group.
Article in Frontiers in veterinary science, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.Veterinary and animal science · 2026Article
- Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models.Frontiers in veterinary science · 2026Article
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16 authors.
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Abstract
Introduction: Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal swabs to describe sequencing data from BRD associated viruses. Changes in virus composition were identified between arrival to a feedlot and 14 days on feed (DOF). These data were also assessed for the simultaneous characterization of bacteria and antimicrobial resistance genes (ARGs). Methods: Nasal swabs were obtained from fall-placed calves (FPC) and yearlings (YRL) from western Canadian commercial feedlots. Evidence of respiratory viruses were identified by sampling 380 animals during processing on arrival to the feedlot and again after 14 DOF using Nanopore metagenomic sequencing. Results: Twenty-one distinct viruses from 12 viral families were identified, with multiple viruses detected in most samples. In FPC arrival samples, the most common BRD associated viruses were bovine rhinitis B virus (BRBV; 46%), bovine coronavirus (BCoV; 32%), influenza D virus (IDV; 17%), bovine respiratory syncytial virus (BRSV; 8.5%), and bovine parainfluenza virus 3 (BPIV-3; 4.2%). The prevalences of bovine herpesvirus type 1 (BoHV-1; 2.7%), BPIV-3 (12%), BRSV (26%), and IDV (51%) were higher in 14 DOF samples compared to arrival samples ( Discussion: Changes in the prevalence of BRD associated viruses early in the feeding period reflect transmission and the potential risk of developing the disease. Frequent detection of BCoV, BRSV, and BPIV-3 in newly arrived feedlot cattle suggests the need for improved vaccination before shipping or limitations in existing commercial vaccine preparations.
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