No abstract

Viruses play a key role in the complex aetiology of bovine respiratory disease (BRD). Bovine viral diarrhoea virus 1 (BVDV-1) is widespread in Australia and has been shown to contribute to BRD occurrence. As part of a prospective longitudinal study on BRD, effects of exposure to BVDV-1 on risk of BRD in Australian feedlot cattle were investigated. A total of 35,160 animals were enrolled at induction (when animals were identified and characteristics recorded), held in feedlot pens with other cattle (cohorts) and monitored for occurrence of BRD over the first 50days following induction. Biological samples collected from all animals were tested to determine which animals were persistently infected (PI) with BVDV-1. Data obtained from the Australian National Livestock Identification System database were used to determine which groups of animals that were together at the farm of origin and at 28days prior to induction (and were enrolled in the study) contained a PI animal and hence to identify animals that had probably been exposed to a PI animal prior to induction. Multi-level Bayesian logistic regression models were fitted to estimate the effects of exposure to BVDV-1 on the risk of occurrence of BRD. Although only a total of 85 study animals (0.24%) were identified as being PI with BVDV-1, BVDV-1 was detected on quantitative polymerase chain reaction in 59% of cohorts. The PI animals were at moderately increased risk of BRD (OR 1.9; 95% credible interval 1.0-3.2). Exposure to BVDV-1 in the cohort was also associated with a moderately increased risk of BRD (OR 1.7; 95% credible interval 1.1-2.5) regardless of whether or not a PI animal was identified within the cohort. Additional analyses indicated that a single quantitative real-time PCR test is useful for distinguishing PI animals from transiently infected animals. The results of the study suggest that removal of PI animals and/or vaccination, both before feedlot entry, would reduce the impact of BVDV-1 on BRD risk in cattle in Australian feedlots. Economic assessment of these strategies under Australian conditions is required.

Bovine viral diarrhoea virus 1 (BVDV-1) is strongly associated with several important diseases of cattle, such as bovine respiratory disease, diarrhoea and haemoragic lesions. To date many subgenotypes have been reported for BVDV-1, currently ranging from subgenotype 1a to subgenotype 1u. While BVDV-1 has a world-wide distribution, the subgenotypes have a more restricted geographical distribution. As an example, BVDV-1 subgenotypes 1a and 1b are frequently detected in North America and Europe, while the subgenotype 1c is rarely detected. In contrast, BVDV-1 subgenotype 1c is by far the most commonly reported in Australia. Despite this, uneven distribution of the biological importance of the subgenotypes remains unclear. The aim of this study was to characterise the in vivo properties of five strains of BVDV-1 subgenotype 1c in cattle infection studies. No overt respiratory signs were reported in any of the infected cattle regardless of strain. Consistent with other subgenotypes, transient pyrexia and leukopenia were commonly identified, while thrombocytopenia was not. The quantity of virus detected in the nasal secretions of transiently infected animals suggested the likelihood of horizontal transmission was very low. Further studies are required to fully understand the variability and importance of the BVDV-1 subgenotype 1c.

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.

Context Genotyping-by-sequencing, the use of sequence reads to genotype single-nucleotide polymorphisms (SNPs), has seen an increase in popularity as a tool for genomic prediction. Oxford Nanopore Technologies (Nanopore) sequencing is an emerging technology that produces long sequence reads in real-time. Recent studies have established the ability for low-coverage Nanopore sequence data to be used for genomic prediction. However, the value proposition of Nanopore sequencing for individuals could be improved if both genotyping and disease diagnosis are achieved from a single sample. Aims This study aimed to demonstrate that Nanopore sequencing can be used for both rapid genotyping and as a disease diagnostic tool using the same sample in livestock. Methods Total DNA extracts from nasal swabs collected from 48 feedlot cattle presenting with clinical signs of bovine respiratory disease (BRD) were sequenced using the Nanopore PromethION sequencer. After 24 h of sequencing, genotypes were imputed and genomic estimated breeding values (GEBVs) for four traits were derived using 641 163 SNPs and corresponding SNP effects. These GEBVs were compared with GEBVs derived from SNP array genotypes and calculated using the same SNP effects. Unmapped sequence reads were classified into taxa using Kraken2 and compared with quantitative real-time polymerase chain reaction (qPCR) results for five BRD-associated pathogens of interest. Key results Sequence-derived genotypes for 46 of the 48 animals were produced in 24 h and GEBV correlations ranged between 0.92 and 0.94 for the four traits. Eleven different BRD-associated pathogens (two viruses and nine bacterial species) were detected in the samples using Nanopore sequence data. A significant (P < 0.001) relationship between Nanopore and qPCR results was observed for five overlapping species when a maximum threshold cycle was used. Conclusions The results of this study indicated that 46 cattle genomes can be multiplexed and accurately genotyped for downstream genomic prediction by using a single PromethION flow cell (ver. R9.4) in 24 h. This equates to a cost of AUD35.82 per sample for consumables. The concordance between qPCR results and pathogen proportion estimates also indicated that some pathogenic species, in particular bacterial species, can be accurately identified from the same test. Implications Using Nanopore sequencing, routine genotyping and disease detection in livestock could be combined into one cost-competitive test with a rapid turnaround time.