Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples

Zhang, Maodong; Huang, Yanyun; Godson, Dale L.; Fernando, Champika; Alexander, Trevor W.; Hill, Janet E.

doi:10.1101/2020.06.10.144782

Cited by 2 publications

(1 citation statement)

References 37 publications

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“…Rapid diagnosis of BRD and characterisation of the causative agent is a key mitigation strategy for disease control in feedlots [49]. The MinION is capable of identifying the viruses responsible for BRD using Oxford Nanopore's rapid sequencing kit [50,51].…”

Section: Rapid Diagnostics Of Pathogens In Livestockmentioning

confidence: 99%

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

Lamb

Hayes

Nguyen

et al. 2020

Genes

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Oxford Nanopore Technologies’ MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: ‘crush-side genotyping’ for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.

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Section: Rapid Diagnostics Of Pathogens In Livestockmentioning

confidence: 99%

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

Lamb

Hayes

Nguyen

et al. 2020

Genes

View full text Add to dashboard Cite

show abstract

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

Esnault

Earley

Cormican

et al. 2022

Viruses

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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.

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Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples

Cited by 2 publications

References 37 publications

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

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

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