Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
Date
2022-08-24
Journal Title
Journal ISSN
Volume Title
Publisher
MDPI
Abstract
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.
Description
Publication history: Accepted - 20 August 2022; Published - 24 August 2022.
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Article
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Keywords
Oxford Nanopore Technologies, MinION;, Epi2ME, rapid viral metagenomics diagnostics, bovine herpesvirus 1, bovine respiratory disease
Citation
Esnault, G., Earley, B., Cormican, P., Waters, S.M., Lemon, K., Cosby, S.L., Lagan, P., Barry, T., Reddington, K. and McCabe, M.S. (2022) ‘Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1’, Viruses. MDPI AG. Available at: https://doi.org/10.3390/v14091859.