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

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 t...

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Bibliographic Details
Published in:Viruses 2022-08, Vol.14 (9), p.1859
Main Authors: Esnault, Gaelle, Earley, Bernadette, Cormican, Paul, Waters, Sinead M, Lemon, Ken, Cosby, S Louise, Lagan, Paula, Barry, Thomas, Reddington, Kate, McCabe, Matthew S
Format: Article
Language:English
Subjects:
Animal experimentation
Animals
Anti-Bacterial Agents
Antibiotics
Antibodies
Bacterial infections
bovine herpesvirus 1
bovine respiratory disease
Bovine respiratory disease complex
Calves
Cattle
Cattle Diseases
Cell culture
Control
Diagnosis
DNA viruses
Epi2ME
Epidemics
Genetic aspects
Genomes
Genomics
Health aspects
Herpes viruses
Herpesvirus 1, Bovine - genetics
Herpesviruses
Infections
Laboratories
Medical equipment
Metagenomics
Metagenomics - methods
MinION
Morbidity
Nanopores
Oxford Nanopore Technologies
Pathogens
Physiological apparatus
rapid viral metagenomics diagnostics
Respiratory diseases
Sequence analysis
Testing
Vaccines
Viruses - genetics
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Summary: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.
ISSN:1999-4915
1999-4915
DOI:10.3390/v14091859