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

Simple item page
dc.contributor.authorEsnault, Gaelle
dc.contributor.authorEarley, Bernadette
dc.contributor.authorCormican, Paul
dc.contributor.authorWaters, Sinead M.
dc.contributor.authorLemon, Ken
dc.contributor.authorCosby, S. Louise
dc.contributor.authorLagan, Paula
dc.contributor.authorBarry, Thomas
dc.contributor.authorReddington, Kate
dc.contributor.authorMcCabe, Matthew S.
dc.date.accessioned2022-09-07T13:50:38Z
dc.date.available2022-09-07T13:50:38Z
dc.date.issued2022-08-24
dc.descriptionPublication history: Accepted - 20 August 2022; Published - 24 August 2022.en_US
dc.description.abstractBovine 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.en_US
dc.identifierhttp://hdl.handle.net/20.500.12518/480
dc.identifier.citationEsnault, 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.en_US
dc.identifier.issn1999-4915 (electronic)
dc.identifier.urihttps://doi.org/10.3390/v14091859
dc.language.isoenen_US
dc.publisherMDPIen_US
dc.rightsCopyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).en_US
dc.subjectOxford Nanopore Technologiesen_US
dc.subjectMinION;en_US
dc.subjectEpi2MEen_US
dc.subjectrapid viral metagenomics diagnosticsen_US
dc.subjectbovine herpesvirus 1en_US
dc.subjectbovine respiratory diseaseen_US
dc.titleAssessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1en_US
dc.typeArticleen_US
dcterms.dateAccepted2022-08-20
dcterms.dateSubmitted2022-06-29

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.pdf
Size:
1.41 MB
Format:
Adobe Portable Document Format
Description:
Final published version
Download

Collections

Journal Articles