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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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Autores principales: Esnault, Gaelle, Earley, Bernadette, Cormican, Paul, Waters, Sinead M., Lemon, Ken, Cosby, S. Louise, Lagan, Paula, Barry, Thomas, Reddington, Kate, McCabe, Matthew S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9501177/
https://www.ncbi.nlm.nih.gov/pubmed/36146668
http://dx.doi.org/10.3390/v14091859
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author Esnault, Gaelle
Earley, Bernadette
Cormican, Paul
Waters, Sinead M.
Lemon, Ken
Cosby, S. Louise
Lagan, Paula
Barry, Thomas
Reddington, Kate
McCabe, Matthew S.
author_facet Esnault, Gaelle
Earley, Bernadette
Cormican, Paul
Waters, Sinead M.
Lemon, Ken
Cosby, S. Louise
Lagan, Paula
Barry, Thomas
Reddington, Kate
McCabe, Matthew S.
author_sort Esnault, Gaelle
collection PubMed
description 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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spelling pubmed-95011772022-09-24 Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1 Esnault, Gaelle Earley, Bernadette Cormican, Paul Waters, Sinead M. Lemon, Ken Cosby, S. Louise Lagan, Paula Barry, Thomas Reddington, Kate McCabe, Matthew S. Viruses Article 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. MDPI 2022-08-24 /pmc/articles/PMC9501177/ /pubmed/36146668 http://dx.doi.org/10.3390/v14091859 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/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/).
spellingShingle Article
Esnault, Gaelle
Earley, Bernadette
Cormican, Paul
Waters, Sinead M.
Lemon, Ken
Cosby, S. Louise
Lagan, Paula
Barry, Thomas
Reddington, Kate
McCabe, Matthew S.
Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
title Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
title_full Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
title_fullStr Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
title_full_unstemmed Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
title_short Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1
title_sort assessment of rapid minion nanopore dna virus meta-genomics using calves experimentally infected with bovine herpes virus-1
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9501177/
https://www.ncbi.nlm.nih.gov/pubmed/36146668
http://dx.doi.org/10.3390/v14091859
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