Cargando…

Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing

The sequencing of viral genomes provides important data for the prevention and control of foot-and-mouth disease (FMD) outbreaks. Sequence data can be used for strain identification, outbreak tracing, and aiding the selection of the most appropriate vaccine for the circulating strains. At present, s...

Descripción completa

Detalles Bibliográficos
Autores principales: Brown, Emma, Freimanis, Graham, Shaw, Andrew E., Horton, Daniel L., Gubbins, Simon, King, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8165188/
https://www.ncbi.nlm.nih.gov/pubmed/34079833
http://dx.doi.org/10.3389/fvets.2021.656256
_version_ 1783701263660089344
author Brown, Emma
Freimanis, Graham
Shaw, Andrew E.
Horton, Daniel L.
Gubbins, Simon
King, David
author_facet Brown, Emma
Freimanis, Graham
Shaw, Andrew E.
Horton, Daniel L.
Gubbins, Simon
King, David
author_sort Brown, Emma
collection PubMed
description The sequencing of viral genomes provides important data for the prevention and control of foot-and-mouth disease (FMD) outbreaks. Sequence data can be used for strain identification, outbreak tracing, and aiding the selection of the most appropriate vaccine for the circulating strains. At present, sequencing of FMD virus (FMDV) relies upon the time-consuming transport of samples to well-resourced laboratories. The Oxford Nanopore Technologies' MinION portable sequencer has the potential to allow sequencing in remote, decentralised laboratories closer to the outbreak location. In this study, we investigated the utility of the MinION to generate sequence data of sufficient quantity and quality for the characterisation of FMDV serotypes O, A, Asia 1. Prior to sequencing, a universal two-step RT-PCR was used to amplify parts of the 5′UTR, as well as the leader, capsid and parts of the 2A encoding regions of FMDV RNA extracted from three sample matrices: cell culture supernatant, tongue epithelial suspension and oral swabs. The resulting consensus sequences were compared with reference sequences generated on the Illumina MiSeq platform. Consensus sequences with an accuracy of 100% were achieved within 10 and 30 min from the start of the sequencing run when using RNA extracted from cell culture supernatants and tongue epithelial suspensions, respectively. In contrast, sequencing from swabs required up to 2.5 h. Together these results demonstrated that the MinION sequencer can be used to accurately and rapidly characterise serotypes A, O, and Asia 1 of FMDV using amplicons amplified from a variety of different sample matrices.
format Online
Article
Text
id pubmed-8165188
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-81651882021-06-01 Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing Brown, Emma Freimanis, Graham Shaw, Andrew E. Horton, Daniel L. Gubbins, Simon King, David Front Vet Sci Veterinary Science The sequencing of viral genomes provides important data for the prevention and control of foot-and-mouth disease (FMD) outbreaks. Sequence data can be used for strain identification, outbreak tracing, and aiding the selection of the most appropriate vaccine for the circulating strains. At present, sequencing of FMD virus (FMDV) relies upon the time-consuming transport of samples to well-resourced laboratories. The Oxford Nanopore Technologies' MinION portable sequencer has the potential to allow sequencing in remote, decentralised laboratories closer to the outbreak location. In this study, we investigated the utility of the MinION to generate sequence data of sufficient quantity and quality for the characterisation of FMDV serotypes O, A, Asia 1. Prior to sequencing, a universal two-step RT-PCR was used to amplify parts of the 5′UTR, as well as the leader, capsid and parts of the 2A encoding regions of FMDV RNA extracted from three sample matrices: cell culture supernatant, tongue epithelial suspension and oral swabs. The resulting consensus sequences were compared with reference sequences generated on the Illumina MiSeq platform. Consensus sequences with an accuracy of 100% were achieved within 10 and 30 min from the start of the sequencing run when using RNA extracted from cell culture supernatants and tongue epithelial suspensions, respectively. In contrast, sequencing from swabs required up to 2.5 h. Together these results demonstrated that the MinION sequencer can be used to accurately and rapidly characterise serotypes A, O, and Asia 1 of FMDV using amplicons amplified from a variety of different sample matrices. Frontiers Media S.A. 2021-05-17 /pmc/articles/PMC8165188/ /pubmed/34079833 http://dx.doi.org/10.3389/fvets.2021.656256 Text en Copyright © 2021 Brown, Freimanis, Shaw, Horton, Gubbins and King. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Veterinary Science
Brown, Emma
Freimanis, Graham
Shaw, Andrew E.
Horton, Daniel L.
Gubbins, Simon
King, David
Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing
title Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing
title_full Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing
title_fullStr Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing
title_full_unstemmed Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing
title_short Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing
title_sort characterising foot-and-mouth disease virus in clinical samples using nanopore sequencing
topic Veterinary Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8165188/
https://www.ncbi.nlm.nih.gov/pubmed/34079833
http://dx.doi.org/10.3389/fvets.2021.656256
work_keys_str_mv AT brownemma characterisingfootandmouthdiseasevirusinclinicalsamplesusingnanoporesequencing
AT freimanisgraham characterisingfootandmouthdiseasevirusinclinicalsamplesusingnanoporesequencing
AT shawandrewe characterisingfootandmouthdiseasevirusinclinicalsamplesusingnanoporesequencing
AT hortondaniell characterisingfootandmouthdiseasevirusinclinicalsamplesusingnanoporesequencing
AT gubbinssimon characterisingfootandmouthdiseasevirusinclinicalsamplesusingnanoporesequencing
AT kingdavid characterisingfootandmouthdiseasevirusinclinicalsamplesusingnanoporesequencing