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Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing
Infectious diseases represent one of the major challenges to sustainable aquaculture production. Rapid, accurate diagnosis and genotyping of emerging pathogens during early‐suspected disease cases is critical to facilitate timely response to deploy adequate control measures and prevent or reduce spr...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8518713/ https://www.ncbi.nlm.nih.gov/pubmed/34101853 http://dx.doi.org/10.1111/jfd.13467 |
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author | Delamare‐Deboutteville, Jerome Taengphu, Suwimon Gan, Han Ming Kayansamruaj, Pattanapon Debnath, Partho Pratim Barnes, Andrew Wilkinson, Shaun Kawasaki, Minami Vishnumurthy Mohan, Chadag Senapin, Saengchan Dong, Ha Thanh |
author_facet | Delamare‐Deboutteville, Jerome Taengphu, Suwimon Gan, Han Ming Kayansamruaj, Pattanapon Debnath, Partho Pratim Barnes, Andrew Wilkinson, Shaun Kawasaki, Minami Vishnumurthy Mohan, Chadag Senapin, Saengchan Dong, Ha Thanh |
author_sort | Delamare‐Deboutteville, Jerome |
collection | PubMed |
description | Infectious diseases represent one of the major challenges to sustainable aquaculture production. Rapid, accurate diagnosis and genotyping of emerging pathogens during early‐suspected disease cases is critical to facilitate timely response to deploy adequate control measures and prevent or reduce spread. Currently, most laboratories use PCR to amplify partial pathogen genomic regions, occasionally combined with sequencing of PCR amplicon(s) using conventional Sanger sequencing services for confirmatory diagnosis. The main limitation of this approach is the lengthy turnaround time. Here, we report an innovative approach using a previously developed specific PCR assay for pathogen diagnosis combined with a new Oxford Nanopore Technologies (ONT)‐based amplicon sequencing method for pathogen genotyping. Using fish clinical samples, we applied this approach for the rapid confirmation of PCR amplicon sequences identity and genotyping of tilapia lake virus (TiLV), a disease‐causing virus affecting tilapia aquaculture globally. The consensus sequences obtained after polishing exhibit strikingly high identity to references derived by Illumina and Sanger methods (99.83%–100%). This study suggests that ONT‐based amplicon sequencing is a promising platform to deploy in regional aquatic animal health diagnostic laboratories in low‐ and medium‐income countries, for fast identification and genotyping of emerging infectious pathogens from field samples within a single day. |
format | Online Article Text |
id | pubmed-8518713 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-85187132021-10-21 Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing Delamare‐Deboutteville, Jerome Taengphu, Suwimon Gan, Han Ming Kayansamruaj, Pattanapon Debnath, Partho Pratim Barnes, Andrew Wilkinson, Shaun Kawasaki, Minami Vishnumurthy Mohan, Chadag Senapin, Saengchan Dong, Ha Thanh J Fish Dis Research Articles Infectious diseases represent one of the major challenges to sustainable aquaculture production. Rapid, accurate diagnosis and genotyping of emerging pathogens during early‐suspected disease cases is critical to facilitate timely response to deploy adequate control measures and prevent or reduce spread. Currently, most laboratories use PCR to amplify partial pathogen genomic regions, occasionally combined with sequencing of PCR amplicon(s) using conventional Sanger sequencing services for confirmatory diagnosis. The main limitation of this approach is the lengthy turnaround time. Here, we report an innovative approach using a previously developed specific PCR assay for pathogen diagnosis combined with a new Oxford Nanopore Technologies (ONT)‐based amplicon sequencing method for pathogen genotyping. Using fish clinical samples, we applied this approach for the rapid confirmation of PCR amplicon sequences identity and genotyping of tilapia lake virus (TiLV), a disease‐causing virus affecting tilapia aquaculture globally. The consensus sequences obtained after polishing exhibit strikingly high identity to references derived by Illumina and Sanger methods (99.83%–100%). This study suggests that ONT‐based amplicon sequencing is a promising platform to deploy in regional aquatic animal health diagnostic laboratories in low‐ and medium‐income countries, for fast identification and genotyping of emerging infectious pathogens from field samples within a single day. John Wiley and Sons Inc. 2021-06-08 2021-10 /pmc/articles/PMC8518713/ /pubmed/34101853 http://dx.doi.org/10.1111/jfd.13467 Text en © 2021 The Authors. Journal of Fish Diseases published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made. |
spellingShingle | Research Articles Delamare‐Deboutteville, Jerome Taengphu, Suwimon Gan, Han Ming Kayansamruaj, Pattanapon Debnath, Partho Pratim Barnes, Andrew Wilkinson, Shaun Kawasaki, Minami Vishnumurthy Mohan, Chadag Senapin, Saengchan Dong, Ha Thanh Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing |
title | Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing |
title_full | Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing |
title_fullStr | Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing |
title_full_unstemmed | Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing |
title_short | Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing |
title_sort | rapid genotyping of tilapia lake virus (tilv) using nanopore sequencing |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8518713/ https://www.ncbi.nlm.nih.gov/pubmed/34101853 http://dx.doi.org/10.1111/jfd.13467 |
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