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https://hdl.handle.net/20.500.12348/5749
A multiplexed RT‑PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV)
dc.creator | Delamare-Deboutteville, J. | en_US |
dc.creator | Meemetta, W. | en_US |
dc.creator | Pimsannil, K. | en_US |
dc.creator | Sangpo, P. | en_US |
dc.creator | Gan, H.M. | en_US |
dc.creator | Chadag, V. | en_US |
dc.creator | Thanh, D. | en_US |
dc.creator | Saengchan, S. | en_US |
dc.date.accessioned | 2024-01-09T21:38:57Z | |
dc.date.available | 2024-01-09T21:38:57Z | |
dc.date.issued | 2023 | en_US |
dc.identifier.citation | Jerome Delamare-Deboutteville, Watcharachai Meemetta, Khaettareeya Pimsannil, Pattiya Sangpo, Han Gan, Vishnumurthy Mohan Chadag, Dong Ha Thanh, Senapin Saengchan. (20/11/2023). A multiplexed RT‑PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV). Scientific Reports (13). | en_US |
dc.identifier.issn | 2045-2322 | en_US |
dc.identifier.uri | https://hdl.handle.net/20.500.12348/5749 | |
dc.description.abstract | Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT‑PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real‑ time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV‑infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real‑time Nanopore‑based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development. | en_US |
dc.format | en_US | |
dc.language | en | en_US |
dc.publisher | Nature Research (part of Springer Nature) (Fully open access journals) | en_US |
dc.rights | CC-BY-4.0 | en_US |
dc.source | Scientific Reports;(2023) | en_US |
dc.subject | rna virus | en_US |
dc.subject | tilapia lake virus (tilv) | en_US |
dc.subject | whole genome sequencing (wgs) | en_US |
dc.subject | nanopore sequencing | en_US |
dc.subject | nile tilapia (oreochromis niloticus) | en_US |
dc.subject | oreochromis species | en_US |
dc.subject | segmented virus | en_US |
dc.title | A multiplexed RT‑PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV) | en_US |
dc.type | Journal Article | en_US |
cg.contributor.funder | Norwegian Agency for Development Cooperation | en_US |
cg.contributor.funder | CGIAR Trust Fund | en_US |
cg.contributor.project | Increased Sustainability in the Aquaculture Sector in SSA, through improved Aquatic Animal Health Management (AHA) | en_US |
cg.subject.agrovoc | phylogenetic analysis | en_US |
cg.subject.agrovoc | bioinformatics | en_US |
cg.subject.agrovoc | fish | en_US |
cg.contributor.affiliation | WorldFish | en_US |
cg.contributor.affiliation | Asian Institute of Technology | en_US |
cg.contributor.affiliation | National Science and Technology Development Agency, National Center for Genetic Engineering and Biotechnology | en_US |
cg.contributor.affiliation | The Norwegian Veterinary Institute | en_US |
cg.contributor.affiliation | Mahidol University, Faculty of science, Center of Excellence for Shrimp Molecular Biology and Biotechnology | en_US |
cg.contributor.affiliation | Asian Institute of Technology, School of Environment, Resources and Development | en_US |
cg.contributor.affiliation | Patriot Biotech Sdn Bhd, Bandar Sunway, Selangor, Malaysia | en_US |
cg.identifier.status | Open access | en_US |
cg.identifier.ISIindexed | ISI indexed | en_US |
cg.contribution.worldfishauthor | Delamare-Deboutteville, J. | en_US |
cg.contribution.worldfishauthor | Chadag, V. | en_US |
cg.description.theme | Sustainable aquaculture | en_US |
dc.identifier.doi | https://dx.doi.org/10.1038/s41598-023-47425-w | en_US |
cg.creator.id | Jerome Delamare-Deboutteville: 0000-0003-4169-2456 | en_US |
cg.creator.id | Vishnumurthy Mohan Chadag: 0000-0002-2574-284X | en_US |
cg.subject.sdg | SDG 3 - Good health and well-being | en_US |
cg.subject.sdg | SDG 4 - Quality education | en_US |
cg.subject.sdg | SDG 9 - Industry, innovation and infrastructure | en_US |
cg.subject.sdg | SDG 12 - Responsible consumption and production | en_US |
cg.subject.sdg | SDG 14 - Life below water | en_US |
cg.subject.actionArea | Resilient Agrifood Systems | en_US |
cg.subject.impactArea | Nutrition, health and food security | en_US |
cg.subject.impactArea | Poverty reduction, livelihoods and jobs | en_US |
cg.subject.impactArea | Environmental health and biodiversity | en_US |
cg.contributor.initiative | Aquatic Foods | en_US |
cg.contributor.initiative | One Health | en_US |
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Sustainable aquaculture [2735]