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dc.creatorTaengphu, S.en_US
dc.creatorDelamare-Deboutteville, J.en_US
dc.creatorSangsuriya, P.en_US
dc.creatorDebnath, P.P.en_US
dc.creatorChadag, V.en_US
dc.creatorThanh, D.en_US
dc.creatorSaengchan, S.en_US
dc.date.accessioned2020-05-04T06:48:55Z
dc.date.available2020-05-04T06:48:55Z
dc.date.issued2020
dc.identifier.citationAquaculture, 526: 735423.en_US
dc.identifier.issn0044-8486en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12348/4178
dc.description.abstractThe gene of RNA viruses, encoding RNA-directed RNA polymerase (RdRp) is relatively conserved due to its crucial function in viral genome replication and transcription making it a useful target for genetic diversity study and PCR detection. In this study, we investigated the genetic diversity of 21 tilapia lake virus (TiLV) genome segment 1 sequences predictively coding for RdRp subunit P1. Those sequences were obtained from infected fish samples collected in Ecuador, Israel, Peru, and Thailand between 2011 and 2019 (nine sequences from this study and 12 sequences from GenBank). Primers were then designed from the highly conserved regions among all 21 TiLV segment 1 sequences and used in semi-nested RT-PCR condition optimization. The result revealed that all 21 TiLV segment 1 sequences showed 95.00–99.94 and 99.00–100% nucleotide and amino acid sequence identity, respectively. These isolates were phylogenically clustered into three separate genetic clades, called i) Israeli-2011 clade (containing of TiLV isolates from Israel collected in 2011, Ecuador, and Peru isolates), ii) Israeli-2012 clade (containing only TiLV isolates collected from Israel in 2012), and iii) Thai clade (containing only sequences obtained from Thailand isolates). The newly established PCR protocol was 100 times more sensitive than our previous segment 3-based protocol when comparatively assayed with RNA extracted from infected fish. The assay was also shown to be specific when tested against negative control samples, i.e. RNA extracted from clinical healthy tilapia and from bacterial and viral pathogens (other than TiLV) commonly found in aquatic animals. Validation experiment with RNA extracted from naturally infected fish specimens collected in 2013–2019 yielded positive test results for all samples tested, confirming that the newly designed primers and detection protocol against TiLV segment 1, is an alternative option for TiLV diagnosis in laboratories where conventional RT-PCR method is preferred.en_US
dc.formatPDFen_US
dc.languageenen_US
dc.publisherElsevieren_US
dc.rightsCC-BY-4.0en_US
dc.subjectdetectionen_US
dc.subjectgenomeen_US
dc.subjecttilven_US
dc.subjecttilv segment 1en_US
dc.subjectsemi-nested pcren_US
dc.subjecttilapia lake virusen_US
dc.subjectfish dieseasesen_US
dc.subjectFishen_US
dc.titleGenetic diversity of tilapia lake virus genome segment 1 from 2011 to 2019 and a newly validated semi-nested RT-PCR methoden_US
dc.typeJournal Articleen_US
dcterms.bibliographicCitationTaengphu, S. et al. (2020). Genetic diversity of tilapia lake virus genome segment 1 from 2011 to 2019 and a newly validated semi-nested RT-PCR method. Aquaculture, 526: 735423.
cg.contributor.crpFISHen_US
cg.contributor.funderCGIAR System Officeen_US
cg.coverage.regionGlobalen_US
cg.identifier.worldfish4668
cg.subject.agrovocaquacultureen_US
cg.subject.agrovocgenomesen_US
cg.subject.agrovocgeneticsen_US
cg.subject.agrovoctilapiaen_US
cg.subject.agrovocbreeding stocken_US
cg.contributor.affiliationWorldFishen_US
cg.contributor.affiliationMahidol University, Faculty of science, Center of Excellence for Shrimp Molecular Biology and Biotechnologyen_US
cg.contributor.affiliationSuan Sunandha Rajabhat Universityen_US
cg.identifier.statusOpen accessen_US
cg.identifier.ISIindexedISI indexeden_US
cg.contribution.worldfishauthorDelamare-Deboutteville, J.en_US
cg.contribution.worldfishauthorDebnath, P.P.en_US
cg.contribution.worldfishauthorChadag, V.en_US
cg.description.themeSustainable aquacultureen_US
dc.identifier.doihttps://dx.doi.org/10.1016/j.aquaculture.2020.735423en_US
cg.creator.idJerome Delamare-Deboutteville: 0000-0003-4169-2456en_US
cg.creator.idVishnumurthy Mohan Chadag: 0000-0002-2574-284Xen_US


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