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Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue

Taura syndrome is a World Organization for Animal Health (OIE)-listed disease of marine shrimp that is caused by Taura syndrome virus (TSV), a single-stranded RNA virus. Here we demonstrate the utility of using 15-year-old archived Davidson’s-fixed paraffin-embedded (DFPE) shrimp tissues for TSV det...

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Autores principales: Ochoa, Lauren Marie, Cruz-Flores, Roberto, Dhar, Arun K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551232/
https://www.ncbi.nlm.nih.gov/pubmed/32948008
http://dx.doi.org/10.3390/v12091030
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author Ochoa, Lauren Marie
Cruz-Flores, Roberto
Dhar, Arun K.
author_facet Ochoa, Lauren Marie
Cruz-Flores, Roberto
Dhar, Arun K.
author_sort Ochoa, Lauren Marie
collection PubMed
description Taura syndrome is a World Organization for Animal Health (OIE)-listed disease of marine shrimp that is caused by Taura syndrome virus (TSV), a single-stranded RNA virus. Here we demonstrate the utility of using 15-year-old archived Davidson’s-fixed paraffin-embedded (DFPE) shrimp tissues for TSV detection and phylogenetic analyses. Total RNA was isolated from known TSV-infected DFPE tissues using three commercially available kits and the purity and ability to detect TSV in the isolated RNA were compared. TSV was successfully detected through RT-qPCR in all the tested samples. Among the TSV-specific primers screened through RT-PCR, primer pair TSV-20 for the RNA-dependent RNA polymerase (RdRp), primers TSV-15 and TSV-16 for the capsid protein gene VP2 and primers TSV-5 for the capsid protein gene VP1 amplified the highest number of samples. To assess the phylogenetic relation among different TSV isolates, the VP1 gene was amplified and sequenced in overlapping segments. Concatenated sequences from smaller fragments were taken for phylogenetic analyses. The results showed that the TSV isolates from this study generally clustered with homologous isolates from the corresponding geographical regions indicating RNA derived from DFPE tissues can be used for pathogen detection and retrospective analyses. The ability to perform genomic characterization from archived tissue will expedite pathogen discovery, development of diagnostic tools and prevent disease spread in shrimp and potentially other aquaculture species worldwide.
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spelling pubmed-75512322020-10-16 Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue Ochoa, Lauren Marie Cruz-Flores, Roberto Dhar, Arun K. Viruses Article Taura syndrome is a World Organization for Animal Health (OIE)-listed disease of marine shrimp that is caused by Taura syndrome virus (TSV), a single-stranded RNA virus. Here we demonstrate the utility of using 15-year-old archived Davidson’s-fixed paraffin-embedded (DFPE) shrimp tissues for TSV detection and phylogenetic analyses. Total RNA was isolated from known TSV-infected DFPE tissues using three commercially available kits and the purity and ability to detect TSV in the isolated RNA were compared. TSV was successfully detected through RT-qPCR in all the tested samples. Among the TSV-specific primers screened through RT-PCR, primer pair TSV-20 for the RNA-dependent RNA polymerase (RdRp), primers TSV-15 and TSV-16 for the capsid protein gene VP2 and primers TSV-5 for the capsid protein gene VP1 amplified the highest number of samples. To assess the phylogenetic relation among different TSV isolates, the VP1 gene was amplified and sequenced in overlapping segments. Concatenated sequences from smaller fragments were taken for phylogenetic analyses. The results showed that the TSV isolates from this study generally clustered with homologous isolates from the corresponding geographical regions indicating RNA derived from DFPE tissues can be used for pathogen detection and retrospective analyses. The ability to perform genomic characterization from archived tissue will expedite pathogen discovery, development of diagnostic tools and prevent disease spread in shrimp and potentially other aquaculture species worldwide. MDPI 2020-09-16 /pmc/articles/PMC7551232/ /pubmed/32948008 http://dx.doi.org/10.3390/v12091030 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ochoa, Lauren Marie
Cruz-Flores, Roberto
Dhar, Arun K.
Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue
title Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue
title_full Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue
title_fullStr Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue
title_full_unstemmed Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue
title_short Detection and Phylogenetic Analyses of Taura Syndrome Virus from Archived Davidson’s-Fixed Paraffin-Embedded Shrimp Tissue
title_sort detection and phylogenetic analyses of taura syndrome virus from archived davidson’s-fixed paraffin-embedded shrimp tissue
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551232/
https://www.ncbi.nlm.nih.gov/pubmed/32948008
http://dx.doi.org/10.3390/v12091030
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