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Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards

SIMPLE SUMMARY: In the present report, we designed a reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) for the detection and quantification of the nervous necrosis virus (NNV), a fish virus of great importance in Mediterranean aquaculture. The advantage of this procedu...

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Autores principales: Olveira, José G., Souto, Sandra, Bandín, Isabel, Dopazo, Carlos P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8069436/
https://www.ncbi.nlm.nih.gov/pubmed/33921441
http://dx.doi.org/10.3390/ani11041100
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author Olveira, José G.
Souto, Sandra
Bandín, Isabel
Dopazo, Carlos P.
author_facet Olveira, José G.
Souto, Sandra
Bandín, Isabel
Dopazo, Carlos P.
author_sort Olveira, José G.
collection PubMed
description SIMPLE SUMMARY: In the present report, we designed a reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) for the detection and quantification of the nervous necrosis virus (NNV), a fish virus of great importance in Mediterranean aquaculture. The advantage of this procedure with respect to others is that it ensures the correct diagnosis of any viral type, at extremely low viral loads, thanks to a limit of detection lower than in previous methods, and demonstrates a better diagnostic sensitivity and specificity than PCR and cell culture isolation. Furthermore, this is the first time that an RT-qPCR procedure has been validated for the quantification of NNV, ensuring the reliability of the quantification, regardless of the calibration standard chosen. Therefore, its use would enable the comparison of data between different laboratories. ABSTRACT: The nervous necrosis virus (NNV) is a threat to fish aquaculture worldwide, especially in Mediterranean countries. Fast and accurate diagnosis is essential to control it, and viral quantification is required to predict the level of risk of new viral detections in field samples. For both, reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) is used by diagnostic laboratories. In the present study, we developed an RT-qPCR procedure for the diagnosis and simultaneous quantification of NNV isolates from any of the four genotypes. The method proved to be highly sensitive in terms of crude virus titer: 5.56–9.88 TCID(50)/mL (tissue culture infectious dose per mL), depending on the viral strain, and averaging 8.8 TCID(50)/mL or 0.08 TCID(50)/reaction. Other standards also yielded very low detection limits: 16.3 genome copies (cps) of purified virus per mL, 2.36 plasmid cps/mL, 7.86 in vitro synthetized RNA cps/mL, and 3.16 TCID(50)/mL of virus from infected tissues. The diagnostic parameters evaluated in fish samples were much higher in comparison to cell culture isolation and nested PCR. In addition, the high repeatability and reproducibility of the procedure, as well as the high coefficient of determination (R(2)) of all the calibration curves with any type of standard tested, ensure the high reliability of the quantification of NNV using this RT-qPCR procedure, regardless of the viral type detected and from the type of standard chosen.
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spelling pubmed-80694362021-04-26 Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards Olveira, José G. Souto, Sandra Bandín, Isabel Dopazo, Carlos P. Animals (Basel) Article SIMPLE SUMMARY: In the present report, we designed a reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) for the detection and quantification of the nervous necrosis virus (NNV), a fish virus of great importance in Mediterranean aquaculture. The advantage of this procedure with respect to others is that it ensures the correct diagnosis of any viral type, at extremely low viral loads, thanks to a limit of detection lower than in previous methods, and demonstrates a better diagnostic sensitivity and specificity than PCR and cell culture isolation. Furthermore, this is the first time that an RT-qPCR procedure has been validated for the quantification of NNV, ensuring the reliability of the quantification, regardless of the calibration standard chosen. Therefore, its use would enable the comparison of data between different laboratories. ABSTRACT: The nervous necrosis virus (NNV) is a threat to fish aquaculture worldwide, especially in Mediterranean countries. Fast and accurate diagnosis is essential to control it, and viral quantification is required to predict the level of risk of new viral detections in field samples. For both, reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) is used by diagnostic laboratories. In the present study, we developed an RT-qPCR procedure for the diagnosis and simultaneous quantification of NNV isolates from any of the four genotypes. The method proved to be highly sensitive in terms of crude virus titer: 5.56–9.88 TCID(50)/mL (tissue culture infectious dose per mL), depending on the viral strain, and averaging 8.8 TCID(50)/mL or 0.08 TCID(50)/reaction. Other standards also yielded very low detection limits: 16.3 genome copies (cps) of purified virus per mL, 2.36 plasmid cps/mL, 7.86 in vitro synthetized RNA cps/mL, and 3.16 TCID(50)/mL of virus from infected tissues. The diagnostic parameters evaluated in fish samples were much higher in comparison to cell culture isolation and nested PCR. In addition, the high repeatability and reproducibility of the procedure, as well as the high coefficient of determination (R(2)) of all the calibration curves with any type of standard tested, ensure the high reliability of the quantification of NNV using this RT-qPCR procedure, regardless of the viral type detected and from the type of standard chosen. MDPI 2021-04-12 /pmc/articles/PMC8069436/ /pubmed/33921441 http://dx.doi.org/10.3390/ani11041100 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/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 (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Olveira, José G.
Souto, Sandra
Bandín, Isabel
Dopazo, Carlos P.
Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards
title Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards
title_full Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards
title_fullStr Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards
title_full_unstemmed Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards
title_short Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards
title_sort development and validation of a sybr green real time pcr protocol for detection and quantification of nervous necrosis virus (nnv) using different standards
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8069436/
https://www.ncbi.nlm.nih.gov/pubmed/33921441
http://dx.doi.org/10.3390/ani11041100
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