Chilean IPNV isolates: Robustness analysis of PCR detection

Background: The genomes of several infectious pancreatic necrosis viruses (IPNVs) isolated in Chile were sequenced with a single amplification approach for both segments A and B. The resulting sequences were then used to determine the conservation of the primer-binding regions used in polymerase cha...

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Autores principales:	Jorquera,Esteban, Morales,Paz, Tapia,David, Torres,Pamela, Eissler,Yoanna, Espinoza,Juan C, Conejeros,Pablo, Kuznar,Juan
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2016
Materias:	IPNV detection Mismatch's Tm analysis QPCR
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000200005
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spelling	oai:scielo:S0717-345820160002000052016-05-17Chilean IPNV isolates: Robustness analysis of PCR detectionJorquera,EstebanMorales,PazTapia,DavidTorres,PamelaEissler,YoannaEspinoza,Juan CConejeros,PabloKuznar,Juan IPNV detection Mismatch's Tm analysis QPCR Background: The genomes of several infectious pancreatic necrosis viruses (IPNVs) isolated in Chile were sequenced with a single amplification approach for both segments A and B. The resulting sequences were then used to determine the conservation of the primer-binding regions used in polymerase chain reaction (PCR)-based diagnostic methods proposed in the literature. Thus, the robustness of each technique was studied, particularly the eventual effect of further mutations within the primer-binding sites. Results: On analysis, most methods currently used to detect Chilean IPNV varieties were deemed adequate. However, the primers were designed to be genogroup specific, implying that most detection methods pose some risk of detecting all strains prevalent in the country, due to the coexistence of genogroups 1 and 5. Conclusions: Negative results must be interpreted carefully given the high genomic variability of IPNVs. Detection techniques (quantitative reverse transcription (qRT)-PCR) based on degenerate primers can be used to minimize the possibilities of false-negative detections.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.19 n.2 20162016-03-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000200005en10.1016/j.ejbt.2016.01.001
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	IPNV detection Mismatch's Tm analysis QPCR
spellingShingle	IPNV detection Mismatch's Tm analysis QPCR Jorquera,Esteban Morales,Paz Tapia,David Torres,Pamela Eissler,Yoanna Espinoza,Juan C Conejeros,Pablo Kuznar,Juan Chilean IPNV isolates: Robustness analysis of PCR detection
description	Background: The genomes of several infectious pancreatic necrosis viruses (IPNVs) isolated in Chile were sequenced with a single amplification approach for both segments A and B. The resulting sequences were then used to determine the conservation of the primer-binding regions used in polymerase chain reaction (PCR)-based diagnostic methods proposed in the literature. Thus, the robustness of each technique was studied, particularly the eventual effect of further mutations within the primer-binding sites. Results: On analysis, most methods currently used to detect Chilean IPNV varieties were deemed adequate. However, the primers were designed to be genogroup specific, implying that most detection methods pose some risk of detecting all strains prevalent in the country, due to the coexistence of genogroups 1 and 5. Conclusions: Negative results must be interpreted carefully given the high genomic variability of IPNVs. Detection techniques (quantitative reverse transcription (qRT)-PCR) based on degenerate primers can be used to minimize the possibilities of false-negative detections.
author	Jorquera,Esteban Morales,Paz Tapia,David Torres,Pamela Eissler,Yoanna Espinoza,Juan C Conejeros,Pablo Kuznar,Juan
author_facet	Jorquera,Esteban Morales,Paz Tapia,David Torres,Pamela Eissler,Yoanna Espinoza,Juan C Conejeros,Pablo Kuznar,Juan
author_sort	Jorquera,Esteban
title	Chilean IPNV isolates: Robustness analysis of PCR detection
title_short	Chilean IPNV isolates: Robustness analysis of PCR detection
title_full	Chilean IPNV isolates: Robustness analysis of PCR detection
title_fullStr	Chilean IPNV isolates: Robustness analysis of PCR detection
title_full_unstemmed	Chilean IPNV isolates: Robustness analysis of PCR detection
title_sort	chilean ipnv isolates: robustness analysis of pcr detection
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2016
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000200005
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_version_	1718441926548520960

Chilean IPNV isolates: Robustness analysis of PCR detection

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