Use of reverse transcription-real time polymerase chain reaction (real time RT-PCR) assays with Universal Probe Library (UPL) probes for the detection and genotyping of infectious pancreatic necrosis virus strains isolated in Chile

Felipe Calleja, Marcos G. Godoy, Juan G. Cárcamo, Isabel Bandín, Alejandro J. Yáñez, Carlos P. Dopazo, Fred S. Kibenge, Ruben Avendaño-Herrera

Resultado de la investigación: Article

21 Citas (Scopus)

Resumen

Reverse transcription-real time polymerase chain reaction (real time RT-PCR) assay with Universal Probe Library (UPL) probes has been developed for the detection and genotyping of Chilean infectious pancreatic necrosis virus (IPNV) isolates from infected cell culture. Partial nucleotide sequences (1175. bp) of the VP2 coding region from a selection of 7 Chilean IPNV isolates showed that they clustered into two main groups strongly correlated with Genogroups 1 and 5 proposed by Blake et al. (2001), corresponding to types West Buxton (WB) and Spajarup (Sp), respectively. Based on the VP2 gene sequences of those 7 Chilean isolates and different reference IPNV strains, 2 sets of candidate primer/UPL probes (# 8 and # 117) were designed and evaluated with a total of 32 field isolates isolated from Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) and Pacific salmon (Oncorhynchus kisutch) farms from 2006 to 2010 in Chile. The UPL probes clearly differentiated the same two major Genogroups that those recognized by sequencing analysis. Among the Chilean isolates examined, 18 yielded amplification with UPL probe # 8, and 14 with probe # 117, respectively corresponding to types Sp and WB, as demonstrated by typing by sequencing. Based on the findings reported below, it has been demonstrated that the combined real time RT-PCR protocol with UPLs approach was efficient in discriminating distinct Genogroups of IPNV cultured in fish cell lines and, therefore, recommended its use for detection and typing of IPN viruses. The study also confirmed the existence of two IPNV type strains in Chilean salmonid aquaculture.

Idioma originalEnglish
Páginas (desde-hasta)80-85
Número de páginas6
PublicaciónJournal of Virological Methods
Volumen183
N.º1
DOI
EstadoPublished - 1 jul 2012

Huella dactilar

Infectious pancreatic necrosis virus
Chile
Reverse Transcription
Real-Time Polymerase Chain Reaction
Salmo salar
Oncorhynchus mykiss
Genotype
Oncorhynchus kisutch
Aquaculture
Salmon
Fishes
Cell Culture Techniques
Viruses
Cell Line
Genes

ASJC Scopus subject areas

  • Virology

Citar esto

@article{695e270af1ca47a8944a213284d6b521,
title = "Use of reverse transcription-real time polymerase chain reaction (real time RT-PCR) assays with Universal Probe Library (UPL) probes for the detection and genotyping of infectious pancreatic necrosis virus strains isolated in Chile",
abstract = "Reverse transcription-real time polymerase chain reaction (real time RT-PCR) assay with Universal Probe Library (UPL) probes has been developed for the detection and genotyping of Chilean infectious pancreatic necrosis virus (IPNV) isolates from infected cell culture. Partial nucleotide sequences (1175. bp) of the VP2 coding region from a selection of 7 Chilean IPNV isolates showed that they clustered into two main groups strongly correlated with Genogroups 1 and 5 proposed by Blake et al. (2001), corresponding to types West Buxton (WB) and Spajarup (Sp), respectively. Based on the VP2 gene sequences of those 7 Chilean isolates and different reference IPNV strains, 2 sets of candidate primer/UPL probes (# 8 and # 117) were designed and evaluated with a total of 32 field isolates isolated from Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) and Pacific salmon (Oncorhynchus kisutch) farms from 2006 to 2010 in Chile. The UPL probes clearly differentiated the same two major Genogroups that those recognized by sequencing analysis. Among the Chilean isolates examined, 18 yielded amplification with UPL probe # 8, and 14 with probe # 117, respectively corresponding to types Sp and WB, as demonstrated by typing by sequencing. Based on the findings reported below, it has been demonstrated that the combined real time RT-PCR protocol with UPLs approach was efficient in discriminating distinct Genogroups of IPNV cultured in fish cell lines and, therefore, recommended its use for detection and typing of IPN viruses. The study also confirmed the existence of two IPNV type strains in Chilean salmonid aquaculture.",
keywords = "Genotyping method, Infectious pancreatic necrosis virus, Real time RT-PCR, Universal Probe Library",
author = "Felipe Calleja and Godoy, {Marcos G.} and C{\'a}rcamo, {Juan G.} and Isabel Band{\'i}n and Y{\'a}{\~n}ez, {Alejandro J.} and Dopazo, {Carlos P.} and Kibenge, {Fred S.} and Ruben Avenda{\~n}o-Herrera",
year = "2012",
month = "7",
day = "1",
doi = "10.1016/j.jviromet.2012.03.022",
language = "English",
volume = "183",
pages = "80--85",
journal = "Journal of Virological Methods",
issn = "0166-0934",
publisher = "Elsevier",
number = "1",

}

Use of reverse transcription-real time polymerase chain reaction (real time RT-PCR) assays with Universal Probe Library (UPL) probes for the detection and genotyping of infectious pancreatic necrosis virus strains isolated in Chile. / Calleja, Felipe; Godoy, Marcos G.; Cárcamo, Juan G.; Bandín, Isabel; Yáñez, Alejandro J.; Dopazo, Carlos P.; Kibenge, Fred S.; Avendaño-Herrera, Ruben.

En: Journal of Virological Methods, Vol. 183, N.º 1, 01.07.2012, p. 80-85.

Resultado de la investigación: Article

TY - JOUR

T1 - Use of reverse transcription-real time polymerase chain reaction (real time RT-PCR) assays with Universal Probe Library (UPL) probes for the detection and genotyping of infectious pancreatic necrosis virus strains isolated in Chile

AU - Calleja, Felipe

AU - Godoy, Marcos G.

AU - Cárcamo, Juan G.

AU - Bandín, Isabel

AU - Yáñez, Alejandro J.

AU - Dopazo, Carlos P.

AU - Kibenge, Fred S.

AU - Avendaño-Herrera, Ruben

PY - 2012/7/1

Y1 - 2012/7/1

N2 - Reverse transcription-real time polymerase chain reaction (real time RT-PCR) assay with Universal Probe Library (UPL) probes has been developed for the detection and genotyping of Chilean infectious pancreatic necrosis virus (IPNV) isolates from infected cell culture. Partial nucleotide sequences (1175. bp) of the VP2 coding region from a selection of 7 Chilean IPNV isolates showed that they clustered into two main groups strongly correlated with Genogroups 1 and 5 proposed by Blake et al. (2001), corresponding to types West Buxton (WB) and Spajarup (Sp), respectively. Based on the VP2 gene sequences of those 7 Chilean isolates and different reference IPNV strains, 2 sets of candidate primer/UPL probes (# 8 and # 117) were designed and evaluated with a total of 32 field isolates isolated from Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) and Pacific salmon (Oncorhynchus kisutch) farms from 2006 to 2010 in Chile. The UPL probes clearly differentiated the same two major Genogroups that those recognized by sequencing analysis. Among the Chilean isolates examined, 18 yielded amplification with UPL probe # 8, and 14 with probe # 117, respectively corresponding to types Sp and WB, as demonstrated by typing by sequencing. Based on the findings reported below, it has been demonstrated that the combined real time RT-PCR protocol with UPLs approach was efficient in discriminating distinct Genogroups of IPNV cultured in fish cell lines and, therefore, recommended its use for detection and typing of IPN viruses. The study also confirmed the existence of two IPNV type strains in Chilean salmonid aquaculture.

AB - Reverse transcription-real time polymerase chain reaction (real time RT-PCR) assay with Universal Probe Library (UPL) probes has been developed for the detection and genotyping of Chilean infectious pancreatic necrosis virus (IPNV) isolates from infected cell culture. Partial nucleotide sequences (1175. bp) of the VP2 coding region from a selection of 7 Chilean IPNV isolates showed that they clustered into two main groups strongly correlated with Genogroups 1 and 5 proposed by Blake et al. (2001), corresponding to types West Buxton (WB) and Spajarup (Sp), respectively. Based on the VP2 gene sequences of those 7 Chilean isolates and different reference IPNV strains, 2 sets of candidate primer/UPL probes (# 8 and # 117) were designed and evaluated with a total of 32 field isolates isolated from Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) and Pacific salmon (Oncorhynchus kisutch) farms from 2006 to 2010 in Chile. The UPL probes clearly differentiated the same two major Genogroups that those recognized by sequencing analysis. Among the Chilean isolates examined, 18 yielded amplification with UPL probe # 8, and 14 with probe # 117, respectively corresponding to types Sp and WB, as demonstrated by typing by sequencing. Based on the findings reported below, it has been demonstrated that the combined real time RT-PCR protocol with UPLs approach was efficient in discriminating distinct Genogroups of IPNV cultured in fish cell lines and, therefore, recommended its use for detection and typing of IPN viruses. The study also confirmed the existence of two IPNV type strains in Chilean salmonid aquaculture.

KW - Genotyping method

KW - Infectious pancreatic necrosis virus

KW - Real time RT-PCR

KW - Universal Probe Library

UR - http://www.scopus.com/inward/record.url?scp=84860551593&partnerID=8YFLogxK

U2 - 10.1016/j.jviromet.2012.03.022

DO - 10.1016/j.jviromet.2012.03.022

M3 - Article

C2 - 22484616

AN - SCOPUS:84860551593

VL - 183

SP - 80

EP - 85

JO - Journal of Virological Methods

JF - Journal of Virological Methods

SN - 0166-0934

IS - 1

ER -