Design and evaluation of a unique RT-qPCR assay for diagnostic quality control assessment that is applicable to pathogen detection in three species of salmonid fish

BMC Veterinary Research

Volumn 9, Issue , 2013, Pages

  Sepúlveda, Dagoberto ^a,e   Bohle, Harry ^b   Labra, Álvaro ^a,c   Grothusen, Horst ^b   Marshall, Sergio H ^a,d  

^a PONTIFICIA UNIVERSIDAD CATÓLICA DE VALPARAÍSO   (Chile)

^b ADL Diagnostic Chile   (Chile)

^c Ministerio de Economía Fomento y Turismo   (Chile)

^d Fraunhofer Chile Research Foundation   (Chile)

^e AARHUS UNIVERSITY   (Denmark)

Author keywords

ELF1 ; Elongation Factor 1 alpha; Endogenous control; Fish disease; Fish virus; Real time PCR; RT qPCR

Indexed keywords

ONCORHYNCHUS KISUTCH; ONCORHYNCHUS MYKISS; SALMO SALAR; SALMONIDAE;

ELONGATION FACTOR 1;

ANIMAL; ANIMAL DISEASE; ARTICLE; CLASSIFICATION; FISH DISEASE; GENETIC VARIABILITY; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; QUALITY CONTROL; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SALMONID; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; FISH DISEASES; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; PEPTIDE ELONGATION FACTOR 1; QUALITY CONTROL; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SALMONIDAE; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY;

EID: 84883821784     PISSN: None     EISSN: 17466148     Source Type: Journal    
DOI: 10.1186/1746-6148-9-183     Document Type: Article

References (32)

1. Schreck CB. Stress and fish reproduction: the roles of allostasis and hormesis. Gen Comp Endocrinol 2010, 165(3):549-556.
2. Sindermann CJ. Disease in marine aquaculture. Helgol Mar Res 1984, 37(1):505-530.
3. Bustin SA. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000, 25(2):169-193.
4. Matejusova I, McKay P, Bland F, Snow M. Application of a sensitive, specific and controlled real time PCR assay to surveillance indicates a low prevalence of viral haemorrhagicsepticaemia virus (VHSV) in wild herring, Clupeaharengus L., in Scottish waters. J Fish Dis 2010, 33(10):841-847.
5. Purcell MK, Hart SA, Kurath G, Winton JR. Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus. J Virol Methods 2006, 132(1):18-24.
6. Hodneland K, Endresen C. Sensitive and specific detection of Salmonidalphavirus using real-time PCR (TaqMan). J Virol Methods 2006, 131(2):184-192.
7. Karatas S, Mikalsen J, Steinum TM, Taksdal T, Bordevik M, Colquhoun DJ. Real time PCR detection of Piscirickettsiasalmonis from formalin-fixed paraffin-embedded tissues. J Fish Dis 2008, 31(10):747-753.
8. Corbeil S, McColl KA, Crane MSJ. Development of a TaqMan quantitative PCR assay for the identification of Piscirickettsiasalmonis. Bull Eur Assn Fish P 2003, 23(3):95-101.
9. Olivares J, Marshall SH. Determination of minimal concentration of Piscirickettsiasalmonis in water columns to establish a fallowing period in salmon farms. J Fish Dis 2010, 33(3):261-266.
10. Bruno D, Collet B, Turnbull A, Kilburn R, Walker A, Pendrey D, McIntosh A, Urquhart K, Taylor G. Evaluation and development of diagnostic methods for Renibacteriumsalmoninarum causing bacterial kidney disease (BKD) in the UK. Aquaculture 2007, 269(1-4):114-122.
11. Snow M, McKay P, McBeath AJA, Black J, Doig F, Kerr R, Cunningham CO, Nylund A, Devold M. Development, application and validation of a taqman® real-time RT-PCR assay for the detection of infectious salmon anaemia virus(ISAV) in atlantic salmon(Salmosalar). Dev Biol 2006, 126:133-145.
12. Bowers RM, Lapatra SE, Dhar AK. Detection and quantitation of infectious pancreatic necrosis virus by real-time reverse transcriptase-polymerase chain reaction using lethal and non-lethal tissue sampling. J Virol Methods 2008, 147(2):226-234.
13. Bland F, McIntosh R, Bain N, Snow M. Development and validation of a range of endogenous controls to support the implementation of practical Taqman real time PCR-based surveillance for fish diseases within aquaculture. J Fish Dis 2012, 35:447-454.
14. Moore LJ, Somamoto T, Lie KK, Dijkstra JM, Hordvik I. Characterisation of salmon and trout CD8 [alpha] and CD8 [beta]. Mol Immunol 2005, 42(10):1225-1234.
15. Ingerslev HC, Pettersen EF, Jakobsen RA, Petersen CB, Wergeland HI. Expression profiling and validation of reference gene candidates in immune relevant tissues and cells from Atlantic salmon (Salmosalar L.). Mol Immunol 2006, 43(8):1194-1201.
16. Jorgensen SM, Kleveland EJ, Grimholt U, Gjoen T. Validation of reference genes for real-time polymerase chain reaction studies in Atlantic salmon. Mar Biotechnol 2006, 8(4):398-408.
17. Peña AA, Bols NC, Marshall SH. An evaluation of potential reference genes for stability of expression in two salmonid cell lines after infection with either Piscirickettsiasalmonis or IPNV. BMC research notes 2010, 3(1):101.
18. Lovoll M, Austbo L, Jorgensen JB, Rimstad E, Frost P. Transcription of reference genes used for quantitative RT-PCR in Atlantic salmon is affected by viral infection. Vet Res 2011, 42(1):8.
19. SuB B, Flekna G, Wagner M, Hein I. Studying the effect of single mismatches in primer and probe binding regions on amplification curves and quantification in real-time PCR. J Microbiol Methods 2009, 76(3):316-319.
20. Jiang Z, Wang Z, Kunej T, Williams GA, Michal JJ, Wu XL, Magnuson NS. A novel type of sequence variation: multiple-nucleotide length polymorphisms discovered in the bovine genome. Genetics 2007, 176(1):403-407.
21. Vignal A, Milan D, SanCristobal M, Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 2002, 34(3):275-306.
22. Kerkel K, Spadola A, Yuan E, Kosek J, Jiang L, Hod E, Li K, Murty VV, Schupf N, Vilain E. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 2008, 40(7):904-908.
23. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797.
24. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999, 41:95-98.
25. Klungthong C, Chinnawirotpisan P, Hussem K, Phonpakobsin T, Manasatienkij W, Ajariyakhajorn C, Rungrojcharoenkit K, Gibbons RV, Jarman RG. The impact of primer and probe-template mismatches on the sensitivity of pandemic influenza A/H1N1/2009 virus detection by real-time RT-PCR. J Clin Virol 2010, 48(2):91-95.
26. Kibbe WA. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res 2007, 35(suppl 2):W43-W46.
27. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009, 55(4):611-622.
28. Devold M, Krossoy B, Aspehaug V, Nylund A. Use of RT-PCR for diagnosis of infectious salmon anaemia virus (ISAV) in carrier sea trout Salmotrutta after experimental infection. Dis Aquat Organ 2000, 40(1):9-18.
29. Dannevig BH, Falk K, Namork E. Isolation of the causal virus of infectious salmon anaemia (ISA) in a long-term cell line from Atlantic salmon head kidney. J Gen Virol 1995, 76(6):1353-1359.
30. Lannan CN, Winton JR, Fryer JL. Fish cell lines: establishment and characterization of nine cell lines from salmonids. In Vitro Cell Dev-Pl 1984, 20(9):671-676.
31. Ganassin RC, Bols NC. Development of a monocyte/macrophage-like cell line, RTS11, from rainbow trout spleen. Fish Shellfish Immun 1998, 8(6):457-476.
32. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001, 29(9):e45.