Table 2 List of qPCR assays used for farm surveillance in main study.
From: A novel high-throughput qPCR chip for solving co-infections in RAS farmed rainbow trout
Target | Assay name | Sequence | Probe type | Reference |
|---|---|---|---|---|
Infectious hematopoietic necrosis virus, IHNV | IHNV N | F:AGAGCCAAGGCACTGTGCG R: TTCTTTGCGGCTTGGTTGA P: AGCGGGACAGGRATGACAATGGTG | BHQ | Primers: Purcell et al.65 Probe: Hoferer et al.66 |
Infectious pancreatic necrosis virus, IPNV | IPNV SP VP2 | F: GCCAAGATGACCCAGTCCAT R: TGACAGCTTGACCCTGGTGAT P: CCGACCGAGAACAT | MGB | Lockhart et al.67 |
IPNV Tapia | F: GTTGATMMASTACACCGGAG R: AGGTCHCKTATGAAGGAGTC P: TACATAGGCAAAACCAAAGGAGACAC | 3IABkFQ | Tapia et al.68 | |
Infectious salmon anemia virus, ISAV | MS ISAV | F: CTACACAGCAGGATGCAGATGT R: CAGGATGCCGGAAGTCGAT P: CATCGTCGCTGCAGTTC | 3IABkFQ | Snow et al.69 |
Onchorhynchus masou herpesvirus, OMV | OMV | F: GCCTGGACCACAATCTCAATG R: CGAGACAGTGTGGCAAGACAAC P: CCAACAGGATGGTCATTA | MGB | Lennox et al.41 |
Piscine myocarditis virus, PMCV | PMCV | F: TTCCAAACAATTCGAGAAGCG R: ACCTGCCATTTTCCCCTCTT P: CCGGGTAAAGTATTTGCGTC | MGB | Løvoll et al.70 |
Pan PRV (PRV-1, -2, -3) | PanPRV | F: TGGGTAACTATCAGACAAGTAACAAC R: GTAGARTCGAGTCCGCCTTCAG P: CAATTTTGGGTAACTGGCGACGGCAATGA | MGB | Zhao et al.71 |
Piscine orthoreovirus genotype 1, PRV-1 | PRV1 | F: TGCTAACACTCCAGGAGTCATTG R: TGAATCCGCTGCAGATGAGTA P: CGCCGGTAGCTCT | MGB | Palacios et al.26 |
Piscine orthoreovirus genotype 3, PRV-3 | L1PRV3 | F: TACAGGTCGTGTTCCCGTTG R: TCCAGCCACGAGGTAGATCA P: TTCAGGTTGGATGGAGCGCG | BHQ | Sørensen et al.6 |
Salmon alphavirus 1, 2, and 3, SAV | SAV QnsP1 | F: CCGGCCCTGAACCAGTT R: GTAGCCAAGTGGGAGAAAGCT P: CTGGCCACCACTTCGA | MGB | Hodneland and Endresen72 |
Viral hemorrhagic septicemia virus, VHSV | VHSV Spjo | F: AAACTCGCAGGATGTGTGCGTCC R: TCTGCGATCTCAGTCAGGATGAA P: TAGAGGGCCTTGGTGATCTTCTG | 31ABkFQ | Jonstrup et al.73 |
Salmon gill pox virus | sgpx | F: ATCCAAAATACGGAACATAAGCAAT R: CAACGACAAGGAGATCAACGC P: CTCAGAAACTTCAAAGGA | BHQ | Gjessing et al.24 |
Aeromonas salmonicida | ae_sal | F: TAAAGCACTGTCTGTTACC R: GCTACTTCACCCTGATTGG P: ACATCAGCAGGCTTCAGAGTCACTG | MGB | Keeling et al.74 |
Candidatus Branchiomonas cysticola | c_b_cys | F: AATACATCGGAACGTGTCTAGTG R: GCCATCAGCCGCTCATGTG P: CTCGGTCCCAGGCTTTCCTCTCCCA | MGB | Mitchell et al.14 |
Flavobacterium psychrophilum | fl_psy_p1 | F: GAAGATGGAGAAGGTAATTTAGTTGATATT R: CAAATAACATCTCCTTTTTCTACAACTTGA P: AAACGGGTATTCTTCTTGCTACA | MGB | Strepparava et al.53 |
Piscichlamydia salmonis | pch_sal | F: TCACCCCCAGGCTGCTT R: GAATTCCATTTCCCCCTCTTG P: CAAAACTGCTAGACTAGAGT | MGB | Nylund et al.75 |
Piscirickettsia salmonis | pisck_sal | F: TCTGGGAAGTGTGGCGATAGA R. TCCCGACCTACTCTTGTTTCATC P: TGATAGCCCCGTACACGAAACGGCATA | MGB | Corbiel et al.76 |
Red mark syndrome Rickettsia-like organism | rlo | F: GGCTCAACCCAAGAACTGCTT R: GTGCAACAGCGTCAGTGACT P: CCCAGATAACCGCCTTCGCCTCCG | BHQ | Lloyd et al.77 |
Renibacterium salmoninarum | rs_msa | F: GGAGCAACTCCGGTTACTGGTA R: TGGCCGTCCTTGAACCAT P: TGGTCTGGCGACAACAACACGTATGGT | BHQ | Bruno et al.52 |
Vibrio anguillarum | vi_ang | F: CCGTCATGCTATCTAGAGATGTATTTGA R: CCATACGCAGCCAAAAATCA P: TCATTTCGACGAGCGTCTTGTTCAGC | MGB | Miller16 |
Vibrio salmonicida | vi_sal | F: GTGTGATGACCGTTCCATATTT R: GCTATTGTCATCACTCTGTTTCTT P: TCGCTTCATGTTGTGTAATTAGGAGCGA | MGB | Miller16 |
Yersinia ruckeri | ye_ruck | F: TCCAGCACCAAATACGAAGG R: ACATGGCAGAACGCAGAT P: AAGGCGGTTACTTCCCGGTTCCC | BHQ | Miller et al.78 |
Tetracapsuloides bryosalmonae, PKD | te_bry | F: GCGAGATTTGTTGCATTTAAAAAG R: GCACATGCAGTGTCCAATCG P: CAAAATTGTGGAACCGTCCGACTACGA | MGB | Bettge et al.79 |
Elongation factor 1 alpha | ELF1a | F: CCCCTCCAGGATGTCTACAAA R: CACACGGCCCACGGGTACT P: ATCGGCGGTATTGGAAC | 31ABkFQ | Jonstrup et al.73 |
