Table 2 Real time RT-PCR assays used in the study
Target (Assay name) | Primer and probe sequences (5′–3′) | Reference | |
|---|---|---|---|
Atlantic salmon Elongation factor 1α (EF1AA) | F | CCCCTCCAGGACGTTTACAAA | [40] |
Probe | ATCGGTGGTATTGGAAC | ||
R | CACACGGCCCACAGGTACA | ||
Parvicapsula pseudobranchicola 18S (Parvi) | F | TCGTAGTCGGATGACAAGAACGT | [29] |
Probe | CCGTATTGCTGTCTTTGA | ||
R | AAACACCCCGCACTGCAT | ||
Desmozoon lepeophtherii 16S (Nuc) | F | CGGACAGGGAGCATGGTATAG | [41] |
Probe | TTGGCGAAGAATGAAA | ||
R | GGTCCAGGTTGGGTCTTGAG | ||
Ichthyobodo spp. 18S (Costia) | F | ACGAACTTATGCGAAGGCA | [42] |
Probe | TCCACGACTGCAAACGATGACG | ||
R | TGAGTATTCACTYCCGATCCAT | ||
“Candidatus Branchiomonas cysticola” 16S (Epit) | F | GAGTAATACATCGGAACGTGTCTAGTG | [43] |
Probe | ACTTAGCGAAAGTTAAGC | ||
R | CTTTCCTCTCCCAAGCTTATGC | ||
Piscine orthoreovirus M2 (PRV) | F | CAATCGCAAGGTCTGATGCA | [43] |
Probe | CTGGCTCAACTCTC | ||
R | GGGTTCTGTGCTGGAGATGAG | ||
Piscine myocarditis virus (PMCV) | F | AGGGAACAGGAGGAAGCAGAA | [43] |
Probe | TGGTGGAGCGTTCAA | ||
R | CGTAATCCGACATCATTTTGTGA | ||
Infectious pancreatic necrosis virus Segm. A (IPNV) | F | ACCCCAGGGTCTCCAGTC | [29] |
Probe | TCTTGGCCCCGTTCATT | ||
R | GGATGGGAGGTCGATCTCGTA | ||
Infectious salmon anemia virus S7 (ISAV) | F | TGGGATCATGTGTTTCCTGCTA | [44] |
Probe | CACATGACCCCTCGTC | ||
R | GAAAATCCATGTTCTCAGATGCAA | ||