Table 1.
Primers and probes.
| Targeted gene | Primer/probe name | Sequence (5’- 3’) | Accession n°/ reference | ||
|---|---|---|---|---|---|
|
Primers for PCR and RT-PCR |
PCR |
RT-PCR |
|
|
|
| CyHV-3 ORF3 |
ORF3InF |
|
• |
TATGCCCACATGATGCTGTT |
DQ657948 |
| |
ORF3InR |
|
• |
CAGTCAGACCCTTCCTCTGC |
|
| CyHV-3 ORF55 |
ORF55InF |
• |
|
AGCGCTACACCGAAGAGTCC |
|
| |
ORF55stopR |
• |
|
TCACAGGATAGATATGTTACAAG |
|
| |
ORF55ATGF |
|
• |
ATGGCTATGCTGGAACTGG |
|
| |
ORF55InR |
|
• |
GGCGCACCCAGTAGATTATG |
|
| CyHV-3 ORF78 |
ORF78InF |
|
• |
TGGACGACGAACACCCTTC |
|
| |
ORF78InR |
|
• |
GGTAGAGGGTACAACCACG |
|
| CyHV-3 ORF132 |
ORF132InF |
|
• |
GGATCCGTTTTCTGGGTCTG |
|
| |
ORF132InR |
|
• |
CTCAATCCCTCACCGACCTC |
|
| CyHV-3 ORF133 |
ORF133InF |
|
• |
GACGAGATCCCTATCCGCAG |
|
| |
ORF133InR |
|
• |
GACCTCGGGTATGGTCGGTA |
|
| CyHV-3 ORF134 |
ORF134stopF |
|
• |
TCAATGTTTGCGCTTGGTTTTC |
|
| |
ORF134ATGR |
|
• |
ATGTTCCTTGCAGTGCTAC |
|
| |
ORF134InF |
• |
|
GGTTTCTCTTTGTAGTTTTCCG |
|
| |
ORF134InR |
• |
|
CACCCCAACTTTTGAGACAAC |
|
| |
ORF134outseqF |
• |
|
GTCAACATGGACGAGCGTGA |
|
| |
ORF134outseqR |
• |
|
GTGGGGATATCAAACACGCA |
|
| CyHV-3 ORF135 |
ORF135InF |
|
• |
ACACCACCAACGAGACATGC |
|
| |
ORF135InR |
|
• |
CTTTTCGGACCAGAAGACCG |
|
| Carp β-actin |
Actin-F |
|
• |
ATGTACGTTGCCATCCAGGC |
M24113 |
| |
Actin-R |
|
• |
GCACCTGAACCTCTCATTGC |
|
|
Primers for amplification of recombination cassettes | |||||
| H1-galK-H2 cassette |
134 galK F |
|
|
ATGTTCCTTGCAGTGCTACTAACCG |
Warming et al. [34] |
| CGACCATCTTCTTCGAGGCTCGGGG | |||||
| CCTGTTGACAATTAATCATCGGCA | |||||
| |
134 galK R |
|
|
TCAATGTTTGCGCTTGGTTTTCATG |
|
| TTCTTGACGTCTTTTGCGACCAGGA | |||||
| TCAGCACTGTCCTGCTCCTT | |||||
| H1-ORF134-H2 |
H1F |
|
|
GCTCATCAATCGCAGCAGCA |
DQ657948 |
| cassette | |||||
| |
H2R |
|
|
CAAGCCATTATCCTGTTGGG |
|
|
Primers and probes for real-time TaqMan PCR quantification of CyHV-3 genome | |||||
| CyHV-3 ORF89 |
KHV-86F |
|
|
GACGCCGGAGACCTTGTG |
AF411803 |
| |
KHV-163R |
|
|
CGGGTTCTTATTTTTGTCCTTGTT |
|
| |
KHV-109P |
|
|
(6FAM)CTTCCTCTGCTCGGCGAGCACG(BHQ1) |
|
| Carp glucokinase |
CgGluc-162F |
|
|
ACTGCGAGTGGAGACACATGAT |
AF053332 |
| |
CgGluc-230R |
|
|
TCAGGTGTGGAGCGGACAT |
|
| |
CgGluc-185P |
|
|
(6FAM)AAGCCAGTGTCAAAATGCTGCCCACT(BHQ1) |
|
|
Primers for RT-qPCR analysis of carp gene expression | |||||
| 40S |
40S-F |
|
|
CCGTGGGTGACATCGTTACA |
AB012087 |
| |
40S-R |
|
|
TCAGGACATTGAACCTCACTGTCT |
|
| IL-1β |
IL-1β-F |
|
|
AAGGAGGCCAGTGGCTCTGT |
AJ245635 |
| |
IL-1β-R |
|
|
CCTGAAGAAGAGGAGGCTGTCA |
|
| TNF-α1 and 2 |
TNF-α1 and 2-F |
|
|
GCTGTCTGCTTCACGCTCAA |
AJ311800 |
| |
TNF-α1 and 2-R |
|
|
CCTTGGAAGTGACATTTGCTTTT |
|
| CXCa |
CXCa-F |
|
|
CTGGGATTCCTGACCATTGGT |
AJ421443 |
| |
CXCa-R |
|
|
GTTGGCTCTCTGTTTCAATGCA |
|
| IL-10 |
IL-10-F |
|
|
CGCCAGCATAAAGAACTCGT |
AB110780 |
| |
IL-10-R |
|
|
TGCCAAATACTGCTCGATGT |
|
| IFNγ-2 |
IFNγ-2-F |
|
|
TCTTGAGGAACCTGAGCAGAA |
AM168523 |
| |
IFNγ-2-R |
|
|
TGTGCAAGTCTTTCCTTTGTAG |
|
| IL-6 |
IL-6M17-F |
|
|
CACATTGCTGTGAGGGTGAA |
AY102633 |
| IL-6M17-R | GCATCCATAGGCTTTCTGCT | ||||
Underlined: 50bp corresponding to CyHV-3 sequence.