TABLE 1.
Primers and probes used in the rRT-PCR assays
| rRT-PCR assay name | EIV subtype | Primer or probea | Sequence (5′ to 3′) (nt location) | GenBank accession no. |
|---|---|---|---|---|
| EqFlu NP | H3N8 | EqFlu NP F | GAAGGGCGGCTGATTCAGA (157-175) | DQ124184 |
| EqFlu NP R | TTCGTCGAATGCCGAAAGTAC (199-219) | |||
| EqFlu NP Pr | bCAGCATAACAATAGAAAGGAc (177-196) | |||
| EqFlu M | EqFlu M F | ACCGAGGTCGAAACGTACGT (38-57) | DQ124188 | |
| EqFlu M R | CGCGATCTCGGCTTTGA (84-100) | |||
| EqFlu M Pr | bCTCTCTATCGTACCATCAGGc (59-78) | |||
| EqFlu HA3 | EqFlu HA3 F | TCACATGGACAGGTGTCACTCA (448-469) | L39914 | |
| EqFlu HA3 R | GGCTGATCCCCTTTTGCA (485-506) | |||
| EqFlu HA3 Pr | bAACGGAAGAAGTGGAGCc (471-487) | |||
| EqFlu HA3-Mia | EqFlu HA3-Mia F | GCAGTGCTTTCAGCAATTGC (346-365) | M29257 | |
| EqFlu HA3-Mia R | AGAGACCGGAGCGATGCA (389-406) | |||
| EqFlu HA3-Mia Pr | dCCATATGACGTCCCTGACTc (369-387) | |||
| EqFlu NP-Pra | H7N7 | EqFlu NP-Pra F | GGCGTCTCAAGGCACCAA (48-65) | M63748 |
| EqFlu NP-Pra R | TCTGGCGTTCTCCACCAGTT (87-106) | |||
| EqFlu NP-Pra Pr | bCGACCTTATGAACAAATGc (67-84) | |||
| EqFlu M-Pra | EqFlu M-Pra F | CGCGCAGAGACTTGAGAATG (97-116) | CY005801 | |
| EqFlu M-Pra R | CATTCCATGAGAGCCTCAAGATCT (136-159) | |||
| EqFlu M-Pra Pr | bTTTGCAGGGAAAAATAc (119-134) | |||
| EqFlu HA7-Pra | EqFlu HA7-Pra F | CAATGGAGAGACTAGCGCATGT (441-462) | X62552 | |
| EqFlu HA7-Pra R | AGAAGCCATTTCATCTCTGCATAA (483-506) | |||
| EqFlu HA7-Pra Pr | eAAGGTCAAGATCTTCCc (465-480) | |||
| EqFlu HA7 | EqFlu HA7 F | TCCTCTGTGTACGTGCAGATAAAATC (59-84) | X62556 | |
| EqFlu HA7 R | GGGTGTCTACTTTGGTTCCATTAGA (106-130) | |||
| EqFlu HA7 Pr | bCCTAGGACGTCATGCTGc (87-103) |
a
F, forward primer; R, reverse primer; Pr, probe.
b
Reporter dye (6-carboxyfluorescein)-labeled nucleotide.
c
Nonfluorescent quencher dye (MGB)-labeled nucleotide.
d
Reporter dye (VIC)-labeled nucleotide.
e
Reporter dye (NED)-labeled nucleotide.