TABLE 1.
Primers for S segments and species-specific RT-PCR
| Primer or probea | Sequence |
|---|---|
| S segment | |
| BUN+ | AGTAGTGTACTCCAC |
| BUN− | AGTAGTGTGCTCCAC |
| LACSFUP | AGTAGTGTACTCCACTTGAATACTTTGA |
| LACSFDP | AGTAGTGTGCTCCACTGAATACATT |
| TAHSFUP | AGTAGTGTACTCCACTTGAATACTTTGAA |
| TAHSFDP | AGTAGTGTGCTCCACTGAATACCTT |
| BUNSFUP | AGTAGTGTACTCCACACTACAAACTTG |
| BUNSFDP | AGTAGTGTGCTCCACCTAAAACTTA |
| GERSFUP | GTAGTGTACTCCACGCATAAAACTTT |
| GERSFDP | AGTAGTGTGCTCCACCTTAAACTTAA |
| OROSFUP | AGTAGTGTACTCCACTAT |
| OROSFDP | AGTAGTGTGGCTCCACAT |
| GROSFUP | AGTAGTGTACTCCACACTACATACCAAT |
| GROSFDP | AGTAGTGTGCTCCACCTAATACCTATA |
| Species specific | |
| LAC FP | CCAGATGGGTCCTTGATCA |
| LAC P | CGAGAATGATGATGAGTCTCAGCACG |
| LAC RP | CAATTGGGTTGATAATAGTTGTTCTG |
| CAL FP | GCGGAGTCAAATGGCAT |
| CAL P | AGAATGGTGCAGAAATTTATTTGGCATTC |
| CAL RP | GGTAAAATTTGAAAGTTTCCAAGAA |
| JC FP | GGATATCTAGCCAGATGGGTTCT |
| JC P | CTCAGATGATGACGAGTCTCAGAGAGAACTC |
| JC RP | ATTGGATTCTGCAATTGGATTT |
| SSH FP | GGATATTTAGCCAGATGGGTTC |
| SSH P | AGAGAATGAAGACGAGTCTCGGCG |
| SSH RP | TTGATGATTGTTGTCTTGATCAA |
| TAH FP | CAAAGCTGCTCTCGCTCG |
| TAH P | CCGGAGAGGAAGGCTAGTCCTAAATTTGGA |
| TAH RP | TTCCAGGAAAATGATWATTGACGA |
| INK FP | CATTGGAACAATGGCCC |
| INK P | TCCCAGGAACAGAAATGTTTCTAGAAGTTTTC |
| INK RP | AGGATCCATCATACCATGCTT |
| GER FP | TGTACTCAATACGAATTTCCCTGG |
| GER P | AGGAACAATGCAGTGCCTGACTACGGTC |
| GER RP | TCCACTGATACGGTGGAAGGTA |
| BUN FP | AATTTTCCTGGCAACCGGA |
| BUN P | AACCCAGTTCCTGACGATGGTCTTACCC |
| BUN RP | AAGGAATCCACTGAGGCGG |
| GRO FP | GAGGCTGGAGAATTCCTGT |
| GRO P | TAATACACATTTTCCTGGAAACCGGA |
| GRO RP | GAATCATCGAGGACTGGACT |
| ORO FP | CATTTGAAGCTAGATACGGACAA |
| ORO P | CAATGCTGGTGTTGTTAGAGTCTTCTTCCT |
| ORO RP | CCATGGGCCTCGATG |
| BAT FP | GACGCGAGATTAAAACTAGTCTCTC |
| BAT P | AAGTGAATGGGAGGTTACGCTTAACCTTG |
| BAT RP | AGGAAAATTTGTATTAAATACAGTAACCTTC |
| Nested | |
| ORO N5 | AAAGAGGATCCAATAATGTCAGAGTTCATTT |
| ORO N3 | GTGAATTCCCACTATATGCCAATTCCGAATT |
a
SFUP, S-segment upstream primer; SFDP, S-segment downstream primer; SFSP, S-segment single primer; FP, forward primer; RP, reverse primer; P, TaqMan probe. All sequences are given in the 5′-to-3′ orientation.