TABLE 4.
Primers used for LDR
| Target region | Downstream primer, sequence (5′-3′) | Tm (°C)b | Allele-specific (upstream) primer,a sequence (5′-3′) | Tm (°C) | LDR product length (bp) |
|---|---|---|---|---|---|
| 1 (NS2a) | WNV831aCOM, (Phos)CTATCATGCTTGCACTCCTAGTCCTAGTGTTTGG(6-FAM) | 74 | WNV831GZp52, (NH2)TCCGTTCCGCCAGAGGGTGAGTGGACRGCCAAGATCAGCATKCCAG | 85-87 | 80 |
| WNV831bCOM, (Phos)CTATACTGATTGCTCTGCTAGTYCTGGTGTTTGG(6-FAM) | 73-74 | ||||
| WNV831cCOM, (Phos)CCATACTGATTGCCCTGCTAGTTCTAGTGTTTGG(6-FAM) | 74 | ||||
| WNV939aCOM, (Phos)GAGACGTCG,TGCACTTGGCACTTATGG(6-FAM) | 71 | WNV939aGZp53, (NH2)TCGCCGTCCGCTGTCTTTGGCGTTTGCTGAAGCRAACTCAGGAG | 84 | 72 | |
| WNV939bCOM, (Phos)GAGACGTGGTACACTTGGCGCTCATGG(6-FAM) | 73 | WNV939bGZp53, (NH2)TCGCCGTCCGCTGTCTTTGGCTTTCGCAGAATCYAATTCRGGAG | 82-84 | ||
| WNV939cCOM, (Phos)GAGATGTGGTGCATCTGGCGCTCATGG(6-FAM) | 73 | WNV939cGZp53, (NH2)TCGCCGTCCGCTGTCTTTGGCCTTTGCAGAATCMAACTCAGGAG | 83-84 | ||
| WNV1021aCOM, (Phos)GACCAACCAAGAGAGTATTTTGCTCATGCTTG(6-FAM) | 71 | WNV1021aGZp54, (NH2)GACCAGGCCTCGACCCACCCGGTGGCTTCCTTTTTGAAGGCAAGGTG | 87 | 79 | |
| WNV1021bCOM, (Phos)GACCAACCAGGAGAACATYTTGTTGATGTTGG(6-FAM) | 71-73 | WNV1021bGZp54, (NH2)GACCAGGCCTCGACCCACCCGGTGGCATCGTTTCTCAAAGCGAGATG | 87 | ||
| WNV1021cCOM, (Phos)GACCAACCAAGAAAACATTCTGCTGATGTTGG(6-FAM) | 71 | WNV1021cGZp54, (NH2)GACCAGGCCTCGACCCACCCGGTAGCATCATTTCTCAAGGCGAGATG | 86 | ||
| 2 (NS5) | WNV5341aCOM, (Phos)GTTGGAATATTGTTACCATGAAGAGTGGAGTCGACGTC(6-FAM) | 76 | WNV5341aGZp55, (NH2)GCCACGCTGCCAGGACTCCGATGAAGAACCACAACTGGTGCAGAGCTATG | 86 | 88 |
| WNV5341bCOM, (Phos)GATGGAACATTGTCACCATGAAGAGYGGRGTGGATGTG(6-FAM) | 77-79 | WNV5341bGZp55, (NH2)GCCACGCTGCCAGGACTCCGATGAAGAGCCCCAACTRGTGCAAAGTTATG | 85-86 | ||
| WNV5341cGZp55, (NH2)GCCACGCTGCCAGGACTCCGATGAAGAGCCCCAGCTAGTGCAGAGCTATG | 88 | ||||
| WNV5427aCOM, (Phos)AGTCATCGTCAAGTGCCGAGGTAGAAGAACACCGC(6-FAM) | 78 | WNV5427aGZp56, (NH2)TCCGGTCTTGGTCGCTTCGCGCGAGCGACACACTGCTCTGTGACATTGGAG | 88 | 86 | |
| WNV5427bCOM, (Phos)AGTCYTCRTCAAGTGCTGAGGTTGAAGAGCATAGG(6-FAM) | 74-76 | WNV5427bGZp56, (NH2)TCCGGTCTTGGTCGCTTCGCTGYTGCGAYACYCTCCTTTGTGACATCGGAG | 85-88 | ||
| WNV5427cCOM, (Phos)AGTCCTCATCAAGTGCTGAAGTTGAAGAACATAGA(6-FAM) | 72 | WNV5427cGZp56, (NH2)TCCGGTCTTGGTCGCTTCGCTGTTGTGACACTCTCCTTTGTGATATCGGAG | 85 | ||
| WNV5548aCOM, (Phos)CCAAAGTGATTGAGAAGATGGAAACACTCC(6-FAM) | 69 | WNV5548aCZp57, (NH2)GTCTTCGCGGTGGGTGCCTGCTGCATCAAAGTGCTATGCCCTTACATGC | 86 | 79 | |
| WNV5548bCOM, (Phos)CRAAAGTCATAGAGAAGATGGAGCTRCTCC(6-FAM) | 69-72 | WNV5548bCZp57, (NH2)GTCTTCGCGGTGGGTGCCTGTTGYGTGAAGGTRCTSTGCCCCTACATGC | 86-88 | ||
| WNV5548cCOM, (Phos)CAAAGGTCATAGAAAAGATGGAGCTGCTCC(6-FAM) | 71 | ||||
| 3 (NS5) | WNV6094aCOM, (Phos)GAGTCAAATACGTCCTCAATGAGACCACGAACTGGCTG(6-FAM) | 78 | WNV6094aGZp58, (NH2)GCGTTTGGTTGGCTGCGGACCACAAAGGCTCCAGAGCCTCCAGAAG | 86 | |
| WNV6094bCOM, (Phos)GAGTGAAGTATGTGCTCAAYGAAACCACCAAYTGGTTG(6-FAM) | 75-77 | WNV6094bGZp58, (NH2)GCGTTTGGTTGGCTGCGGACCACGAAAGCTCCBGAACCGCCAGAAG | 86-87 | 84 | |
| WNV6094cCOM, (Phos)GAGTGAAGTACGTGCTCAAYGAGACCACCAAYTGGTTG(6-FAM) | 77-79 | ||||
| WNV6094dCOM, (Phos)GAGTTAAGTATGTGCTCAATGAAACCACCAATTGGTTG(6-FAM) | 73 | ||||
| WNV6168aCOM, (Phos)TGYTCCCGGGAGGAATTTATYGGAAAAGTCAACAG(6-FAM) | 73-76 | WNV6168aGZp59, (NH2)GGACCTCGGCCACGCTCTGCTTAGCCCGCGAYAARAAACCCAGGATG | 86-88 | 82 | |
| WNV6168bCOM, (Phos)TGCTCGCGAGAGGAATTTATAAGGAAGGTCAATAG(6-FAM) | 73 | WNV6168bGZp59, (NH2)GGACCTCGGCCACGCTCTGCCTGGCACGAGAAAAGCGTCCCAGAATG | 88 | ||
| WNV6168cCOM, (Phos)TGCTCTCGAGAGGARTTCATAAGAAAGGTCAACAG(6-FAM) | 73-74 | WNV6168cGZp59, (NH2)GGACCTCGGCCACGCTCTGCCTGGCCAGAGAAAAACGTCCCAGAATG | 87 | ||
| WNV6244aCOM, (Phos)GGAAGAACGCCCGGGAAGCTGTAGAGGATCC(6-FAM) | 77 | WNV6244aTZp60, (NH2)GCCACTCGTCCGTCCGCCACAGGAGCGATGTTTGAAGAACAGAACCAAT | 85 | 80 | |
| WNV6244bCOM, (Phos)GGAGGAGTGCTAGAGAAGCGGTTGAAGATCC(6-FAM) | 75 | WNV6244bTZp60, (NH2)GCCACTCGTCCGTCCGCCACGGGTGCCATGTTTGAAGARCAGAAYCAAT | 85-86 | ||
| WNV6244cCOM, (Phos)GGAGGAGCGCCAGAGAAGCAGTTGAAGATCC(6-FAM) | 76 |
a
The zip code complements on the upstream primers are in bold.
b
Tm, melting temperature.