TABLE 1.
Oligonucleotide primers and probes used in the conventional RT-PCR and TaqMan RT-PCR
| Assay | Serotype | Identification | Sequence (5′-3′) | Size (bp) | Gene | No. of strainsc |
|---|---|---|---|---|---|---|
| Conventional RT-PCR with cross-reactive primers | Dus (forward) | TCAATATGCTGAAACGCGCGAGAAACCG | 511 | C-PrM. | ||
| Duc (reverse) | TTGCACCAACAGTCAATGTCTTCAGGTTC | |||||
| Conventional RT-PCR with type-specific primers | 1 | D1s (forward) | GGACTGCGTATGGAGTTTTG | 490 | E-NS1 | |
| D1c (reverse) | ATGGGTTGTGGCCTAATCAT | |||||
| 2 | D2S (forward) | GTTCCTCTGCAAACACTCCA | 230 | E | ||
| D2c (reverse) | GTGTTATTTTGATTTCCTTG | |||||
| 3 | D3s (forward) | GTGCTTACACAGCCCTATTT | 320 | E-NS1 | ||
| D3c (reverse) | TCCATTCTCCCAAGCGCCTG | |||||
| 4 | D4s (forward) | CCATTATGGCTGTGTTGTTT | 398 | NS2a-NS2b | ||
| D4c (reverse) | CTTCATCCTGCTTCACTTCT | |||||
| TaqMan RT-PCR with type- specific primers and probes | 1 | D1MGBEn469s (forward) | GAACATGGRACAAYTGCAACYAT | 67 | E | 76d |
| D1MGBEn493pa (probe) | ACACCTCAAGCTCC | |||||
| D1MGBEn536r (reverse) | CCGTAGTCDGTCAGCTGTATTTCA | |||||
| 2 | D2MGBEn493s (forward) | ACACCACAGAGTTCCATCACAGA | 68 | E | 203e | |
| D2MGBEn545pa (probe) | CGATGGARTGCTCTC | |||||
| D2MGBEn568r (reverse) | CATCTCATTGAAGTCNAGGCC | |||||
| 3 | D3MGBEn1s (forward) | ATGAGATGYGTGGGAGTRGGAAAC | 70 | E | 59f | |
| D3MGBEn27pa (probe) | AGATTTTGTGGAAGGYCT | |||||
| D3MGBEn71r (reverse) | CACCACDTCAACCCACGTAGCT | |||||
| 4 | D4TEn711s (forward) | GGTGACRTTYAARGTHCCTCAT | 75 | E | 30g | |
| D4TEn734pb (probe) | CCAAGAGACAGGATGTGACAGTGCTRGGATC | |||||
| D4TEn786c (reverse) | WGARTGCATRGCTCCYTCCTG |
Labeled at the 5′ end with the FAM reporter dye and at the 3′ end with the quencher dye TAMRA.
MGB probes were labeled at the 5′ end with the FAM reporter dye and were not labeled at the 3′ end with the quencher dye TAMRA.
Retrieved from GenBank to design primers and probes.
AF425639, AF514876, AF514878, AF514883, AF514885, AJ574760, AY206457, AB111064-78, AF226685, AF298807-8, AF311956-58, AF425609-38, AF513110, AJ438941, AY145121-23, AY153755, D00501-05, M23027, M87512, S64849, U88535-37, and X76219.
A91810, AF004019-20, AF01041, AF022434-41, AF038402-3, AF093674, AF100459-69, AF19661, AF163096, AF195032-44, AF19678-88, AF204177-78, AF231715-20, AF264053-4, AF276619, AF295694-709, AF359579, AF363069-92, AF398106-14, AF410345-79, AF469175-6, AF489932, AF509530, AY037116, AY044442, AY079923-24, D00345-6, D10514, AB111448-54, L04561, L10040-55, M15075, M19197, M20558, M24444-51, M29095, M84727-28, U87411-12, X15214, X15433-34, X54319, and X65240.
AF147456-60, AF317645, AF349753, AF533079, AY038605, AY135419, AY145712-30, AB111080-84, L11422-42, L11619-20, L41125, and NC_001475.
AF231722-25, AF289029, AF326573, AF375822, AB111085-88, NC_002640, and U18425-42.