TABLE 3 .
Oligonucleotides used for RT-qPCR of viral gRNA and sgmRNA
| Amplicon | Oligonucleotidea | Oligonucleotide sequence (5′→3′)b | Methodc |
|---|---|---|---|
| gRNA | Rep-VS | TTCTTTTGACAAAACATACGGTGAA | SYBR |
| Rep-RS | CTAGGCAACTGGTTTGTAACATCTTT | SYBR | |
| sgmRNA S | LCS1-VS | CCAACTCGAACTAAACTTTGGTAACC | SYBR |
| LCS1-RS | TCAATGGCATTACGACCAAAAC | SYBR | |
| sgmRNA 3a | rt3a-VS2 | CGGACACCAACTCGAACTAAACTTAC | SYBR |
| rt3a-RS | ATCAAGTTCGTCAAGTACAGCATCTAC | SYBR | |
| sgmRNA E | Ldrt-VS | CGTGGCTATATCTCTTCTTTTACTTTAACTAG | SYBR |
| mRNAE-RS | CAATGCCCTAGGAAACGTCATAG | SYBR | |
| sgmRNA M | Ldrt-VS | CGTGGCTATATCTCTTCTTTTACTTTAACTAG | SYBR |
| mRNAM-RS | GCATGCAATCACACACGCTAA | SYBR | |
| sgmRNA N | Ldrt-VS | CGTGGCTATATCTCTTCTTTTACTTTAACTAG | SYBR |
| N82−RS | TCTTCCGACCACGGGAATT | SYBR | |
| sgmRNA 7 | Ldrt-VS | CGTGGCTATATCTCTTCTTTTACTTTAACTAG | SYBR |
| 7 (38)-RS | AAAACTGTAATAAATACAGCATGGAGGAA | SYBR | |
| gRNA | Rep-VS | TTCTTTTGACAAAACATACGGTGAA | TaqMan |
| Rep-RS | CTAGGCAACTGGTTTGTAACATCTTT | TaqMan | |
| Rep-MGB | FAM-AGGGCACCGTTGTCA-MGB | TaqMan | |
| sgmRNA 7 | Ldrt-VS | CGTGGCTATATCTCTTCTTTTACTTTAACTAG | TaqMan |
| 7 (38)-RS | AAAACTGTAATAAATACAGCATGGAGGAA | TaqMan | |
| mRNA7-MGB | FAM-CGAACTAAACGAGATGCT-MGB | TaqMan |
a
VS, virus sense; RS, reverse sense; MGB, minor groove binder group.
b
FAM, 6-carboxyfluorescein.
c
SYBR, SYBR green-based detection chemistry for qPCR; TaqMan, TaqMan-based detection for qPCR.