Table 2.
Primers sequences employed for the Degenerate/Consensus PCR according VanDevanter et al. (2a) and the Consensus Panherpes PCR according to Ehlers et al. (2b). Primers used for Sanger Sequencing following the Degenerate/Consensus PCR according to VanDevanter et al. are shown in italic. Degenerate and inosine-substituted equivalents are shown in bold. Ia = Deoxyinosine.
| 2a. Consensus Panherpes Polymerase Chain Reaction Primers | |
|---|---|
| First PCR | |
| Forward | Reverse |
| DFA: 5′-GAY TTY GCN AGY YTN TAY CC-3′ | KG1: 5′-GTC TTG CTC ACC AGN TCN ACN CCY TT-3′ |
| ILK: 5′-TCC TGG ACA AGC AGC ARN YSG CNM TNA A-3I’ | |
| Second PCR | |
| Forward | Reverse |
| TGV: 5′-TGT AAC TCG GTG TAY GGN TTY ACN GGN GT-3′ | IYG: 5′-CAC AGA GTC CGT RTC NCC RTA DAT-3′. |
| Approximate product: 215- to 315-bp | |
| Sanger Sequencing | |
| Forward | Reverse |
| TGVseq: 5′-CAT CTG ATG TAA CTC GGT GTA-3′ bottom line | IYGseq: 5′-GAC AAA CAC AGA GTC CGT-3′ |
|
2b. Consensus Panherpes PCR with Consensus/Degenerate
and Deoxyinosine-Substituted Primers | |
| First PCR | |
| Forward | Reverse |
| DFA: 5′-GAY TTY GCN AGY YTN TAY CC-3′ | KG1: 5′-GTC TTG CTC ACC AGN TCN ACN CCY TT-3′ |
| ILK: 5′-TCC TGG ACA AGC AGC ARN YSG CNM TNA A-3′ | |
| Deoxyinosine-substituted equivalent | Deoxyinosine-substituted equivalent |
| DFA: 5′-GAY TTY GCIa AGY YTIa TAY CC-3I′ | KG1: 5′-GTC TTG CTC ACC AGIa TCIa ACIa CCY TT-3′ |
| ILK: 5′-TCC TGG ACA AGC AGC ARIa YSG CIaM TIaA-3′ | |
| Second PCR | |
| Forward | Reverse |
| TGV: 5′-TGT AAC TCG GTG TAY GGN TTY ACN GGN GT-3′ | IYG: 5′-CAC AGA GTC CGT RTC NCC RTA DAT-3′ |
|
Deoxyinosine-substituted equivalent TGV: 5′-TGT AAC TCG GTG TAY GGIa TTY ACIa GGIa GT-3′ |
Deoxyinosine-substituted equivalent IYG: 5′-CAC AGA GTC CGT RTC IaCC RTA IaAT-3′ |