TABLE 6.
Primers and probes
| Virus | Oligonucleotide name |
Concn (nM) |
Sequence (5′–3′)a | Positions of the amplicon in the genome (length) |
Target gene |
Reference sequence (GenBank) |
|---|---|---|---|---|---|---|
| HSV-1 | HSV-1 FWDLP1 | 300 | GTTGAGCTAGCCAGCGA | 93560–93683 (124 bp) | UL42 | X14112.1 |
| HSV-1 REVLP1 | 300 | CGTTAAGGACCTTGGTGAGC | ||||
| HSV-1 probeLP1 | 250 | FAM-CGCGAACTGACGAGCTTTGTG-BHQ1 | ||||
| HSV-2 | HSV-2 FWD-2-2 | 400 | CACACCACACGACAACAA | 46783–46872 (90 bp) | UL23 | Z86099.2 |
| HSV-2 REVLP1 | 400 | TAGTTCAAACACGGAAGCC | ||||
| HSV-2 probeLP1 | 200 | JOE-CGGCGATGACGGCAATAAA-BHQ1 | ||||
| VZV | VZV FWDLP1 | 200 | GCGCAAGGCTATTAGAGC | 48283–48145 (139 bp) | ORF28 | KU529566.1 |
| VZV REVLP1 | 200 | ACATGGCAGAAATCCCTG | ||||
| VZV probeLP1 | 150 | TxRd-CGCATACCCGGAAGTTCTTCAGAT-BHQ2 | ||||
| EBV | EBV FWD | 200 | CGGAAGCCCTCTGGACTTC | 153036–152947 (90 bp) | BALF5 | KF717093.1 |
| EBV REV | 300 | CCCTGTTTATCCGATGGAATG | ||||
| EBV Probe | 300 | FAM-TGTACACGCACGAGAAATGCGCC-BHQ1 | ||||
| HCMV | H5 FWD211 | 400 | GTGYTCCGTGAATCGTTAC | 80396–80329 (68 bp) | UL54 | AB329634.1 |
| H5 rev 211 | 500 | AGTCKACCTCGATATCACAAGTCG | ||||
| H5 Probe 20 | 300 | TxRd-ACCCTGCTGCCGCCAGT-BHQ2 | ||||
| KSHV | HHV8 fwd 3.1 | 200 | ATATACGGCGACACTGACTC | 13603–13761 (159 bp) | ORF9 | AP017458.1 |
| HHV8 REV 10 | 200 | GAGCAGAAGGCACTTGAAG | ||||
| H8 Probe 300 | 200 | JOE-CGGAGGAGCTAGCGTCAATCA-BHQ1 | ||||
| HHV-6A | HHV6A FWD1-3 | 500 | CGGCCTCCAGAGTTGTAA | 133969–133894 (76 bp) | U90 | KP257584.1 |
| HHV6A REV 10 | 500 | TGTCCCTTCAACTACTGAATC | ||||
| HHV6A LNA Probe A1 | 100 | FAM-AC[+A]T[+G]TTGC[+T]A[+G]AAA[+G][+A]CT-BHQ1 | ||||
| HHV6A LNA Probe A2 | 100 | FAM-AC[+A]T[+G]TTGC[+T]A[+C]AAA[+G][+A]CT-BHQ1 | ||||
| HHV-6B | H6B FOTY1 | 300 | TTTGACAGGAGTTGCTGAG | 136176–136258 (83 bp) | U90 | AB021506.1 |
| H6B ROTY 1 | 300 | GGATTCAGGAAAAAGGTTCTAA | ||||
| H6B PROBE MVP | 200 | JOE-AGGAAGCGTTTCGGTACACTTGGAG-BHQ1 | ||||
| HHV-7 | HHV7 1. FWD | 400 | CTCGCAGATTGCTTGTTG | 88332–88490 (159 bp) | U57 | AF037218.1 |
| HHV7 1. REV | 400 | GCATACACCAACCCTACTGTAA | ||||
| H7 MOP PROBE | 300 | TxRd-TTAGGCATCACGTTGGCATTG-BHQ2 |
a
Nucleotides in brackets refer to locked nucleic acids.