TABLE 1.
Primers and probes
| Primer or probe | Positiona | Sequence (5′-3′) | Virus and/or fragment size (bp) |
|---|---|---|---|
| Universal primersd | |||
| BJU-1b | (2518–2539) | GGGCAGCCTATGTATGG(T,C)cATGG | JCV, 354 |
| BJU-2 | (2868–2889) | TCTGGACATGGATCAAGCACTG | BKV(Dun), 372 |
| BKV(AS), 360 | |||
| Virus-specific probes | |||
| BDN-1.1 | (2798–2819) | TCTGACCTTTGGGAATCTTCAG | BKV(Dun) specific |
| BAS-1.1 | (2534–2553) | GCTGTGAGGGTTTTCTGAAT | BKV(AS) specific |
| JMG-1.1 | (2650–2671) | TACAGATGTGAAAAGTGCAGTT | JCV specific, Mad-1 and Cin |
| BK virus-specific primers and probes | |||
| BES-3 | (4222–4243) | AATATTATGCCCAGCACACATG | 151 |
| BES-6 | (4393–4372) | CTTTCCCTCTGATCTACACCAG | |
| BES-3.1 | (4287–4304) | TATACAGAATTTGAGCTT | |
| BES-3.3 | (4287–4304) | TATACAGAATTAAAGCTT | |
| BLS-3 | (1818–1837) | GCTTCCCTGTTACAGCACAG | 95 |
| BLS-4 | (1912–1893) | GTACAGTTACAGCCTCCCAC | |
| BLS-3.1 | (1843–1867) | ATTCCCCTCCCCAATTTAAATGAGG | |
| BTP-1 | (3049–3070) | TACAGGCCTAAACCAAATTAGC | 168 |
| BTP-2 | (3216–3195) | GAGTATCCTGTCCCTAAAACCC | |
| BTP-1.1 | (3121–3138) | CTCTGAGTTTTGTAAGGA | |
| BRR-1 | (5018–5047) | CTTTCTCGAGGTGAAATTCCTTACACTTCC | 513 |
| BRR-2 | (377–348) | CAGTACTAGTGGGGACAAGGCCAAGATTCC | |
| JC virus-specific primers and probes | |||
| JES-3 | (4085–4106) | AATATTATGACCCCCAAAACCA | 151 |
| JES-6 | (4256–4235) | CTTTCCTGTAGATCTGCATGCA | |
| JES-3.1 | (4178–4197) | GGTATACACAGCAAAAGAAG | |
| JTP-1 | (2990–3011) | GCAGCTTAGTGATTTTCTCAGG | 141 |
| JTP-2 | (3109–3130) | CACCAAAACAAAAGAACACAGG | |
| JTP-1.1 | (3053–3077) | CTGTAAAGTTCTAGGCACTGAATAT | |
| JRR 5 | (4979–5009) | TCCATGGATCCCTCCCCTATTCAGCACTTTGT | 473 |
| JRR 6 | (315–285) | TTTCACTGCAGCCTTACGTGACAGCTGGCGA |
a
Each virus numbered after BKV(Dun), JCV(Mad-1), and SV40 (10).
b
Primers are represented with whole numbers, probes are represented with decimal numbers.
c
T and C combined at this position in order to match both BKV and JCV sequences.
d
For amplification of both BKV and JCV.