TABLE 2.
Oligonucleotide primers used for PCR amplification and sequencing of JCV and SV40
| Virus type (region)a | Position (nt)b | Amplification reaction | Primer | Product size (bp) | Annealing temp (°C) | Sequence |
|---|---|---|---|---|---|---|
| JCV (VP1 region) | 1710–1734 | Nested-left | JLP15 | 215 | 63 | 5′-ACAGTGTGGCCAGAATTCCACTACC-3′c |
| JCV (VP1 region) | 1902–1924 | Nested-right | JLP16 | 5′-TAAAGCCTCCCCCCCAACAGAAA-3′c | ||
| JCV (IG region) | 2062–2087 | First-left | EP1A | 737 | 59 | 5′-TGAATGTTGGGTTCCTGATCCCACC-3′ |
| JCV (IG region) | 2774–2798 | First-right | EP2A | 5′-ACCCATTCTTGACTTTCCTAGAGAG-3′ | ||
| JCV (IG region) | 2099–2124 | Nested-left | P1A | 668 | 59 | 5′-CAAGATATTTTGGGACACTAACAGG-3′d |
| JCV (IG region) | 2742–2766 | Nested-right | P2A | 5′-CCATGTCCAGAGTCTTCTGCTTCAG-3′d | ||
| JCV (IG region) | 2511–2536 | Nested-right | JCSR | 478 | 55 | 5′-TGATTACAGCATTTTTGTCTGCAAC-3′ |
| JCV (IG region) | 2364–2388 | Nested-left | JCSL | 5′-GGAAGTCCTTCTGTTAATTAAATCAG-3′ | ||
| JCV (R region) | 4992–5011 | First-left | JR1 | 586 | 55 | 5′-CCCTATTCAGCACTTTGTCC-3′e |
| JCV (R region) | 428–447 | First-right | JR2 | 5′-CAAACCACTGTGTCTCTGTC-3′e | ||
| JCV (R region) | 5060–5079 | Nested-left | JR3 | 382 | 55 | 5′-GGGAATTTCCCTGGCCTCCT-3′e |
| JCV (R region) | 297–317 | Nested-right | JR4 | 5′-ACTTTCACAGAAGCCTTACG-3′e | ||
| SV40 (TAg) | 2614–2633 | First-left | SV1 | 336 | 46 | 5′-AATTTGTGATGCTATTGCTT-3′ |
| SV40 (TAg) | 2932–2950 | First-right | SV2 | 5′-TTGGAGTTTTAGAAAGGCT-3′ | ||
| SV40 (TAg) | 2746–2766 | Nested-left | SV3 | 157 | 50 | 5′-CTACAAATGTGGTATGGCTGA-3′ |
| SV40 (TAg) | 2883–2903 | Nested-right | SV4 | 5′-AGCCAGGAAAATGCTGATAA-3′ | ||
| SV40 (TAg) | 2609–2631 | First-left | SV1A | 336 | 55 | 5′-TGTGAAATTTGTGATGCTATTGC-3′ |
| SV40 (TAg) | 2922–2945 | First-right | SV2A | 5′-GTTTTAGATTGGCTAAGAAACAGT-3′ | ||
| SV40 (TAg) | 2746–2766 | Nested-left | SV5 | 119 | 50 | 5′-CTACARATGTGRTATGGCTGA-3′fg |
| SV40 (TAg) | 2844–2864 | Nested-right | SV6 | 5′-AAGAACATGGAAGACTCAGGG-3′f |
a
VP1, virion protein 1; TAg, T antigen.
b
For JCV, the sequence positions are relative to the JCV-Mad-1 sequence; for SV40, the sequence positions are relative to a standard SV40 sequence.
c
From the work of Agostini et al. (5).
d
Modified from the work of Kunitake et al. (23).
e
From the work of Monaco et al. (27).
f
From the work of Lednicky et al. (24).
g
R = A + G.