Table 2.

Oligonucleotide primers used for PCR amplification and sequencing of JCV and SV40

Virus type (region)aPosition (nt)bAmplification reactionPrimerProduct size (bp)Annealing temp (°C)Sequence
JCV (VP1 region)1710–1734Nested-leftJLP15215635′-ACAGTGTGGCCAGAATTCCACTACC-3′c
JCV (VP1 region)1902–1924Nested-rightJLP165′-TAAAGCCTCCCCCCCAACAGAAA-3′c
JCV (IG region)2062–2087First-leftEP1A737595′-TGAATGTTGGGTTCCTGATCCCACC-3′
JCV (IG region)2774–2798First-rightEP2A5′-ACCCATTCTTGACTTTCCTAGAGAG-3′
JCV (IG region)2099–2124Nested-leftP1A668595′-CAAGATATTTTGGGACACTAACAGG-3′d
JCV (IG region)2742–2766Nested-rightP2A5′-CCATGTCCAGAGTCTTCTGCTTCAG-3′d
JCV (IG region)2511–2536Nested-rightJCSR478555′-TGATTACAGCATTTTTGTCTGCAAC-3′
JCV (IG region)2364–2388Nested-leftJCSL5′-GGAAGTCCTTCTGTTAATTAAATCAG-3′
JCV (R region)4992–5011First-leftJR1586555′-CCCTATTCAGCACTTTGTCC-3′e
JCV (R region)428–447First-rightJR25′-CAAACCACTGTGTCTCTGTC-3′e
JCV (R region)5060–5079Nested-leftJR3382555′-GGGAATTTCCCTGGCCTCCT-3′e
JCV (R region)297–317Nested-rightJR45′-ACTTTCACAGAAGCCTTACG-3′e
SV40 (TAg)2614–2633First-leftSV1336465′-AATTTGTGATGCTATTGCTT-3′
SV40 (TAg)2932–2950First-rightSV25′-TTGGAGTTTTAGAAAGGCT-3′
SV40 (TAg)2746–2766Nested-leftSV3157505′-CTACAAATGTGGTATGGCTGA-3′
SV40 (TAg)2883–2903Nested-rightSV45′-AGCCAGGAAAATGCTGATAA-3′
SV40 (TAg)2609–2631First-leftSV1A336555′-TGTGAAATTTGTGATGCTATTGC-3′
SV40 (TAg)2922–2945First-rightSV2A5′-GTTTTAGATTGGCTAAGAAACAGT-3′
SV40 (TAg)2746–2766Nested-leftSV5119505′-CTACARATGTGRTATGGCTGA-3′f,g
SV40 (TAg)2844–2864Nested-rightSV65′-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.