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. 2008 Jun 11;82(16):7863–7874. doi: 10.1128/JVI.00310-08

TABLE 2.

List of primers used in nested PCR and in sequencing reaction

Region and primera Sequence (5′→3′) Length Terminal position
5′ 3′
CA
    Gag out CA F GACTGTATCTACTGCCACAGC 21-mer 927 947
    Gag out CA R TTCTTGGCAGGCCCTCAGTTTT 22-mer 1674 1653
    Gag int CA F GGGATTAGACACCAGACCATC 21-mer 972 992
    Gag int CA R CTGGGCTCTGCTTGTTGTTCT 21-mer 1376 1356
V3-V4
    Env out F GCGCAAGTAGTGTGGAGACT 20-mer 6791 6810
    Env out R CTGCATAACTTCTTCCGGCAC 21-mer 8080 8060
    Hd int F GGATGGTGGAACCAAGTAGC 20-mer 7334 7353
    Env int R GGTAAATCCGATGTGCAAGACC 22-mer 7887 7866
RT
    RT out F GGAGTAGGAGGAGGAAAAAGAGGAAC 26-mer 2157 2182
    RT out R GCCCATCCACTTATATGGGGGC 22-mer 3029 3008
    RT int F GGGCCTCAGGTAAAACAGTGGC 22-mer 2391 2412
    RT int R GTCTTCCGGGGTTTCAAATCCCCAC 25-mer 2993 2969
a

Primers for the CA region were based on those of Hohdatsu et al. (12), and primers for the V3-V4 region, with exception of Env out R, were based on those of Bachman et al. (3). All RT primers were based on the TM2 subtype B sequence.