Table 2.
Primer and probe sequences used by the different laboratories and number of mismatches within the ACHIEV2E HIV-2 group A and group B standards and samples
| Region and primer or probe | Sequence | No. of hits in 25 HIV-2 genomesa | No. of mismatches |
|||
|---|---|---|---|---|---|---|
| HIV-2 sample A | HIV-2 sample B | HIV-2 standard A | HIV-2 standard B | |||
| LTR | ||||||
| Belgium For | TCGCCGCCTGGTCATTC | 22 | 1 | 2 | 1 | 0 |
| Belgium Rev | GCCGCCCTTACTGCCTTCA | 24 | 1 | 1 | 0 | 0 |
| Gambia For | ATTGAGCCCTGGGAGGTTCTCTCCA | 22 | —b | — | — | — |
| Gambia Rev | TTCGGGCGCCAACCTGCTAGGGATTTT | 23 | 1 | 0 | 0 | 0 |
| Switzerland TMFPR1 | AACAAACCACGACGGAGTGC | 17 | 0 | 0 | ||
| Switzerland TMRPR1 | CCACACGCTGCCTTTGGTA | 11 | 1 | 1 | ||
| Switzerland TMPROBE1 | TCGGCCCGCGCITTTCTAGG | 13 | 1 | 0 | ||
| Switzerland TMFPRB | AATCAACCACGACGGAGAGC | 10 | 0 | 0 | ||
| Switzerland TMRPRB | CTCCTCACGCTGCCTGGT | 11 | 0 | 0 | ||
| Switzerland TMPROBEB | CCGGCCTGCGCTTTTACAGG | 9 | 1 | 0 | ||
| UK HIV-2 For | GCAGGTAGAGCCTGGGTGTTC | 23 | — | — | — | — |
| UK HIV-2 Rev | CTTGCTTCTAAYTGGCAGCTTTATT | 18 | 3 | 2 | 0 | 1 |
| UK HIV-2 probe | TGGGCAGAYGGCTCCACGC | 22 | 0 | 1 | 0 | 0 |
| USA For | GCGGAGAGGCTGGCAGAT | 22 | — | — | — | — |
| USA Rev | GAACACCCAGGCTCTACCTGCTA | 22 | — | — | — | — |
| USA probe | AGAGAACCTCCCAGG | 22 | — | — | — | — |
| gag | ||||||
| France F3 For | GCGCGAGAAACTCCGTCTTG | 21 | 2 | 2 | ||
| France L140 Rev | TCCAACAGGCTCTCTGCTAATCC | 24 | 3 | 0 | 0 | 0 |
| France probe | TAGGTTACGGCCCGGCGGAAAGA | 25 | 1 | 0 | 0 | 1 |
| France R1 Rev | AACATATTGTGTGGGCAGCGAA | 15 | 0 | 4 | 0 | 6 |
a
Number of primer targets with 2 mismatches or less in 25 full HIV-2 genomes listed in GenBank. Only mismatches in the first half of the genome are included.
b
—, target outside sequenced region.