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| For example, 7810–7785 and 6557–6582 (HXB2 nts) in env were conserved for almost all M group HIV-1 strains in addition to the primer binding sites in gag and pol. Moreover, the amplicon length was designed to be associated with conservative or variation of targeted gene, the largest gag-pol amplicon represents the most conserved gene region in HIV-1; the high variable env gene region was split into two fragments for amplification (pol-env and env-nef). The selected sets of primers were further examined to match the Chinese prevalent strains Thai-B and BC recombinant strains.2,5,16-18 Specially, recombinant pattern of BC recombinant forms were taken into consideration as another important factor in designing primers. The primers binding sites were designed to avoid the recombinant breakpoints of BC recombinant strains (Figure). In addition, degenerate bases within the primers were also used to cover the genetic diversity present at the primer binding sites. |
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