FIG 1.

Proportion of nucleotides in 200-bp fragments that match the HIV-1 2012 subtype B consensus sequence. A consensus sequence was generated from a total of 675 aligned full-length subtype B sequences from the Los Alamos HIV Sequence Database, and the number of bases in 200-bp fragments that matched the consensus sequence was calculated. The most highly conserved regions are present where the original gSCA primers were designed and in the 3′ region of pol, where the iSCA primers and probe target.