Figure 6

Resistance mutations associated with gRNA-RRE/env preserve the env reading frame.

CRISPR gRNA-RRE/env targets the RRE and the env gene. (a) The net change in number of bases of the 23 bp gRNA or the 234 bp RRE sequence for all reads derived from NL4-3 infection. Most reads have no frame change, but net additions of 1 and 2 bp are present. (b) Indel reads were characterized for altered reading frame for both NL4-3 and R7 infections at the 23 bp gRNA sequence. The total number of bases either increased (Added) or decreased (Subtracted). In frame insertions or deletions were either +3 or −3 bases, respectively. Frameshifts were altered by 1 or 2 bases. (c) LANL protein sequence logo of the HIV-1 subtype B Env amino acids L520 to G527 encoded by the bases targeted by gRNA-RRE/env. The most common variant encodes NL4-3 Env A525, but 6% of patient samples encode NL4-3 Env T525.