FIG 8.

Asymmetrical 5′ and 3′ LTRs from sequenced proviruses. (A) Proviral 5′- and 3′-LTR sequences from donor C-02. (B) Proviral 5′- and 3′-LTR sequences from donor C-03. (C) Proviral 5′- and 3′-LTR sequences from donor F-07. (D) Proviral 5′- and 3′-LTR sequences from donor K-01. (E) Proviral 5′- and 3′-LTR sequences from donor R-09. The 5′- and 3′-LTR sequences were extracted from the assembled proviral consensus FASTA files and aligned using MUSCLE (28). Proviruses were defined as having asymmetrical LTRs when a large deletion was present in one LTR but not the other and the two LTRs had sequence identity within 3 mismatches. Open blue boxes indicate regions absent in the amplicon and not sequenced. Vertical blue dashed lines demarcate LTR regions R and U5. Numbers to the right of each aligned provirus indicate the length of the LTR sequence. TAR, trans-activation response element.