MOESM4 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

Additional file 4: Figure S4. Highlighter plots of transmitter and recipient Env sequences. The consensus of the single genome amplification (SGA) sequences of recipients were used as master sequences indicated on top and Env sequences of recipients (R) and transmitters (T) were aligned to it. Amino acid mismatches are illustrated by a colored bar. Sequences are derived from single genome amplification (SGA_X), cloning (cl_X) and from next generation sequencing of primary virus isolate and plasma virus. Note that haplotypes for primary virus isolates and plasma are only spanning gp120 and only those at a frequency above 1 % are depicted. Clones indicated in blue and red were used in follow up experiments for recipient and transmitter, respectively.