Comparison of the type 1 IFN resistance of viruses generated from IMCs of founder and 6-month consensus virus sequences. (A) Diagrammatic representation of the nucleotide differences between the founder and 6-month consensus (6-mo) IMC pairs from subjects CH058, CH077, CH236, CH470 and CH850. The founder and 6-mo IMC sequences from each subject are represented by horizontal grey lines. The horizontal axis indicates nucleotide positions in the alignment beginning at the start of the U3 region of the 5‘ LTR and extending to the end of the U5 region of the 3’ LTR, based on HXB2 reference sequence numbering (http://www.hiv.lanl.gov/content/sequence/HIV/REVIEWS/HXB2.html). Nucleotide differences between the founder and 6-mo IMC sequences are indicated by tic-marks on the 6-mo sequence, with the colour of the tic-mark indicating the base present in the 6 mo IMC (A in green, T in red, G in orange and C in light blue). Non-synonymous changes are labelled. The total number of nucleotide differences between each founder and 6-mo IMC pair is indicated. (B) IFNα (left panels) and IFNβ (right panels) Vres (upper half of figure) and IC50 (lower half of figure) values of viruses generated from the founder and 6-mo IMCs depicted in (A). The data shown are the mean of results from a minimum of 2 independent IFNα or IFNβ assays performed with each virus using different donor PBMC mixes.