Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial
Figure 6
Estimated vaccine efficacy as a function of distance to contactsites of the CRF01_AE vaccine sequences.
SmoothMarks [20] estimates of vaccine efficacy (VE) against acquisition with an HIV-1 CRF01_AE virus with genetic distance v from the 92TH023 or CM244 vaccine sequences, with 95% confidence intervals, using Env mindist amino acid sequences and computed with the HIVb PAM substitution matrix[16] across the contactsites. For each panel, the first p-value is for testing whether there is any VE against any virus genotype, and the second p-value is for testing whether VE declines with the distance v. The PAM distances are directly proportional to Hamming distances, where a PAM distance of v approximately equals a Hamming distance of 0.85×v. Given that contactsites contains 176 residues, the span of contactsites distances 0.08 to 0.25 correspond to 13–39 amino acid mismatches.