Background:  Although HIV-1 env polymorphism correlates with natural disease progression, a relationship with response to combination ART is unknown. We hypothesized that pre-therapy genomic complexity in env favors a positive therapy outcome.

Methods:  HIV-1 env V1V2-length quasispecies were evaluated by spectratyping, a sensitive method to evaluate genetic length polymorphisms. Correlation of env V1V2 length and extent of length polymorphisms with clinical disease status was determined via Spearman rank order correlation (SROC) test for 14 untreated pediatric subjects. Association of pre-therapy viral genomic complexity with therapy outcome was assessed using Mann-Whitney S test by comparison of env V1V2-length diversity in pre-therapy viruses between children (n = 5) who achieved complete viral suppression and those (n = 9) who failed to control viral replication after ART. Change in env V1V2-length distribution post-therapy was followed in a 1-year longitudinal study. V3 genotype between viral successes and viral failures pre- and post-therapy were compared by Mann-Whitney S test, and correlated to V1/V2 lengths by SROC test.   

Results:  Number of HIV-1 env V1V2-length variants in pre-therapy viruses ranged from 1 to 16 among the individuals. V1V2 length extended from 273 to 360 bp among all variants across subjects, but was closely clustered in a related length range within each individual. Although pre-therapy V1V2 length or length polymorphisms were unrelated to pre-therapy CD4 percentage or viral levels, a significant relationship between V1V2-length diversity and therapy outcome was identified (p = 0.02). Children with more diversified pre-therapy env V1V2-length quasispecies developed complete viral suppression, while subjects harboring viruses with uniform or limited number of env V1V2-length variants prior to ART failed to control viral replication after therapy. Net V3 charge was independent of length in env V1, V2, or V1V2, but was related to CCR5 co-receptor use in viral success or CXCR4 use in viral failure (p = <0.001). Distribution and diversity of env V1V2 length was stable in all viral successors and 6 of 9 viral failures over 1 year of therapy.

Conclusions:  Spectratyping is equivalent to sequencing to detect env V1V2-length variants. Genomic diversity in pre-therapy env, coupled with CCR5 co-receptor use, correlates with favorable response to ART, may reflect immunity, and can serve as a novel surrogate marker for therapy outcome.