Background: The detection of viruses that evolve to escape antibody neutralization in HIV infection indicates that neutralizing antibodies are exerting immunological pressure on the virus in vivo. We hypothesize that particular regions of the HIV envelope involved in this escape can be mapped through a direct comparison of a series of genetically related autologous viruses and their corresponding envelopes.

Methods: Neutralizing antibodies and virologic escape were measured in two acute infection cohorts from Trinidad and Tobago. A cMAGI-based neutralization assay was used to assess antibody neutralization of autologous virus from sequential time points. We performed detailed mapping of the development of neutralizing antibodies and escape in one individual to identify the viral epitopes involved. Envelopes from the initial “sensitive” isolate and from the “escape” isolate (in the presence of neutralizing antibodies) were sequenced and cloned into an HIV pseudotyped virus. Recapitulation of the neutralizing antibody escape phenomena was tested using the cloned pseudotyped virus with the autologous serum. In addition, differences in the kinetics of virus growth were assessed.

Results: In the first cohort, we found that 16 out of the 20 (80%) individuals developed neutralizing antibodies within 1 year of infection. In the second cohort, we noted one individual with early development of neutralizing antibodies and escape by 71 days. Sequence analysis of both the bulk PCR products and the cloned envelopes from the “initial” and the “escape” variant indicated several changes associated with neutralizing sensitivity. In the escape variant, a deletion of 1–2 glycosylation sites in the V1 region, and the appearance of a glycosylation site in the V4 region were the marked changes from the initial sensitive isolate. In a pseudotyped virus/neutralization assay, the “escape” virus clone exhibited the same property of escape from autologous neutralizing sera as did the virus quasispecies. The two viruses had similar growth kinetics.

Conclusions: Regions in the HIV envelope that involve the deletion of glycosylation sites in the V1 region and an addition of a glycosylation site in the V4 region are likely candidates for mediating virus escape from neutralizing antibodies. Understanding the viral epitopes involved in subverting the immune response could aid the development of new therapeutic and vaccine strategies.