Background:  Careful examination of viral dynamics during treatment can provide important insights into HIV pathogenesis. Here, we examined viral evolution during and after enfuvirtide (T20) treatment with an objective of defining the characteristics of viral evolution during advanced HIV immunodeficiency.

Methods:  We examined the viral quasi-species from 9 patients who experienced incomplete viral suppression on a T20-based regimen, and who subsequently interrupted enfuvirtide while remaining on a stable background regimen (T20 partial treatment interruption). An average of 8 clones was sequenced from 3 time-points:  pre-T20, post-T20 failure, and post-T20 interruption. We used a Bayesian hierarchical phylogenetic model to assess the evolutionary relatedness of the virus that emerged after T20 interruption to the strains sequenced before initiation of T20 and strains sequenced before the interruption. This method allowed us to explicitly test evolutionary hypotheses across patients and time points simultaneously while allowing for individual patient evolutionary parameters to vary.

Results:  Interruption of T20 was associated with rapid loss of gp41-associated resistance mutations in all subjects. This loss of resistance reflected continued viral evolution of the dominant quasi-species at the time of the interruption rather than re-emergence of an archived virus (Bayes factor = 30.2, p = 0.01). Furthermore, we found that patients with the highest support for ongoing viral evolution during interruption period (>99% posterior probability) had a greater increase in diversity during T20 therapy (n = 4). Patients with no change in diversity also had strong support for the evolution tree (>90% posterior probability, n = 2). In contrast, patients who had a decrease in diversity during early T20 therapy had mixed support or weak support for the evolution tree (n = 3).

Conclusions:  In contrast to observations when all drugs are interrupted, loss of resistance during T20 interruption often occurs because of ongoing viral evolution (and back-mutation), rather than emergence of an archived virus. This was particularly true in patients whose virus remained diverse or became more diverse during enfuvirtide therapy. Collectively, these observations suggest ongoing immunologic pressure against envelope in advanced disease, with the emergence of virus population that is immunologically more fit than previous generation of viruses.