Investigating Signs of Recent Evolution in the Pool of Proviral HIV Type 1 DNA during Years of Successful HAART

Abstract

In order to shed light on the nature of the persistent reservoir of human immunodeficiency virus type 1 (HIV-1), we investigated signs of recent evolution in the pool of proviral DNA in patients on successful HAART. Pro-viral DNA, corresponding to the C2-V3-C3 region of the HIV-1 env gene, was collected from PBMCs isolated from 57 patients. Both "consensus" (57 patients) and clonal (7 patients) sequences were obtained from five time points spanning a 24-month period. The main computational strategy was to use maximum likelihood to fit a set of alternative phylogenetic models to the clonal data, and then determine the support for models that imply evolution between time points. Model fit and model-selection uncertainty was assessed using the Akaike information criterion (AIC) and Akaike weights. The consensus sequence data was also analyzed using a range of phylogenetic techniques to determine whether there were temporal trends indicating ongoing replication and evolution. In summary, it was not possible to detect definitive signs of ongoing evolution in either the bulk-sequenced or the clonal data with the methods employed here, but our results could be consistent with localized expression of archival HIV genomes in some patients. Interestingly, stop-codons were present at the same two positions in several independent clones and across patients. Simulation studies indicated that this phenomenon could be explained as the result of parallel evolution and that some sites were inherently more likely to evolve into stop codons.

HIV-1 Continues To Replicate and Evolve in Patients with Natural Control of HIV Infection

“…Although the level of viremia is significantly reduced in both cases, control persists despite ongoing full cycles of replication in HIV-1 controllers whereas replication, in many studies, has been found to be completely blocked in patients on a fully suppressive cART regimen (2,7,41,60).…”

“…Although the topic remains controversial (6), many studies have found that combination therapy effectively blocks the infection of new cells, as confirmed both by the absence of sequence evolution (2,7,41,60) and by the lack of reduction in HIV-1 RNA when cART is intensified with a fourth drug (12,17,18,40). Thus, the persistent viremia in patients on successful cART stems from a reservoir of long-lived cells in the absence of de novo infection.…”

The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence

“…However, multiple lines of evidence indicate that ART effectively curtails new infection of susceptible cells. Because HIV-1 replication is invariably accompanied by the progressive accumulation of mutations (138) reflecting the error prone nature of reverse transcriptase (139) and possibly hypermutation by the host restriction factor APOBEC3G (40, 140–143), the lack of sequence evolution in the viral reservoir (22, 97, 100, 144, 145) indicates that ART blocks ongoing cycles of viral replication. A recent report claiming viral evolution is confounded by sampling only in the first 6 months of ART, a period during which short-lived populations of infected cells not representative of the stable reservoir are dominant (146).…”

The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time

“…Investigations into whether HIV-1 replication continues during suppressive therapy have been carried out with peripheral blood and GALT samples but have led to potentially contradictory results. Some studies have found an absence of genetic evolution in viral reservoirs (23)(24)(25)(26)(27)(28)(29) and no reduction of plasma RNA during intensification of cART…”