Impact of highly active antiretroviral therapy and immunologic status on hepatitis C virus quasispecies diversity in human immunodeficiency virus/hepatitis C virus-coinfected patients

Abstract

This study analyzes the effect of highly active antiretroviral therapy (HAART), and thus immunologic status, on hepatitis C virus (HCV) load and quasispecies diversity in patients coinfected with the human immunodeficiency virus (HIV) and HCV. Three cohorts of coinfected patients were analyzed retrospectively over a period of 7 to 10 months: group A was antiretroviral drug naïve at baseline and then on HAART for the remainder of the study, group B did not receive antiretroviral therapy at any point, and group C was on HAART for the entire study. HCV quasispecies diversity was analyzed by sequencing hypervariable region 1. In a longitudinal analysis, there was no significant change from baseline in any immunologic, virologic, or quasispecies parameter in any of the three groups. However, in comparison to groups A and B, group C had significantly higher CD4+- and CD8+-cell counts, a trend toward a higher HCV load, and significantly increased number of HCV clones, entropy, genetic distance, and ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (Ka/Ks). In addition, CD4+-cell count was positively correlated with HCV load, genetic distance, and Ka. Interestingly, patients infected with HCV genotype 2 or 3 had a significantly higher CD4+-cell count, HCV load, genetic distance, and Ka/Ks than those infected with genotype 1. These results suggest that there is no immediate effect of HAART on HCV but that, with prolonged HAART, immune restoration results in an increase in HCV load and quasispecies diversity.

FIG. 1.

Phylogenetic analysis of E1/E2 nucleotide sequences from the baseline time point of all patients. A phylogenetic tree was constructed from a total of 160 E1/E2 sequences using the neighbor-joining method and Kimura two-parameter model. The horizontalbranch lengths are drawn to scale, and the scale bar represents 0.1 nucleotide substitutions per site. The clone number is indicated at the end of each horizontal branch tip, and the brackets at the far right indicate groupings based on patient source. Patients in group A are indicated as A1 through A7, patients in group B as B1 through B3, and patients in group C as C1 through C6. Clone numbers are indicated by patient source followed by sequence number (e.g., A1-1, A1-2, etc.).

FIG. 2.

Phylogenetic analysis of E1/E2 nucleotide sequences from two independent RT-PCRs. Phylogenetic trees were constructed from 10 E1/E2 sequences for each RT-PCR (for a total of 20 sequences per sample) using the neighbor-joining method and Kimura two-parameter model. Representative trees are shown for two samples, A and B. The horizontal branch lengths are drawn to scale, and the scale bar indicates nucleotide substitutions per site. The clone number is indicated at the end of each horizontal branch tip. For each sample, clones from RT-PCR 1 are indicated as 1-1 through 1-10, and clones from RT-PCR 2 are indicated as 2-1 through 2-10.