Compartmentalization of hepatitis C virus (HCV) during HCV/HIV coinfection

Abstract

Extrahepatic replication has important implications for the transmission and treatment of hepatitis C virus (HCV). We analyzed longitudinal HCV diversity in peripheral-blood mononuclear cells (PBMCs) and serum during HCV monoinfection and HCV/HIV coinfection to determine whether distinct amino acid signatures characterized HCV replicating within PBMCs. Analysis of E1-HVR1 sequences demonstrated higher serum genetic distances among HCV/human immunodeficiency virus (HIV)-coinfected persons. Moreover, consensus PBMC sequences were rarely identical to those in the corresponding serum, suggesting divergence in these 2 compartments. Three of 5 HCV/HIV-coinfected participants showed evidence of HCV compartmentalization in PBMCs. Additionally, signature sequence analysis identified PBMC-specific amino acids in all HCV/HIV-coinfected persons. To our knowledge, this is the first study to identify specific amino acids that may distinguish HCV variants replicating in PBMCs. It is provocative to speculate that extrahepatic HCV diversity may be an important determinant of treatment response and thus warrants additional study, particularly during HCV/HIV coinfection.

Figure 1

Phylogenetic tree of consensus E1-HVR1 amino acid sequences from serum (black symbols) and peripheral-blood mononuclear cell (PBMC; white symbols) compartments at visits A (circles), B (squares), and C (triangles). Database reference sequences are indicated by their genotype. Arrow 1 indicates a time point at which the consensus amino acid sequences from the serum and PBMC compartments are identical for patient 48 (hepatitis C virus [HCV]/HIV coinfected). Arrow 2 indicates 2 time points at which the consequence amino acid sequences in the PBMC compartment are identical for patient 30 (HCV/HIV coinfected). *HCV/HIV-coinfected individuals.

Figure 2

Phylogenetic tree analysis of quasispecies E1-HVR1 amino acid sequences from the serum (black circles) and peripheral-blood mononuclear cell (PBMC; white circles) compartments of hepatitis C virus (HCV)/HIV–coinfected women. Relevant bootstrap values >70 (of 100) are shown for PBMC-specific viral variants (highlighted by large, open circles). HCV genotype 2 was used as the reference sequence.

Figure 2

Phylogenetic tree analysis of quasispecies E1-HVR1 amino acid sequences from the serum (black circles) and peripheral-blood mononuclear cell (PBMC; white circles) compartments of hepatitis C virus (HCV)/HIV–coinfected women. Relevant bootstrap values >70 (of 100) are shown for PBMC-specific viral variants (highlighted by large, open circles). HCV genotype 2 was used as the reference sequence.

Figure 3

Signature sequence analysis. Amino acid positions at which the peripheral-blood mononuclear cell (PBMC) and serum clonal distributions are significantly different at a threshold of 70% are underlined. “S30A” and “P30A” indicate, for example, a serum sample and a PBMC sample, respectively, from patient 30 at time point A. Nos. in parentheses indicate the no. of amino acid signatures present in PBMCs at that time point. Shown are the consensus amino acids at each position. In several instances, a given amino acid may appear to be identical between the 2 compartments; however, the frequency distribution of the 10 viral variants that make up that consensus is different between the 2 compartments. The bar highlights the 27 amino acids of HVR1.