Spontaneous clearance of primary acute hepatitis C virus infection correlated with high initial viral RNA level and rapid HVR1 evolution

Abstract

The aim of this study is to determine whether early viral dynamics and evolution predict outcome of primary acute hepatitis C virus (HCV) infection. HCV- and human immunodeficiency virus-negative injection drug users were enrolled prospectively and followed monthly to identify acute HCV infection using RNA detection. Subjects with more than 1 month between HCV-RNA-negative and -positive visits were excluded to ensure stringent acute infection. Differences in medians of log-transformed viral RNA levels and evolutionary rates in each gene of a 5'-hemigenomic amplicon were assessed using Mann-Whitney's rank-sum test. Correlation coefficient was calculated using Spearman's rank order. Initial viremia level was 50-fold higher in subjects with spontaneous clearance (compared with persistence) of primary acute HCV infection (median, 7.1 versus 5.4 log(10) IU/mL; P = 0.002). Initial viremia level in subjects with interleukin (IL)28B-C allele at rs12979860 and clearance was higher than that in subjects with IL28B-T allele and persistence (P = 0.001). Evolutionary rates in the hypervariable region 1 (HVR1) region of the E2 gene were significantly higher in self-resolvers than those in persistence subjects during early infection, whereas other genes or regions had comparable rates. All major substitutions in HVR1 in persistence subjects were convergent changes, whereas over the same time interval clearance subjects displayed divergent evolution, indicating different immune responses between the two groups.

Conclusion: Spontaneous clearance of acute HCV infection is predicted by high initial viremia as well as favorable IL28B genotype and is associated with rapid envelope-sequence evolution. This linkage of host genetics, viral dynamics, and evolution provides new directions for mechanistic studies. (HEPATOLOGY 2012;55:1684-1691).

Figure 1. Comparison of initial viral RNA levels and viral kinetics in subjects with self-resolving and persistent infections

(A) Median viral RNA of each individual during segmented period of time during acute infection. (B) Dynamic change of viral RNA levels in each individual during acute infection. (C) Median viral RNA and ALT curves for clearance and persistence groups. Dashed horizontal lines indicate lower limit of detection for HCV RNA (50 IU/mL).

Figure 2. Initial viral RNA and early viral kinetics in correspondence with IL-28B genotype and infection outcome

(A) Initial viral RNA for four outcome/IL-28B groups. Boxes indicate median and inter-quartile ranges of log-transformed HCV RNA, with 5^th and 95^th percentiles indicated. IL-28B genotypes are indicated on X axis (C for C/C and T for C/T or T/T). Significant P values (Rank Sum) are shown. (B) Median viral RNA curves for each outcome/IL-28B group during the first year of infection.

Figure 3. Comparison of evolutionary rates for each gene/region of the 5’-hemigenome between cleared and persistent subjects

Rate of nonsynonymous evolution is depicted as filled (clearance) or empty (persistence) circles for each gene/region and each individual. E2 is divided into E2-HVR1 (HVR1) and E2-nonHVR1 (nHVR1) regions. P values (rank sum) are shown for each comparison of rates.

Figure 4. Amino acid sequence evolution of HVR1 in clearance and persistence subjects

Consensus sequences of HVR1 for genotype 1a HCV are shown above. Type 1 logos (with letter height proportional to frequency) illustrate initial viral quasispecies. Type 2 logos (51) compare amino acid sequences to initial sequences, with the height of each amino acid indicating the log2 unlikelihood of observing the amino acid at a given position. Amino acids that change toward the 1a consensus are depicted with hollow letters. Subjects with comparable visit intervals are depicted in parallel for comparison. Red colored subjects are those with nAb data reported previously (27). Subjects 8 and 13 (indicated by asterisks) who had intervals between HCV RNA negativity and positivity over 1 month but less than 3 months were also included. Amino acid sequence evolution with nAb titers of subject 29 have been shown elsewhere.(30)