High diversity of hepatitis C viral quasispecies is associated with early virological response in patients undergoing antiviral therapy

Abstract

Differential response patterns to optimal antiviral therapy, peginterferon alpha plus ribavirin, are well documented in patients with chronic hepatitis C virus (HCV) infection. Among many factors that may affect therapeutic efficiency, HCV quasispecies (QS) characteristics have been a major focus of previous studies, yielding conflicting results. To obtain a comprehensive understanding of the role of HCV QS in antiviral therapy, we performed the largest-ever HCV QS analysis in 153 patients infected with HCV genotype 1 strains. A total of 4,314 viral clones spanning hypervarible region 1 were produced from these patients during the first 12 weeks of therapy, followed by detailed genetic analyses. Our data show an exponential distribution pattern of intrapatient QS diversity in this study population in which most patients (63%) had small QS diversity with genetic distance (d) less than 0.2. The group of patients with genetic distance located in the decay region (d>0.53) had a significantly higher early virologic response (EVR) rate (89.5%), which contributed substantially to the overall association between EVR and increased baseline QS diversity. In addition, EVR was linked to a clustered evolutionary pattern in terms of QS dynamic changes.

Conclusion: EVR is associated with elevated HCV QS diversity and complexity, especially in patients with significantly higher HCV genetic heterogeneity.

Figure 1

Neighbor-Joining tree of 153 dominant clones representing individual patients and 45 reference sequences from GenBank. Bootstrap test was done with 500 replicates and shown at major branches. Among 153 patients, 38 were infected with HCV genotype 1b and 115 were genotype 1a. The latter was further clustered into three subgroups with more than 90% bootstrap support. EVR, early virologic response.

Figure 2

The correlation between early virologic response patterns (EVR or Non-EVR) and genetic diversity at the baseline. While EVR group showed a higher genetic diversity than Non-EVR group. The difference between two groups did not reach statistical significance (two-tailed t test) except for HVR1 dN, which indicated a higher pressure for the positive selection in the EVR group.

Figure 3

The correlation between early virologic response patterns (EVR or Non-EVR) and genetic diversity at the baseline. While EVR group showed a higher genetic diversity than Non-EVR group, the difference between two groups did not reach statistical significance (two-tailed t test) except for dN value in HVR1.

Figure 4

Comparisons of genetic complexity between EVR and Non-EVR groups. Pretreatment HCV genetic complexity (left side) and its average change over time (right side) were compared between two groups at wither amino acid or nucleotide level. AA, amino acid; Nu, nucleotide.

Figure 5

Histogram of baseline QS diversity in the study population. The number of patients at each category of genetic distance (d) based on HVR1 was calculated. The distribution of QS diversity in this study population fit an exponential distribution (p=0.132 by KS test) in which most patients (about 63%) had a small d value less than 0.2. The χ_min, estimated using described formula in MATLAB, is about 0.53, which put genetic distance from 19 patients in the decay region (shaded area). This group of patients had a much higher EVR rate (89.5%) compared to the overall EVR rate (68%, p=0.032) or patients with genetic distance less than 0.53 (65%, p=0.016). KS test, One-sample Kolmogorov-Smirnov test.