Abstract
Backgrounds. Hepatitis C virus (HCV) exists as population of closely related genetic variants known as quasispecies. HCV quasispecies diversity is strongly influenced by host immune pressure on virus. Quasispecies diversity is expected to decline as host immune response to HCV decreases over natural course of progressing from chronic hepatitis C (CHC) to hepatocellular carcinoma (HCC). Methods. Ultradeep pyrosequencing (UDPS) was used to evaluate degree of quasispecies diversity in 49 patients infected with HCV including 26 with CHC and 23 with HCC. Whole structural protein of HCV genome was subjected to UDPS. Results. Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups. Area under curve of ROC analysis for differentiating HCC from CHC was >0.8 for all of 14 amino acid positions. Conclusion. HCV quasispecies diversity as indicator of declining host immune functions was easily assessed by UDPS technology. Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC. Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.
Highlights
Hepatitis C virus (HCV) is an enveloped RNA virus [1]
It is known that the progression of chronic hepatitis C to hepatocellular carcinoma (HCC) is accompanied by anergy of host immune system [8]
A total of 1,822,601 sequence reads were obtained from 49 samples using Ultradeep pyrosequencing (UDPS) in the average number of sequence reads as 37,196 per sample
Summary
HCV is capable of producing highly diverse variants, so called quasispecies, by initiating replications based on RNAdependent, error-prone RNA polymerase [2, 3]. These HCV quasispecies are considered as one of the mechanisms by which HCV evades host immune pressure [4]. It is known that the progression of chronic hepatitis C to HCC is accompanied by anergy of host immune system [8]. These changes in host immune response to the virus affect the diversity in HCV quasispecies
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