Consequently, the genome-wide sliding window analysis revealed that statistical significance in most regions were compromised upon exclusive inclusion of high-frequency mutations. Interestingly, the HCV HVR1, a domain used frequently in viral diversity studies, is less powerful in distinguishing SVR from null responders. Thus conflicting data obtained with common methods appears to be the result of lowresolution of mutation detection. Our analysis further reveals that multiple forces together shape the viral population structure. Although not absolute, synonymous and nonsynonymous mutations are commonly interpreted as the reflection of selective and neutral forces, respectively. Confirming to this assertion, sliding window analysis of nonsynonymous, but not synonymous mutations, shows an apparent peak in the HVR1, a well-documented region under high immune selection. The higher number of nonsynonymous mutations thus suggests a stronger immune pressure in the SVR group compared to the null responders. Second, among 36,665 mutations detected in HCV coding region from 56 patients, 24,375 are low-frequency synonymous mutations from which statistical significance stems mostly. Given comparable numbers of structural HCV HVR1 variants between SVR and null responders, viral compartmentation, often associated with distinct HCV HVR1 variants, might play a negligible role in the contribution to observational difference of the mutation load. Therefore genetic drift and its magnitude might be a reasonable explanation for both mutation accumulation and differential mutation loads in SVR and null responders. Third, two HCV domains, respectively located in NS5a and NS5b, showed significant mutation Perifosine customer reviews load-dependent clustering. The NS5b encodes RNA-dependent RNA polymerase that drives an error-prone viral replication. Mutations in NS5b or nearby regions, together with increasing number of indels, may have a direct effect on strains’ intrinsic mutation rates. Lastly, it was interesting to note that the low mutation load was associated with IL28B CC type, one of single strongest predictors in interferon-based HCV antiviral therapy. Taken together, these data may delineate a scenario regarding the generation and modulation of HCV mutation load. Besides direct contribution of nonsynonymous mutations, the HCV-target immunity, both innate and adaptive, modulate viral replication dynamics that affect the strength of genetic drift by coupling with viral intrinsic mutation rates. While molecular mechanisms underpinning these observations remain largely unknown, it is clear that no single factors from either virus or host side could dominate the mutation load in chronic HCV infection. A power law distribution among patients indeed signifies the operation of potential multiple-level hierarchies on the modulation of HCV mutation load. In conclusion, by establishing a method for genome-wide quantitation of HCV mutation load, the current study explains previous conflicting observation and intensifies a dominant role of natural selection in HCV population in response to interferonbased antiviral therapy.