Estimation of genetic diversity in NS3 region of Hepatitis C virus using 454 pyrosequencing

Viruses are highly diverse in their genetic constitution, both within and between infected hosts. They adapt to the host’s environment with a high mutation rate and make identification and consequent treatment very difficult, especially if the treatment targets a particular genetic feature. Hepatitis C Virus (HCV), which causes nearly 200 million chronic infections worldwide, is being studied using various bioinformatics approaches. It is curable with treatments which vary in dosage and duration based on the genotype of the virus. It is hypothesized that direct antiviral therapies which target viral proteins create a selection pressure in the virus. This ultimately leads to the emergence of viral strains in which the gene coding for the target protein is mutated, further complicating treatment. There is a need for highly accurate genotyping capabilities, so variants are correctly identified and appropriate treatment can be administered. We propose a case study in which viral samples from 45 patients with chronic HCV are being sequenced using a Roche GS Junior at different stages of treatment. Using variant callers like GS Amplicon Variant Analyzer and other tools the variants in the viral population over the course of treatment are observed. It is of interest to know if the increase in viral diversity is linked with onset of the treatment, and the difference in viral population for each outcome of the treatment (responders vs non-responders). This would ultimately help in understanding the evolution of the virus and further insights into drug designing and personalized treatment.