AMPLIFICA TION OF HVR1 REGION OF HEPA TITIS C VIRUS WITH PA TIENT SPECIFIC NESTED PCR PRIMERS

Abstract

The understanding of the function of the hyper variable region (HVR) at the NH2-terminus of the E2 protein remains very limited. Comparison of published sequences of HCV has led to the identification of a number of distinct virus types that may differ from each other by as much as 33% over the whole viral genome allowing the virus to escape cellular and humoral immunity. This phenomenon is related to the capacity of HCV to escape immune recognition, by frequent mutations HVR1 region. Several investigations have observed that the antibodies present in a proportion of infected patients had significant cross reactivity with apparently unrelated HVR1 sequences presented as synthetic peptides. To study the HVR1 cross reactivity and evolution in individuals with varying liver disease severity, nested PCR was performed to obtain patient specific 150 bp long HVR1 genome. For this, previously amplified first round single molecule amplimers were reamplified using new patient specific sense and antisense primers. The patient specific sense primers did not work in the second round amplification. So, the target DNA was amplified by three rounds of nested PCR, using patient specific primers on the third round. Key Words: HCV, patient specific HVR1, nested PCR