Quasispecies Analysis of HCV Breakthroughs Occurring During the HALT-C Trial Lead-In Treatment Phase

Investigators:

He-Jun Yuan, Mamta Jain, William M. Lee

Hypotheses/Aims

We hypothesize that comparison of baseline samples with those obtained at the time of relapse will demonstrate unique differences in viral sequence (escape mutations) that will identify HCV interferon-resistant quasi-species that emerge under interferon pressure.

1. Analyze the HCV sequences both at baseline and at the time of viral breakthrough when patients are still on the peg-IFN therapy by clone analysis assay. Changes in the sequence in the E2 and NS5a regions will be analyzed to determine whether either specific mutations or the number of mutations in some regions are responsible for viral breakthrough.
2. Further comparisons of HCV sequence diversity will be determined using heteroduplex assays on sera from the same 10 compliant patients, at baseline, last positive sample before viral breakthrough and at the time of return of virus while under treatment. The dynamic changes in sequence diversity and complexity will be noted. This work will allow us to see whether there is a change in sequence diversity if more IFN resistant quasi-species were selected by the augmented immune pressure. Cloning and sequencing of these samples may also be undertaken if indicated.