Evolution of hepatitis C virus NS5A region in breakthrough patients during pegylated interferon and ribavirin therapy

Abstract

Investigating the evolution of the hepatitis C viral (HCV) genome in the small number of patients that experience viral breakthrough might shed light on the problem of resistance to interferon therapy. Within the HCV genome, sequence diversity of the viral nonstructural 5A protein-coding region (NS5A) has been linked to interferon responsiveness. We analyzed the temporal sequence changes within NS5A in genotype 1a patients: 6 breakthrough (BT), 12 sustained virologic responders (SVR) and 12 non-responders (NR), all of whom had received full dose peg-interferon and ribavirin therapy. The entire NS5A region was amplified by reverse transcription (RT)-PCR followed by direct sequencing of serum samples from baseline and three on-treatment time points for each group. Comparing baseline sequences with week 12 and later time points, BT patients resembled SVR patients in having a higher number of amino acid substitutions at week 12 than NR patients; however, the number of amino acid substitutions in this group decreased at and after BT. Substitutions were focused in the V3 and flanking regions in BT patients but not in SVR patients. The high number of substitutions in NS5A in both BT and SVR groups suggests that selective pressure is associated with viral response to therapy. Our results provide evidence that amino acid substitutions within the NS5A coding region may reflect a host response that drives selective pressure for viral adaptation.

Coevolution of the Hepatitis C Virus Polyprotein Sites in Patients on Combined Pegylated Interferon and Ribavirin Therapy

“…However, since these models were generated using only 40 sequences from 20 patients, it is critical to demonstrate that the interrelationships identified for these patients are representative of those for other patients. For this purpose, two predictive models were constructed using the same Virahep-C data set and tested using the HCV NS5A sequences from baseline specimens obtained from patients in the HALT-C study (131). Because no additional data were available for E2 from patients with NR and UR outcomes investigated in a single study, only the NS5A models were validated.…”

“…For some analyses, a total of 298 HCV 1a fulllength consensus polyprotein sequences from GenBank were used. In addition, full-length NS5A protein consensus sequences from 18 treatment-naïve patients (6 UR and 12 NR) identified through the HALT-C trial (131) were used as a test data set to validate the NS5A predictive models constructed from the Virahep-C data. A full listing of the GenBank accession numbers of all sequences used in this study can be found in the supplemental material.…”

“…The validation of the NS5A predictive models was conducted using the consensus sequences of the NS5A protein from the HALT-C study (131), which were not part of any of the analyses described herein. Estimation of the NS5A BNC and NS5A-LP accuracy of prediction of treatment outcome for HCV NS5A variants from the HALT-C study was based on the overall percent classification correctness.…”

Polymorphisms of Hepatitis C Virus Non-Structural Protein 5A and Core Protein and Clinical Outcome of Pegylated-Interferon/Ribavirin Combination Therapy

“…It does not exclude the possibility, however, that the same region plays an important role in modulating the interaction with various host systems, including IFN responsiveness. It is also possible that the genetic flexibility of this region, especially IRRDR, is accompanied by compensatory changes elsewhere in the viral genome and that these compensatory changes affect overall viral fitness and responses to IFN therapy [25] .…”

NS5A Sequence Heterogeneity of Hepatitis C Virus Genotype 4a Predicts Clinical Outcome of Pegylated-Interferon–Ribavirin Therapy in Egyptian Patients

“…This flexibility might play an important role in modulating the interaction with various host systems, including IFN-induced antiviral machineries. It is also possible that the genetic flexibility of IRRDR is accompanied by compensatory changes elsewhere in the viral genome and that these compensatory changes affect overall viral fitness and responses to IFNbased therapy (8,29,41). Also, it is worth noting that IRRDR is among the most variable sequences across the different genotypes and subtypes of HCV (25) whereas its upstream and downstream sequences show a higher degree of sequence conservation (15).…”