Mutations in E2-PePHD, NS5A-PKRBD, NS5A-ISDR, and NS5A-V3 of Hepatitis C Virus Genotype 1 and Their Relationships to Pegylated Interferon-Ribavirin Treatment Responses

Abstract

Mutations in several subgenomic regions of hepatitis C virus (HCV) have been implicated in influencing the response to interferon (IFN) therapy. Sequences within HCV NS5A (PKR binding domain [PKRBD], IFN sensitivity-determining region [ISDR], and variable region 3 [V3]) were analyzed for the pretreatment serum samples of 60 HCV genotype 1-infected patients treated with pegylated IFN plus ribavirin (1b, n ‫؍‬ 47; 1a, n ‫؍‬ 13) but with different treatment outcomes, those with sustained virologic responses (SVR; n ‫؍‬ 36) or nonresponders (NR; n ‫؍‬ 24). Additionally, the sequence of the PKR/eIF-2␣ phosphorylation homology domain (E2-PePHD) region was determined for 23 patients (11 SVR and 12 NR). The presence of >4 mutations in the PKRBD region was associated with SVR (P ‫؍‬ 0.001) and early virologic responses (EVR; 12 weeks) (P ‫؍‬ 0.037) but not rapid virologic responses (4 weeks). In the ISDR, the difference was almost statistically significant (68% of SVR patients with mutations versus 45% without mutations; P ‫؍‬ 0.07). The V3 region had a very high genetic variability, but this was not related to SVR. Finally, the E2-PePHD (n ‫؍‬ 23) region was well conserved. The presence of >4 mutations in the PKRBD region (odds ratio [OR] ‫؍‬ 9.9; P ‫؍‬ 0.006) and an age of <40 years (OR ‫؍‬ 3.2; P ‫؍‬ 0.056) were selected in a multivariate analysis as predictive factors of SVR. NS5A sequences from serum samples taken after 1 month of treatment and posttreatment were examined for 3 SVR and 15 NR patients to select treatment-resistant viral subpopulations, and it was found that in the V3 and flanking regions, the mutations increased significantly in posttreatment sera (P ‫؍‬ 0.05). The genetic variability in the PKRBD (>4 mutations) is a predictive factor of SVR and EVR in HCV genotype 1 patients treated with pegylated IFN and ribavirin.

Sequencing of E2 and NS5A regions of HCV genotype 3a in Brazilian patients with chronic hepatitis

“…In this way the populations of each region were distributed into two groups (E2 aa 636-708, > or ≤ 1; PePHD, without mutations or ≥ 1; CRS, without or ≥ 1; ISDR, without or ≥ 1; PKR-binding, > or ≤ 1; NLS, without or 1; extended-V3, > or ≤ 3; NS5A aa 1979-2414, > or ≤ 13). This approach was used by Muñoz de Rueda et al (2008) Nucleotide sequence accession numbers -Nucleotide sequence data reported in this paper was submitted to GenBank (http://www.ncbi.nlm.nih.gov/) with the accession EF207987-EF208018 for the NS5A sequences and EF210487-EF210519 for the E2 sequences.…”

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

“…However, consideration of individual sites allows only for the identification of connections to the therapy outcome in the form of a trend and does not have a strong predictive power. Correlation of the IFN-RBV therapy outcomes has been reported with site polymorphisms in the core (36), E2 (87,106), and NS5A (88,106) proteins. Although these observations revealed numerous associations between the HCV genetic polymorphism and evolution toward IFN-RBV resistance, these associations were never explored in terms of their interrelationships and formulated into an integrative model capable of revealing accurate quantitative connections between HCV genetic changes and therapy outcomes.…”

High ability to predict the treatment outcome of peginterferon and ribavirin combination therapy based on the reduction in HCV RNA levels at 4 weeks after starting therapy and amino acid substitutions in the hepatitis C virus in patients infected with HCV genotype 1b

“…These factors include the amino acid substitutions in the core [3,4], and envelop 1 (E1) [4], E2 [5][6][7], non-structural protein 4B (NS4B) [8], and NS5A regions of HCV [6,7,[9][10][11]. Especially, strong associations between amino acid substitutions at residue 70 of the core region of HCV and the amino acid sequence of residues 2209-2248 of the NS5A region of HCV (i.e., the interferon sensitivity-determining region, ISDR) were reported in Japanese patients infected with HCV genotype 1b [12].…”