Dissection of two drug-targeted regions of Hepatitis C virus subtype 4a infecting Egyptian patients

Abstract

Recently, treatment of HCV infection has been improved after the development of direct acting antivirals (DAAs) which target different viral proteins (NS3-4A, NS5A and NS5B). The activity and effectiveness of these DAAs are affected by the presence of resistance associated substitutions (RASs). This study aimed to characterize HCV genotypes circulating among Egyptian HCV patients, to dissect the full sequences of HCV NS3-4A and NS5B regions, and to characterize RASs associated with NS3-4A and NS5B inhibitors in HCV treatment-naïve patients. Genotyping of 80 HCV samples from treatmentnaïve patients was done using restriction fragment length polymorphism and phylogenetic analysis based on some full NS5B sequences. Results showed the prevalence of HCV subtype 4a. Twenty four new full sequences of NS3-4A and NS5B regions of subtype 4a were deposited in the GenBank database. In general, the substitutions associated with NS3-4A-targeting drugs were absent predicting possible responsiveness of Egyptian HCV patients to these drugs. In addition, the absence of amino acid substitutions associated with resistance to Sofosbuvir may predict good response to treatment with Sofosbuvir. Some amino acid substitutions associated with resistance to different classes of non-nucleoside inhibitors were detected. Further investigations on treated Egyptian HCV patients may evaluate the effectiveness of the massively used drugs. Many predicted T-cell-binding epitopes in NS3-4A and NS5B regions were found to be highly conserved in the currently studied isolates; a finding that might be important for HCV vaccine development. We demonstrated potential NS3 epitopes that could be used in engineering T cells against HCV epitopes.

Identifying Different Mutation Sites Leading to Resistance to the Direct-Acting Antiviral (DAA) Sofosbuvir in Hepatitis C Virus Patients from Egypt

“…For the right palm, residues 360-370 are important for maintaining a proper secondary structure, forming motif E of the palm domain [37]. The presence of an amino acid substitution in these residues may hinder HCV polymerase activity [38]. First, one sample displayed the amino acid substitution D318Y, and two samples demonstrated a D319V mutation.…”

“…Moreover, C316A/L polymorphism was present in two samples. Residues T532-R570 are responsible for regulating polymerase activity and lie in the NS5B C-terminus [38]. Sample 3 displayed eight amino acid substitutions, whereas sample 4 showed 21 amino acid substitutions: I5389L, A540P, G543A, R544K, T552N, G554A, Y555C, S556P, G557V, D559S, I560L, Y561T, H562S, S563K, V564P, S565L, H566G, A567E, R568I, P569R, and R570K.…”

“…The presence of 21 amino acid substitutions indicates high variability in this region. A membrane anchor is formed from amino acids 571-591 in the NS5B C-terminus [38]. We recorded amino acid substitutions in three of the five samples, with 13 amino acid substitutions in this region: W571E, F572K, W573R, F574G, C575I, L576M, L577R, L578N, L579R, A580 Q/S, A581V, Y586F, and N590A.…”