Document Type : Original Article
Authors
1
Botany Department, Faculty of Science, Mansoura University
2
Professor of Tropical Medicine, Tropical Medicine Department, Faculty of Medicine, Mansoura University
3
professor of Biochemistry and Molecular Medicine, Biochemistry Department, Faculty of Medicine, Mansoura University
4
Professor of microbiology/Molecular Biology Botany Department, Faculty of Science, Mansoura University
Abstract
HCV genotype testing was an essential technique before starting treatment, it's necessary to have a better understanding of molecular epidemiology and genetic variability of HCV genotypes. NS5B is a 65-kDa RNA-dependent RNA polymerase that is substantially conserved across all HCV genotypes. It was one of seven nonstructural proteins found in HCV and is required for the virus's replication. This protein is an excellent target for the development of a pan-genotypic, direct-acting antiviral (DAA) with a high resistance barrier, so The goal of this work was to genotype HCV strains circulating in the Dakahlia Governorate by adopting direct sequencing and phylogenetic study of a portion of the HCV genome encoding NS5B in order to compare the NS5B protein in the local HCV genotype 4a with that found in other countries. Using the Jalview tool for molecular evolutionary and phylogenetic research, it was discovered that the HCV NS5B gene of the local genotype 4a detected in Egypt was closely related to their counterpart in Egypt, EF694396.1:21-309, and showed high genomic diversity of genotype 4 from other parts of the world. It also illustrated that the Egyptian isolates can be classified into four clusters. J Netpred algorithm shows that secondary structure of NS5B protein composed of seven alpha helices that were specified at 9-21 (EKDIRAEEEVYQC amino acids), 26-40 (PEARKVITALTERLY amino acids), 70-84 (NTLTCYLKATAAIRA amino acids ), 108-120 (VEEDNRALRAFTE amino acids ), 122-124 (MTR amino acids), 168-175 (ETPLARAA amino acids), 184-198 (VNSWLGNIIVYAPTI amino acids), and at 203-214 (VLMTHFFSILQS amino acids ) and 10 β -sheets at 40-46 ( YVGGPMH amino acids), 51-55 (DLCGY amino acids) , 91-94 (TMLV amino acids ), 99-104 (LVVIAE amino acids), 134-140 (QPAYDLE amino acids ), 142-143 (IT amino acids), 149-154 (VSVAHD amino acids), 159-164 (KVYYLT amino acids), 177(E amino acid) and at 221-233 (ALDFDMYGVTYSI amino acids). The 3-D structure prediction model for the NS5B protein of different HCV genotype 4a isolates showed 4 chains: A, B, Q and R. In conclusion, the Egyptian genotype 4a was structurally unique and should lead to development of a specific viral drug resistance mechanisms, which results in the need to devise its own antiviral medicines.
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