IN SILICO ANALYSIS OF NS5B GENE OF HCV GENOTYPE 4 IN NORTH EGYPT
- Department of Bioinformatics, Genetic Engineering and Biotechnology Research Institute (GEBRI),University of Sadat City, Egypt.
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441, Dammam, Saudi Arabia.
- Department of Molecular Biology, Genetic Engineering and Biotechnology Research Institute (GEBRI),University of Sadat City, Egypt.
- Department of Molecular Diagnostics and Therapeutics, Genetic Engineering and Biotechnology Research Institute (GEBRI),University of Sadat City, Egypt.
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Background:Hepatitis C is a liver disease caused by the hepatitis C virus (HCV). HCV genotypes and subtypes are related to antiviral therapy response. Our purpose was to identify genotypes and subtypes of HCV isolates collected from Menoufia, Egypt and to analyze the effect of the known drug resistance mutations on the RdRp catalytic domain of HCV-NS5B protein.
Methods:Serum of 5 HCV samples was used for RNA extraction and amplification of NS5B gene, followed by direct DNA sequencing and sequence analysis of the partial NS5B sequence.
Results:Multiple sequence alignment and phylogenetic analysis of our isolates and those represent genotypes 1-6, retrieved from GenBank database showed that Menoufia-isolates 1, 2, 4 and 5 were classified as genotype 4a, however, isolate Menoufia-3 was grouped with genotype 4c. Four known mutations related to drug resistance were detected in different HCV genotypes; Q309R was detected in Menoufia-isolates 1, 2, 4 and 5; D244N, Q309R and D310N were common in genotype 3 (80-100%). Protein functional analysis indicated that the detected drug resistance mutations did not alter the RdRb catalytic domain of NS5B protein.
Conclusions:Our data showed that HCV genotype 4 is still the most prevalent genotype in Egypt and Subtype 4a is predominant.In silicodetection of drug resistance mutations in HCV-infectedpatients before treatment is considered as a helpful tool could be used as a marker for clinical decisions to determine the suitable treatment.
[Amal Mahmoud, Tamer M. Roshdy and Moustafa A. Sakr (2020); IN SILICO ANALYSIS OF NS5B GENE OF HCV GENOTYPE 4 IN NORTH EGYPT Int. J. of Adv. Res. 8 (Aug). 1227-1235] (ISSN 2320-5407). www.journalijar.com
Department of Bioinformatics, Genetic Engineering and Biotechnology Research Institute (GEBRI),University of Sadat City, Egypt.
Egypt
