الفهرس 
IntroductionOnly 14 pages are availabe for public view
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Abstract
Background: Hepatitis C virus (HCV) is a major health problem worldwide where around 71 million people suffer from chronic HCV. In Egypt, some studies revealed that most of HCV infections are due to genotype 4 especially HCV subtype 4a that became epidemic and broadly dispersed. Quasispecies or rare variants are mutated variants that cause a big challenge towards drug and immune system resistance. Recent studies showed that the deep Next Generation Sequencing (NGS) technology presents a better understanding of variants dynamics in HCV quasispecies as it is easily to identify low frequency variants due to the high coverage of NGS. Aim: The main concern of this work is to identify the rare variants of HCV virus using Deep Next Generation Sequencing Technique (Mi-seq Sequencer, Illumina).Methods: Viral RNA was isolated from plasma using a viral RNA extraction kit according to manufacturer protocol. RNA sample libraries were prepared with the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA). RNA fragmentation, cDNA synthesis/indexing, PCR amplification/clean-up, and library normalization/pooling steps were conducted according to the manufacturer’s instructions. Sequencing process was performed using MiSeq sequencer with the MiSeq reagent kit v2 (300 cycles; Illumina).Results: from our data, HCV Genotype 4a was the most prevalent subtype between samples. Co-infection with Hepatitis G virus (HPgV) was detected in one patient from naïve group. Also, we succeeded to detect different rare SNP along the genome that lead to form different HCV variants in each sample in both groups.Conclusion: In this study, we succeeded to detect and determine nearly the whole HCV genome sequence and the genetic diversity (rare variants) directly in plasma of both groups (naïve and relapsed) patients without using any specific primers by using deep Illumina sequencing. Furthermore, we can identify a novel variant of HPgV in a paitent infected with HCV.