Abstract
The current study was designed to determine the Hepatitis C Virus (HCV) genotypes in a representative sample of HCV chronically infected patients in Saudi Arabia. All HCV isolates were genotyped by sequencing of the 5′UTR region and newly identified HCV isolates were identified. Specific universal primers targeting 5′UTR region were used for both amplification and sequencing of all isolates that resulted in 244 bp fragment which represent about 80% of 5′UTR region. Most of HCV isolates in this study were genotype 4 (76.4%) where only few isolates were recognized as genotype 1 (19.6%). All results were compared to HCV reference sequences from LOS ALAMOS HCV database, considering only the complete full genomes for the main phylogenetic analysis. Sequences that showed maximum identity (98% –100%) were selected. Most isolates were identical with HCV genotype 4 references. Some isolates were similar to different subtypes of HCV genotypes 4, 1 and 6. Phylogenetic analysis showed resemblance of most isolates to similar ones from the Far East, North America and Egypt. Using sequence Weblogo, Alignment analysis of isolated HCV genotypes 4 and 1 showed 92% and 95.5% nucleotide conservation, respectively. There was no predominant nucleotide in the varied sites, in both genotypes. All isolated sequences were submitted to GenBank database.
Highlights
Hepatitis C virus (HCV) is estimated to infect 170 million people worldwide
We present frequency and percentages of nominal variables for groups’ genotype 1 and 4 mean, standard deviation (SD) and median for numerical variables
The values of HCV viral load varied from 1,2000 copies/ml to 11,500,000 copies/ml, albumin (Alb) varied from 12 g/l to 98 g/l (38610).Total bilirubin varied from 3 mmol/l to 81 mmol/l (13612), aspartite aminotransferase (AST) varied from 12 U/l to 175 U/l (41629), alanine aminotransferase (ALT) varied from 21 U/l to 288 U/l (64643), alkaline phosphatase varied from 52 U/l to 509 U/l (120667), and total proteins varied from 42 g/l to 100 g/l (7568) (Table 1)
Summary
Hepatitis C virus (HCV) is estimated to infect 170 million people worldwide. Chronic infection with HCV leads to progressive liver disease ending in liver cirrhosis and hepatocellular carcinoma [1]. HCV isolates are classified into at least six major genotypes (genotypes 1–6), whose nucleotide sequences differ by 31–33% [5]. 8. To detect the HCV genotype, search nucleotide database using the gotten final sequence in the following site: http://blast.
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