HCV genotyping using statistical classification approach

Hepatitis C virus has a positive-sense single-stranded RNA genome of about 9.6 kb containing one long open reading frame (ORF) with untranslated regions at both ends [1]. The polyprotein is processed into structural and nonstructural proteins. The core and the two envelope proteins (E1 and E2) are part of the virion. So far, six major genotypes (HCV-1 to HCV-6) have been described, each containing multiple subtypes (e.g., 1a, 1b, etc.). The isolates formerly published as genotypes 7 to 11 are now considered subtypes within genotypes 3 (genotype10) and 6 (genotype 7, 8, 9, and 11) [2,3].Infection by HCV is the leading cause of chronic liver disease worldwide [4]. The overall prevalence of HCV infection in the United States is 1.8%, with most of the patients unaware of their infection and risk for developing cirrhosis and hepatocellular carcinoma [5]. The most prevalent genotypes in the U.S. were 1 (71.0%), 2 (14.3%), and 3 (11.6%), followed by less common types 4 (1.7%), and 6 (1.5%). The remaining types represent less than 1% of the population. The prevalence of each genotype in the population was relatively stable [6].The genotype of the HCV strain appears to be an important determinant of the severity and aggressiveness of liver infection, as well as patient response to antiviral therapy [7]. HCV genotypes display significant differences in their global distribution and prevalence, making genotyping a useful method for determining the source of HCV transmission in an infected localized population. Due to the chronic nature of HCV infection and the tremendous burden on healthcare resources, clinicians and researchers have looked for key epidemiological, pathological and viral characteristics that may provide insight into disease progression, severity and response to therapy to permit the administration of effective therapeutic regimens as well as long-term management of infected individuals [8]. The best available therapy for HCV infection, interferon in combinatio