Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region

Abstract

Hepatitis C virus (HCV) shows substantial nucleotide sequence diversity distributed throughout the viral genome, with many variants showing only 68 to 79 % overall sequence similarity to one another. Phylogenetic analysis ofnucleofide sequences derived from part of the gene encoding a non-structural protein (NS-5) has provided evidence for six major genotypes of HCV amongst a worldwide collection of 76 samples from HCV-infected blood donors and patients with chronic hepatitis. Many of these HCV types comprised a number of more closely related subtypes, leading to a current total of 11 genetically distinct viral populations. Phylogenetic analysis of other regions of the viral genome produced relationships between published sequences equivalent to those found in NS-5, apart from the more highly conserved 5' non-coding region in which only the six major HCV types, but not subtypes, could be differentiated. A new nomenclature for HCV variants is proposed in this communication that reflects the twotiered nature of sequence differences between different viral isolates. The scheme classifies all known HCV variants to date, and describes criteria that would enable new variants to be assigned within the classification as they are discovered.

The genotype of the hepatitis C virus in patients with HCV-related B cell non-Hodgkin’s lymphoma

“…23 There are clear differences in genotype prevalence among various geographic areas: type 1a, for instance, is prevalent in the United States; types 1b, 2a and 2b are more frequent in Japan and Taiwan; type 3 is the most common elsewhere in Asia, and type 4 in the Middle East. [25][26][27][28] In Italy, type 1b is the most common, accounting for more than 60% of infected cases.…”

“…The first 8 is based on the amplification of cDNA using two sets of primers specific for the 5′UTR and for the E region of HCV genome and subsequent Southern blot hybridization, using four 32 P-labeled genotype-specific oligonucleotide probes. 22 This assay allows the identification of four genotypes, respectively, 1a, 1b, 2, 3, according to Simmonds classification 23 but is very laborious and does not allow the identification of some clinically relevant types and subtypes. Due to these limitations a second assay (2nd generation Line Probe Assay, LiPA; Innogenetics, Brussels, Belgium) was recently adopted.…”

Trends in HCV prevalence, risk factors and distribution of viral genotypes in injecting drug users: findings from two cross-sectional studies

“…Interestingly, a significantly lower rate of HCV RNA amplification for the NS5b region was obtained when samples collected in the first (1994)(1995)(1996)(1997)18 . 1%) and second (1999-2001, 61 .…”

“…The evolutionary distances were computed using the Maximum Composite Likelihood method [30] and were expressed as the number of base substitutions per site. HCV sequences were classified into genotypes, according to Simmonds et al [18].…”

Cytokine profile of liver- and blood-derived nonspecific T cells after liver transplantation: T helper cells type 1/0 lymphokines dominate in recurrent hepatitis C virus infection and rejection

“…Values for bilirubin (normal Ͻ1 mg/mL), alkaline phosphatase (normal; 40 to 190 U/L), ␥-glutamyltransferase (normal; 4 to 18 U/L), alanine aminotransferase (normal; 5 to 19 U/L), and aspartate aminotransferase (normal; 5 to 15 U/L) were not significantly different among groups (Table 1). HCV genotype 1 14 was found nearly exclusively in group A (15 of 15 patients; 21 T-cell lines) and group B patients (10 of 11 patients; 14 intrahepatic T-cell lines). In control patients with CH-C (group C), 18 of 25 patients had genotype 1, 6 patients had genotype 3a, and 1 patient had genotype 2a (Table 1).…”