Sequence analysis of hepatitis C virus genotypes 1 to 5 reveals multiple novel subtypes in the Benelux countries

Abstract

Hepatitis C virus (HCV) isolates from a cohort of 315 patients from the Benelux countries (Belgium, The Netherlands, Luxembourg) were genotyped by means of reverse hybridization Inno-LiPA (line probe assay). Genotypes la, lb, 2a, 2b, 3a, 4a and 5a were detected. From the cohort, isolates representing all types and those showing an aberrant LiPA pattern were further analysed by sequencing parts of the 5' UTR, core (nt 1 to 326; aa residues 1 to 108) and core/E1 (nt 477 to 924; aa residues 159 to 308) regions. Molecular evolutionary analysis of the core and core/E1 regions allowed discrimination between known and additional subtypes, especially within types 2 and 4. The core region is not suitable for classification of new subtypes because of the relatively high level of conservation. The core/E 1 region displays a higher level of sequence variation and allows much more distinct discrimination between subtypes. Genotypes 2 and 4 are particularly heterogeneous, with at least 7 and 10 subtypes, respectively. In contrast to previous reports from Europe, HCV isolates from the cohort constituted a highly heterogeneous population of virus variants, especially within genotypes 2 and 4.

Hepatitis C Virus Genotyping versus Serotyping in Egyptian Patients

“…This suggests that the presence of anti-NS4 antibodies is not indicative of ability to be typed by the serotyping assay. In this respect our results confirm those of van Doorn et al [10].…”

“…The overall sensitivity of serotyping and genotyping techniques was 81.16% with a concordance of 73.3%. Similar results were reported by van Doorn et al [10]. Seven of the 11 samples nonreactive in serotyping did not contain anti-NS4 antibodies as measured by the line immunoassay [12].…”

“…The overall sensitivity of serotyping does not differ significantly between the major types. In our study, as in those of Stuyver et al [9] and van Doorn et al [10], type 4 appeared to be highly heterogeneous, comprising multiple subtypes. However, the levels of sensitivity and concordance of the serotyping assay for these subtypes are as high as those for the other types because the sequence heterogeneity of the subtype-specific NS4 epitopes is sufficiently restricted to permit reactivity with type 4 peptides in the assay [4].…”

SEQUENCE SIMILARITY BETWEEN THYROID SELF-PROTEIN AND HEPATITIS C VIRUS POLYPROTEIN: possible triggering mechanism of autoimmune thyroiditis

“…In the case of HCV2c, the ID had 3033 AA protein sequences (27) . The HCV2d, the ID contained 149 AA protein sequences (34) .The HCV2e study allowed us to obtain ID of 119 AA protein sequences (33) . In the case of HCV2f, the ID had 93 AA protein sequences (33) .…”

Hepatitis C Virus Genotype 5a Subgenomic Replicons for Evaluation of Direct-Acting Antiviral Agents

“…However, a similar system for genotype 5 is still lacking. This genotype is restricted mainly to South Africa (15) and has been associated with sporadic cases of HCV infection in Canada, Brazil, The Netherlands, Spain, and Belgium (16)(17)(18). In 2004, a high prevalence of genotype 5a was reported in central France (19).…”