Genotype Distribution and Molecular Epidemiology of Hepatitis C Virus in Blood Donors from Southeast France

Abstract

The genotype distribution of hepatitis C virus (HCV) in blood donors from southeast France was tracked for a period of 13 years (1991 to 2003). Virus genomes from 321 samples were analyzed by amplification and sequencing of the NS5b and E1 regions. The most frequent genotypes were 1b (30.2%), 1a (27.7%), and 3a (22.4%). Although it was less common, genotype 2 was characterized by the presence of strains belonging to 11 different subtypes, including 5 that had never been characterized. Genotypes 1a, 1b, 3a, and 4a presented typical "epidemic" profiles, with a large number of isolates per subtype and short mean genetic distances between isolates. Type 2 isolates displayed a typical "endemic" profile, with a large number of subtypes and very few isolates in each subtype. The epidemiology of HCV infection in southeast France changed radically during the study period in relation to modifications in the etiology of infection. We observed the emergence of new epidemic subtypes (subtypes 1a and 3) linked to intravenous drug use and a decrease in the types linked to blood transfusion and nosocomial infection (epidemic subtype 1b and endemic type 2). Comparison of strains from blood donors with strains from a cohort of inpatients in the same region during 2001 and 2002 demonstrated for the first time that the monitoring of blood donors is a generally valid indicator of HCV epidemiology in terms of genotype distribution.

Analysis of the 5′ Noncoding Region versus the NS5b Region in Genotyping Hepatitis C Virus Isolates from Blood Donors in France

“…Indeed, the degree of sequence variation of NS5b correlates well with HCV subtype definition (37,38), by contrast with the 5Ј NCR, which is highly conserved and, hence, does not provide a tool for differentiation between subtypes. Conserved primers in the NS5b have been described previously that allow the amplification of all genotypes of HCV (3,17,20). Moreover, the existence of a previously defined reference panel in HCV databases for the NS5b regions considerably facilitates subtype identification (15,25,31).…”

“…A 339-nucleotide segment from position 8370 to 8708 in the NS5b region was amplified and sequenced (3). If amplification in the NS5b region failed, a 357-nucleotide segment from position 1029 to 1385 in the E1 region was analyzed (2).…”

“…For practical reasons, the 5Ј NCR was also chosen as the target for various genotyping methods, including the InnoLipa HCV II test (33, 34), sequencing (8,9,10,26), and the duplex mobility assay (39). However, recent studies involving NS5b region analysis (3,29,35) show that 5Ј NCR sequence analysis can lead to genotyping errors (5, 35). In this study, we used NS5b region sequence analysis to determine the HCV subtype distribution of 357 isolates collected from blood donors in France between 2002 and 2003.…”

Hepatitis C virus genotype distribution in Turkey remains unchanged after a decade: Performance of phylogenetic analysis of the NS5B, E1, and 5’UTR regions in genotyping efficiency

“…This sample was determined as 2a and 1b with the sequences of the NS5B and E1 regions, respectively. When conserved primers of the NS5B and E1 regions were used (17,18), amplification was less successful, with failures in amplification in 6 and 4 samples, respectively. The major factor of these missing samples might be the variability in the primer-binding sequences of the target genome.…”

Unique NS5b Hepatitis C Virus Gene Sequence Consensus Database Is Essential for Standardization of Genotype Determinations in Multicenter Epidemiological Studies

“…The constitution of this bank could first be based on international available sequences (Los Alamos [4], JSPs Kakehni, euHCVdb, and NIBSC [8] databases), where each sequence is annotated by its genotype, but should also take into account the geographical distribution and the epidemiological situation of the country. Moreover, due to the rapid evolution of HCV and consequently the continual characterization of new genotypes (especially in types 2 and 4 [1,10]), this consensual bank should regularly include newly described subtypes. This multicenter study demonstrates that any laboratory with expertise in sequencing techniques would be able to provide a reliable HCV genotype for clinical and epidemiological purposes as long as they are provided a consensus reference sequence database.…”