Comparison of hepatitis C virus NS5b and 5' noncoding gene sequencing methods in a multicenter study.
A national evaluation study was performed in 11 specialized laboratories with the objective of assessing their capacities to genotype hepatitis C virus (HCV) and define the applicability of a given genotyping method. The panel consisted of 14 samples positive for HCV RNA of different genotypes (including 3 samples with two different artificially mixed genotypes) and 1 HCV-negative sample. Seventeen sets of data were gathered from the 11 participating laboratories. The sensitivities ranged from 64.3 to 100% and from 42.7 to 85.7% for the methods that used sequencing of the NS5b region and the 5' noncoding (5' NC) region, respectively. When the data for the artificially mixed samples were excluded, NS5b genotyping gave correct results for 80% of the samples, 1.7% of the samples were misclassified, and 18.3% of the samples had false-negative results. By 5' NC-region genotyping methods, 58.3% of the results were correct, 29.7% were incomplete, 8.3% were misclassifications, 1.2% were false positive, and 2.4% were false negative. Only two procedures based on NS5b sequencing correctly identified one of the three samples with mixtures of genotypes; the other methods identified the genotype corresponding to the strain with the highest viral load in the sample. Our results suggest that HCV 5' NC-region genotyping methods give sufficient information for clinical purposes, in which the determination of the subtype is not essential, and that NS5b genotyping methods are more reliable for subtype determination, which is required in epidemiological studies.
Laperche
Syria
S
Centre National de Référence pour les Hépatites B et C en Transfusion, Département des Agents Transmissible par le Sang, Institut National de la Transfusion Sanguine, 6 rue Alexandre-Cabanel, 75015 Paris, France.
Lunel
Françoise
F
Izopet
Jacques
J
Alain
Sophie
S
Dény
Paul
P
Duverlie
Gilles
G
Gaudy
Catherine
C
Pawlotsky
Jean-Michel
JM
Plantier
Jean-Christophe
JC
Pozzetto
Bruno
B
Thibault
Vincent
V
Tosetti
François
F
Lefrère
Jean-Jacques
JJ
D020121:5' Untranslated Regions / Q000235:genetics*; D017931:DNA Primers; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics; D006526:Hepatitis C / Q000453:epidemiology / Q000821:virology; D006801:Humans; D007753:Laboratories; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase
D020121:5' Untranslated Regions; D017931:DNA Primers; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase