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Journal of Clinical Microbiology, February 2005, p. 733-739, Vol. 43, No. 2
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.2.733-739.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Comparison of Hepatitis C Virus NS5b and 5' Noncoding Gene Sequencing Methods in a Multicenter Study

Centre National de Référence pour les Hépatites B et C en Transfusion, Département des Agents Transmissibles par le Sang, Institut National de la Transfusion Sanguine,¹ Laboratoire de Virologie, Centre Hospitalo-Universitaire Pitié-Salpêtrière,¹¹ Département des Agents Transmissibles par le Sang, Institut National de la Transfusion Sanguine, Paris,¹⁴ Laboratoire de Virologie-Bactériologie, Centre Hospitalo-Universitaire, Angers,² Laboratoire de Virologie, Centre Hospitalo-Universitaire Purpan, Toulouse,³ Laboratoire de Virologie-Bactériologie, Centre Hospitalo-Universitaire, Limoges,⁴ Laboratoire de Virologie-Bactériologie Associé au CNR des Hépatites B et C, Centre Hospitalo-Universitaire Avicenne, Bobigny,⁵ Laboratoire de Virologie, Centre Hospitalo- Universitaire, Amiens,⁶ Laboratoire de Virologie-Bactériologie, Centre Hospitalo-Universitaire Bretonneau, Tours,⁷ Laboratoire de Virologie-Bactériologie, Centre Hospitalo-Universitaire Henri-Mondor, Créteil,⁸ Laboratoire de Virologie-Bactériologie, Centre Hospitalo-Universitaire, Rouen,⁹ Laboratoire de Virologie-Bactériologie, Centre Hospitalo-Universitaire, Saint Etienne,¹⁰ Laboratoire de Virologie-Bactériologie, Centre Hospitalo-Universitaire, Grenoble,¹² Laboratoire d'Hématologie, Centre Hospitalo-Universitaire, Amiens, France,¹³

Received 28 July 2004/ Returned for modification 16 September 2004/ Accepted 10 October 2004

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.

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