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Journal of Clinical Microbiology, June 2006, p. 2051-2056, Vol. 44, No. 6
0095-1137/06/$08.00+0     doi:10.1128/JCM.02463-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

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

Unité des Virus Emergents EA3292, Etablissement Français du Sang, Alpes-Méditerranée, Marseille, France,¹ Institut National de Transfusion Sanguine, Paris, France,² Faculté de Médecine, Université de la Méditerranée, Marseille, France³

Received 29 November 2005/ Returned for modification 6 February 2006/ Accepted 22 February 2006

The 5' noncoding region (5' NCR) of the hepatitis C virus (HCV) has become the standard for genotyping even though several reports show that its use can result in classification errors. The purpose of this study was to perform genotyping based on sequence analysis of the NS5b region in a set of 357 HCV strains isolated from blood donors in France in 2002 and 2003. Results were compared with those previously obtained using 5' NCR analysis, and HCV subtype distribution was reevaluated. Twenty-six of 120 strains (22%) initially identified as genotype 1b by 5' NCR region sequence analysis were reclassified as genotype 1a by NS5b region sequence analysis. Similarly, 14 of 23 strains (61%) initially identified as 2a/2c were reclassified as non-2a and non-2c subtypes, and 12 of 22 strains (45%) initially identified as 4c/4d subtypes were reclassified as non-4c and non-4d subtypes. Sequence analysis of the NS5b region also revealed 5 putative new subtype 2 variants and 2 putative new subtype 4 variants. Although these findings demonstrated full agreement between 5' NCR and NS5b sequence analysis with regard to type classification, genotyping based on phylogenetic analysis of the NS5b region is more accurate for subtype determination than genotyping based on analysis of the 5' NCR. Sequence analysis of the NS5b region is mandatory for epidemiologic studies.

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