Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions the 5 untranslated region (UTR) fails to classify subtypes.docVIP

Virology Journal BioMedCentral Research Open Access Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5 untranslated region (UTR) fails to classify subtypes Peter T Hraber*, William Fischer, William J Bruno, Thomas Leitner and Carla Kuiken Address: Theoretical Biology and Biophysics, T-10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545 USA Email: Peter T Hraber* - phraber@; William Fischer - wfischer@; William J Bruno - billb@; Thomas Leitner - tkl@; Carla Kuiken - kuiken@ * Corresponding author Published: 14 December 2006 Received: 06 November 2006 Accepted: 14 December 2006 Virology Journal 2006, 3:103 doi:10.1186/1743-422X-3-103 This article is available from: /content/3/1/103 ? 2006 Hraber et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The duration of treatment for HCV infection is partly indicated by the genotype of the virus. For studies of disease transmission, vaccine design, and surveillance for novel variants, subtype-level classification is also needed. This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions. Results: Different regions of the HCV genome yield inconsistent phylogenies, which can lead to erroneous conclusions about classification of a given infection. In particular, the highly conserved 5 untranslated region (UTR) yields phylogenetic trees with topologies that differ from the HCV polyprotein and complete genome phylogenies. Phylogenetic trees from the NS5B gene reliably cluster related subtypes,