ArticleVirology journal2006
Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes.
Article in Virology journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Epidemiological trends of HCV subtypes in China.Virus genes · 2026Article
- Genotype Distribution and Migration Patterns of Hepatitis C Virus in Shandong Province, China: Molecular Epidemiology and Phylogenetic Study.JMIR medical informatics · 2025Article
- Mixed Infections Unravel Novel HCV Inter-Genotypic Recombinant Forms within the Conserved IRES Region.Viruses · 2024Article
- Article
- Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences.The Journal of general virology · 2020Article
- Limits and patterns of cytomegalovirus genomic diversity in humans.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection.BMC bioinformatics · 2014Article
- Epidemiological aspects of HCV infection in non-injecting drug users in the Brazilian state of Pará, eastern Amazon.Virology journal · 2014Article
- Molecular epidemiology and putative origin of hepatitis C virus in random volunteers from Argentina.World journal of gastroenterology · 2013Article
- Naturally occurring genotype 2b/1a hepatitis C virus in the United States.Virology journal · 2011Article
- Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.BMC bioinformatics · 2011Article
- Hepatitis C virus genotyping using an oligonucleotide microarray based on the NS5B sequence.Journal of clinical microbiology · 2010Article
- Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index.The Journal of general virology · 2008Article
- Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses.Virology journal · 2008Article
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5 authors.
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Abstract
backgroundThe 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.
resultsDifferent 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, and yield topologies consistent with those of the whole genome and polyprotein.
conclusionThese results extend those from previous studies and indicate that, unlike the NS5B gene, the 5' UTR contains insufficient variation to resolve HCV classifications to the level of viral subtype, and fails to distinguish genotypes reliably. Use of the 5' UTR for clinical tests to characterize HCV infection should be replaced by a subtype-informative test.
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