title: Comparison of quasispecies diversity of HCV between chronic hepatitis c and hepatocellular carcinoma by Ultradeep pyrosequencing.
abstract: BACKGROUND
  Hepatitis C virus (HCV) exists as population of closely related genetic variants known as quasispecies. HCV quasispecies diversity is strongly influenced by host immune pressure on virus. Quasispecies diversity is expected to decline as host immune response to HCV decreases over natural course of progressing from chronic hepatitis C (CHC) to hepatocellular carcinoma (HCC).
  
  
  METHODS
  Ultradeep pyrosequencing (UDPS) was used to evaluate degree of quasispecies diversity in 49 patients infected with HCV including 26 with CHC and 23 with HCC. Whole structural protein of HCV genome was subjected to UDPS.
  
  
  RESULTS
  Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups. Area under curve of ROC analysis for differentiating HCC from CHC was >0.8 for all of 14 amino acid positions.
  
  
  CONCLUSIONS
  HCV quasispecies diversity as indicator of declining host immune functions was easily assessed by UDPS technology. Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC. Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.
authors.affiliation: Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.
authors.forename: Chang-Wook
authors.initials: CW
authors.lastname: Park
authors.affiliation: Department of Laboratory Medicine, Gyeongsang National University Hospital and Gyeongsang National University School of Medicine, Jinju 660-701, Republic of Korea.
authors.forename: Min-Chul
authors.identifier: 0000-0002-0609-7734
authors.initials: MC
authors.lastname: Cho
authors.affiliation: Department of Laboratory Medicine, Sure Quest Laboratory, Yongin 446-916, Republic of Korea.
authors.forename: Keumrock
authors.initials: K
authors.lastname: Hwang
authors.affiliation: Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.
authors.forename: Sun-Young
authors.identifier: 0000-0002-1108-8381
authors.initials: SY
authors.lastname: Ko
authors.affiliation: Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.
authors.forename: Heung-Bum
authors.initials: HB
authors.lastname: Oh
authors.affiliation: Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea.
authors.forename: Han Chu
authors.initials: HC
authors.lastname: Lee
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral; D016174:Hepacivirus / Q000235:genetics* / Q000472:pathogenicity; D019698:Hepatitis C, Chronic / Q000235:genetics* / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000821:virology