Comparison of quasispecies diversity of HCV between chronic hepatitis C and hepatocellular carcinoma by ultradeep pyrosequencing

Chang Wook Park, Min Chul Cho, Keumrock Hwang, Sun-Young Ko, Heung Bum Oh, Han Chu Lee

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Backgrounds. 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. Conclusion. 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.

Original languageEnglish
Article number853076
JournalBioMed Research International
Volume2014
DOIs
Publication statusPublished - 2014 Jan 1

Fingerprint

Chronic Hepatitis C
Viruses
Hepacivirus
Hepatocellular Carcinoma
Amino Acids
Protein C
ROC Curve
Area Under Curve
Genome
Genes
Technology
Pressure

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Comparison of quasispecies diversity of HCV between chronic hepatitis C and hepatocellular carcinoma by ultradeep pyrosequencing. / Park, Chang Wook; Cho, Min Chul; Hwang, Keumrock; Ko, Sun-Young; Oh, Heung Bum; Lee, Han Chu.

In: BioMed Research International, Vol. 2014, 853076, 01.01.2014.

Research output: Contribution to journalArticle

@article{4edcd89f43ee48cca848ea94404f11f3,
title = "Comparison of quasispecies diversity of HCV between chronic hepatitis C and hepatocellular carcinoma by ultradeep pyrosequencing",
abstract = "Backgrounds. 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. Conclusion. 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.",
author = "Park, {Chang Wook} and Cho, {Min Chul} and Keumrock Hwang and Sun-Young Ko and Oh, {Heung Bum} and Lee, {Han Chu}",
year = "2014",
month = "1",
day = "1",
doi = "10.1155/2014/853076",
language = "English",
volume = "2014",
journal = "BioMed Research International",
issn = "2314-6133",
publisher = "Hindawi Publishing Corporation",

}

TY - JOUR

T1 - Comparison of quasispecies diversity of HCV between chronic hepatitis C and hepatocellular carcinoma by ultradeep pyrosequencing

AU - Park, Chang Wook

AU - Cho, Min Chul

AU - Hwang, Keumrock

AU - Ko, Sun-Young

AU - Oh, Heung Bum

AU - Lee, Han Chu

PY - 2014/1/1

Y1 - 2014/1/1

N2 - Backgrounds. 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. Conclusion. 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.

AB - Backgrounds. 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. Conclusion. 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.

UR - http://www.scopus.com/inward/record.url?scp=84903625300&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84903625300&partnerID=8YFLogxK

U2 - 10.1155/2014/853076

DO - 10.1155/2014/853076

M3 - Article

C2 - 24999482

AN - SCOPUS:84903625300

VL - 2014

JO - BioMed Research International

JF - BioMed Research International

SN - 2314-6133

M1 - 853076

ER -