Computational reconstruction of bole1a, a representative synthetic hepatitis C virus subtype 1a genome

Supriya Munshaw, Justin Bailey, Lin Liu, William Osburn, Kelly P. Burke, Andrea Cox, Stuart Campbell Ray

Research output: Contribution to journalArticle

Abstract

Hepatitis C virus (HCV) research is hampered by the use of arbitrary representative isolates in cell culture and immunology. The most replicative isolate in vitro is a subtype 2a virus (JFH-1); however, genotype 1 is more prevalent worldwide and represents about 70% of infections in the United States, and genotypes differ from one another by 31% to 33% at the nucleotide level. For phylogenetic and immunologic analyses, viruses H77 and HCV-1 (both subtype 1a) are commonly used based on their historic importance. In an effort to rationally design a representative subtype 1a virus (Bole1a), we used Bayesian phylogenetics, ancestral sequence reconstruction, and covariance analysis on a curated set of 390 full-length human HCV 1a sequences from GenBank. By design, Bole1a contains variations present in widely circulating strains and matches more epitope-sized peptides in a full-genome comparison to subtype 1a isolates than any other sequence studied. Parallel analyses confirm that selected epitopes from the Bole1a genome were able to elicit a robust T cell response. In a proof of concept for infectivity, the envelope genes (E1 and E2) of Bole1a were expressed in an HIV pseudoparticle system containing HCV envelope genes and HIV nonenvelope genes with luciferase expression. The resulting Bole1a pseudoparticle robustly infected Hep3B cells. In this study, we demonstrate that a rationally designed, fully synthetic HCV genome contains representative epitopes and envelope genes that assemble properly and mediate entry into target cells.

Original languageEnglish (US)
Pages (from-to)5915-5921
Number of pages7
JournalJournal of Virology
Volume86
Issue number10
DOIs
StatePublished - May 2012

Fingerprint

Hepatitis C virus
Hepacivirus
Genome
genome
epitopes
Epitopes
Viruses
viruses
Genes
genes
Genotype
HIV
genotype
phylogeny
Nucleic Acid Databases
luciferase
Allergy and Immunology
Luciferases
immunology
cell culture

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Computational reconstruction of bole1a, a representative synthetic hepatitis C virus subtype 1a genome. / Munshaw, Supriya; Bailey, Justin; Liu, Lin; Osburn, William; Burke, Kelly P.; Cox, Andrea; Ray, Stuart Campbell.

In: Journal of Virology, Vol. 86, No. 10, 05.2012, p. 5915-5921.

Research output: Contribution to journalArticle

@article{c9646bdccd7245faad5c514cf8b72ed3,
title = "Computational reconstruction of bole1a, a representative synthetic hepatitis C virus subtype 1a genome",
abstract = "Hepatitis C virus (HCV) research is hampered by the use of arbitrary representative isolates in cell culture and immunology. The most replicative isolate in vitro is a subtype 2a virus (JFH-1); however, genotype 1 is more prevalent worldwide and represents about 70{\%} of infections in the United States, and genotypes differ from one another by 31{\%} to 33{\%} at the nucleotide level. For phylogenetic and immunologic analyses, viruses H77 and HCV-1 (both subtype 1a) are commonly used based on their historic importance. In an effort to rationally design a representative subtype 1a virus (Bole1a), we used Bayesian phylogenetics, ancestral sequence reconstruction, and covariance analysis on a curated set of 390 full-length human HCV 1a sequences from GenBank. By design, Bole1a contains variations present in widely circulating strains and matches more epitope-sized peptides in a full-genome comparison to subtype 1a isolates than any other sequence studied. Parallel analyses confirm that selected epitopes from the Bole1a genome were able to elicit a robust T cell response. In a proof of concept for infectivity, the envelope genes (E1 and E2) of Bole1a were expressed in an HIV pseudoparticle system containing HCV envelope genes and HIV nonenvelope genes with luciferase expression. The resulting Bole1a pseudoparticle robustly infected Hep3B cells. In this study, we demonstrate that a rationally designed, fully synthetic HCV genome contains representative epitopes and envelope genes that assemble properly and mediate entry into target cells.",
author = "Supriya Munshaw and Justin Bailey and Lin Liu and William Osburn and Burke, {Kelly P.} and Andrea Cox and Ray, {Stuart Campbell}",
year = "2012",
month = "5",
doi = "10.1128/JVI.05959-11",
language = "English (US)",
volume = "86",
pages = "5915--5921",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "10",

}

TY - JOUR

T1 - Computational reconstruction of bole1a, a representative synthetic hepatitis C virus subtype 1a genome

AU - Munshaw, Supriya

AU - Bailey, Justin

AU - Liu, Lin

AU - Osburn, William

AU - Burke, Kelly P.

AU - Cox, Andrea

AU - Ray, Stuart Campbell

PY - 2012/5

Y1 - 2012/5

N2 - Hepatitis C virus (HCV) research is hampered by the use of arbitrary representative isolates in cell culture and immunology. The most replicative isolate in vitro is a subtype 2a virus (JFH-1); however, genotype 1 is more prevalent worldwide and represents about 70% of infections in the United States, and genotypes differ from one another by 31% to 33% at the nucleotide level. For phylogenetic and immunologic analyses, viruses H77 and HCV-1 (both subtype 1a) are commonly used based on their historic importance. In an effort to rationally design a representative subtype 1a virus (Bole1a), we used Bayesian phylogenetics, ancestral sequence reconstruction, and covariance analysis on a curated set of 390 full-length human HCV 1a sequences from GenBank. By design, Bole1a contains variations present in widely circulating strains and matches more epitope-sized peptides in a full-genome comparison to subtype 1a isolates than any other sequence studied. Parallel analyses confirm that selected epitopes from the Bole1a genome were able to elicit a robust T cell response. In a proof of concept for infectivity, the envelope genes (E1 and E2) of Bole1a were expressed in an HIV pseudoparticle system containing HCV envelope genes and HIV nonenvelope genes with luciferase expression. The resulting Bole1a pseudoparticle robustly infected Hep3B cells. In this study, we demonstrate that a rationally designed, fully synthetic HCV genome contains representative epitopes and envelope genes that assemble properly and mediate entry into target cells.

AB - Hepatitis C virus (HCV) research is hampered by the use of arbitrary representative isolates in cell culture and immunology. The most replicative isolate in vitro is a subtype 2a virus (JFH-1); however, genotype 1 is more prevalent worldwide and represents about 70% of infections in the United States, and genotypes differ from one another by 31% to 33% at the nucleotide level. For phylogenetic and immunologic analyses, viruses H77 and HCV-1 (both subtype 1a) are commonly used based on their historic importance. In an effort to rationally design a representative subtype 1a virus (Bole1a), we used Bayesian phylogenetics, ancestral sequence reconstruction, and covariance analysis on a curated set of 390 full-length human HCV 1a sequences from GenBank. By design, Bole1a contains variations present in widely circulating strains and matches more epitope-sized peptides in a full-genome comparison to subtype 1a isolates than any other sequence studied. Parallel analyses confirm that selected epitopes from the Bole1a genome were able to elicit a robust T cell response. In a proof of concept for infectivity, the envelope genes (E1 and E2) of Bole1a were expressed in an HIV pseudoparticle system containing HCV envelope genes and HIV nonenvelope genes with luciferase expression. The resulting Bole1a pseudoparticle robustly infected Hep3B cells. In this study, we demonstrate that a rationally designed, fully synthetic HCV genome contains representative epitopes and envelope genes that assemble properly and mediate entry into target cells.

UR - http://www.scopus.com/inward/record.url?scp=84861108064&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84861108064&partnerID=8YFLogxK

U2 - 10.1128/JVI.05959-11

DO - 10.1128/JVI.05959-11

M3 - Article

VL - 86

SP - 5915

EP - 5921

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 10

ER -