Variability of the Hepatitis C Virus Genome

Simmonds, Peter

doi:10.1159/000060468

Cited by 37 publications

(14 citation statements)

References 130 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The error-prone RNA-dependent RNA polymerase (RdRp) NS5B, and the resulting high mutation frequencies during replication, contributes to the substantial genetic and antigenic heterogeneity of HCV, with seven major genotypes showing Ͼ30% nucleotide sequence divergence from each other and numerous subtypes identified to date (5,(50)(51)(52). The distribution of genotypes varies by geographical location and risk groups for infection; the predominant genotypes within the United States, Europe, Australia, and East Asia (Japan, Taiwan, Thailand, and China) are 1, 2, and 3.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Development of an Intergenotypic Hepatitis C Virus (HCV) Cell Culture Method To Assess Antiviral Susceptibilities and Resistance Development of HCV NS3 Protease Genes from HCV Genotypes 1 to 6

Imhof

Simmonds

2010

J Virol

View full text Add to dashboard Cite

Protease inhibitors (PIs) of hepatitis C virus (HCV) provide an additional or alternative therapy for chronic infection. However, assessment of their efficacy and ability to inhibit replication of different genotypes is hampered by the lack of a convenient animal model or a method for in vitro culture of HCV other than the type 1/2-based replicons and the infectious genotype 2a clone JFH1. To address this problem, we constructed a panel of replication-competent chimeric Jc1 (pFK JFH1/J6/C-846) clones containing protease and NS4A coding sequences from all six major genotypes, enabling the determination of replication and the susceptibility to PIs. Chimeras showed substantial variability in replication kinetics, attributable in part to naturally occurring polymorphisms and differing requirements for adaptive mutations in NS3 and NS4A. Through calculation of 50% inhibitory concentrations (IC 50 s) of BILN 2061, measuring reduction in the number of focus-forming units/ml (FFU/ml) and replication inhibition, consistent genotype-associated differences in antiviral susceptibilities were observed. IC 50 s for genotype 1b, 4a, and 6a-derived chimeras (1 to 3 nM) were approximately 100-fold lower than those for genotypes 2a, 3a, and 5a (range, 80 to 720 nM), implying major differences in response to therapy. In vitro passage in increasing concentrations of BILN 2061 rapidly induced resistance-associated mutations at position 168 in chimeras of all 6 genotypes and at position 156 in genotypes 1b and 4a, each with substantial variability in the identity of substituted amino acids. The system will allow future comprehensive phenotypic characterization of naturally occurring and treatment-induced mutations for PIs in trial or entering clinical use.Worldwide, about 170 million individuals are estimated to be infected with hepatitis C virus (HCV) (1, 48). Chronic HCV infection is a leading cause of chronic liver diseases, such as cirrhosis and hepatocellular carcinoma (6). HCV has a positive-sense, single-stranded RNA genome of approximately 9,600 nucleotides, belonging to the family Flaviviridae (7). A single polyprotein of around 3,000 amino acids (53) is translated and processed by cellular and viral proteases to generate 10 different structural and nonstructural proteins (16,18,19).The error-prone RNA-dependent RNA polymerase (RdRp) NS5B, and the resulting high mutation frequencies during replication, contributes to the substantial genetic and antigenic heterogeneity of HCV, with seven major genotypes showing Ͼ30% nucleotide sequence divergence from each other and numerous subtypes identified to date (5, 50-52). The distribution of genotypes varies by geographical location and risk groups for infection; the predominant genotypes within the United States, Europe, Australia, and East Asia (Japan, Taiwan, Thailand, and China) are 1, 2, and 3. Genotype 4 is largely confined to the Middle East, Egypt, and Central Africa, whereas genotypes 5 and 6 are found predominantly in South Africa and Southeast Asia, respectively (49).The c...

show abstract

mentioning

confidence: 99%

“…Wells were scored positive if at least 1 positive cell was detected. TCID 50 was calculated according to the method of Reed and Muench (41).…”

mentioning

confidence: 99%

Development of an Intergenotypic Hepatitis C Virus (HCV) Cell Culture Method To Assess Antiviral Susceptibilities and Resistance Development of HCV NS3 Protease Genes from HCV Genotypes 1 to 6

Imhof

Simmonds

2010

J Virol

View full text Add to dashboard Cite

show abstract

“…In contrast, the E1 and E2/NS1 regions present the highest degree of sequence variability among different isolates; in particular, the N terminal portion of E2/NS1 contains a hypervariable region of 30 amino acids, which shows extensive variation between virtually all known isolates. 7 The major extracellular loop of CD81, a cell-surface protein widely expressed on B and T lymphocytes and other cells including hepatocytes, has been shown to bind E2. 8 The recent success of isolating a cDNA clone capable of generating infectious RNA transcripts may be an important step toward the development of a tissue culture system.…”

mentioning

confidence: 99%

Pathogenesis of chronic hepatitis C: Immunological features of hepatic injury and viral persistence

1999

View full text Add to dashboard Cite

The immune response to viral antigens is thought to be responsible for viral clearance and disease pathogenesis during hepatitis C virus (HCV) infection. In chronically infected patients, the T-cell response to the HCV is polyclonal and multispecific, although it is not as strong as the response in acutely infected patients who display a more vigorous T-cell response. Importantly, viral clearance in acutely infected patients is associated with a strong CD4 ؉ helper T-cell response. Thus, the dominant cause of viral persistence during HCV infection may be the development of a weak antiviral immune response to the viral antigens, with corresponding inability to eradicate infected cells. The most striking feature of hepatitis C is its tendency toward chronicity. The hepatitis C virus (HCV) contains a positive-stranded RNA genome of about 10 kilobases, which contains a single uninterrupted open reading frame that encodes a protein of 3010-3011 amino acids. 1,2 The virus is classified as a Flavivirus. HCV infects an estimated 400 million people, corresponding to more than 3% of the world population. 3 Numerous partial and complete nucleotide sequences have been derived from geographically widespread HCV isolates. The data indicate substantial sequence diversity within, and especially between, each geographic area. The European and American isolates appear to be more closely related to each other than to the Japanese isolates. Based on a polymerase chain reaction-based algorithm, a classification system has been proposed by Okamoto 4 and revised by Simmonds. 5 Different viral sequences (quasispecies) have been isolated from the same patient upon sequential sampling, and multiple isolates have been reported in a single sample. 6 The degree of similarity between isolates at the amino acid level varies from genome region to region. The nucleocapsid protein (core) has the highest sequence homology among all isolates sequenced to date. In contrast, the E1 and E2/NS1 regions present the highest degree of sequence variability among different isolates; in particular, the N terminal portion of E2/NS1 contains a hypervariable region of 30 amino acids, which shows extensive variation between virtually all known isolates. 7 The major extracellular loop of CD81, a cell-surface protein widely expressed on B and T lymphocytes and other cells including hepatocytes, has been shown to bind E2. 8 The recent success of isolating a cDNA clone capable of generating infectious RNA transcripts may be an important step toward the development of a tissue culture system. 9,10 The only animal model, the chimpanzee, mirrors several features of human HCV infection. Most importantly, the frequency of persistent infection is high in both species, and virus replication occurs despite evidence of cellular and humoral immune responses. 11,12 A key difference is that necroinflammatory lesions in chronically infected chimpanzees are almost always mild, whereas in humans, the disease spectrum is very wide, ranging from mild to severe hepatitis and end-sta...

show abstract

“…The HCV genome contains a linear, positive-strand RNA molecule of " 9500 nucleotides, with variability apparent in the viral genome and several genotypes described (Choo et al, 1989 ;Chamberlain et al, 1997 ;Simmonds, 1998). Information on the mechanism of HCV replication at the molecular level has so far depended upon the expression of its partial or entire genome and comparative analysis with genomes of distantly related flaviviruses or pestiviruses (Zanotto et al, 1996 ;Clarke, 1997).…”

mentioning

confidence: 99%

Hepatitis C virus NS5A protein modulates cell cycle regulatory genes and promotes cell growth.

Ghosh

Steele

Meyer

et al. 1999

Journal of General Virology

164

124

View full text Add to dashboard Cite

Variability of the Hepatitis C Virus Genome

Cited by 37 publications

References 130 publications

Development of an Intergenotypic Hepatitis C Virus (HCV) Cell Culture Method To Assess Antiviral Susceptibilities and Resistance Development of HCV NS3 Protease Genes from HCV Genotypes 1 to 6

Development of an Intergenotypic Hepatitis C Virus (HCV) Cell Culture Method To Assess Antiviral Susceptibilities and Resistance Development of HCV NS3 Protease Genes from HCV Genotypes 1 to 6

Pathogenesis of chronic hepatitis C: Immunological features of hepatic injury and viral persistence

Hepatitis C virus NS5A protein modulates cell cycle regulatory genes and promotes cell growth.

Contact Info

Product

Resources

About