Development of Intergenotypic Chimeric Replicons To Determine the Broad-Spectrum Antiviral Activities of Hepatitis C Virus Polymerase Inhibitors

Herlihy, Koleen J.; Graham, Joanne P.; Kumpf, Robert A.; Patick, Amy K.; Duggal, Rohit; Shi, Stephanie T.

doi:10.1128/aac.00533-08

Cited by 48 publications

(57 citation statements)

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“…especially rare and that the replication complex is typically encoded on the same genomic strand that it will replicate and transcribe (2). It is also interesting that when replication complexes are exchanged between different genotypes, the replication efficiency is substantially reduced (15). The pseudodiploidy of the HIV genome certainly increases the likelihood of recombination occurring due to the ability of the virus to package two RNA templates (17), while the secondary RNA structure in the HCV genome may limit the production of viable hybrid HCVs (59,68).…”

Section: Figmentioning

confidence: 99%

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

Raghwani

Thomas

Koekkoek

et al. 2012

J Virol

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Since its initial identification in St. Petersburg, Russia, the recombinant hepatitis C virus (HCV) 2k/1b has been isolated from several countries throughout Eurasia. The 2k/1b strain is the only recombinant HCV to have spread widely, raising questions about the epidemiological background in which it first appeared. In order to further understand the circumstances by which HCV recombinants might be formed and spread, we estimated the date of the recombination event that generated the 2k/1b strain using a Bayesian phylogenetic approach. Our study incorporates newly isolated 2k/1b strains from Amsterdam, The Netherlands, and has employed a hierarchical Bayesian framework to combine information from different genomic regions. We estimate that 2k/1b originated sometime between 1923 and 1956, substantially before the first detection of the strain in 1999. The timescale and the geographic spread of 2k/1b suggest that it originated in the former Soviet Union at about the time that the world's first centralized national blood transfusion and storage service was being established. We also reconstructed the epidemic history of 2k/1b using coalescent theory-based methods, matching patterns previously reported for other epidemic HCV subtypes. This study demonstrates the practicality of jointly estimating dates of recombination from flanking regions of the breakpoint and further illustrates that rare genetic-exchange events can be particularly informative about the underlying epidemiological processes. Hepatitis C virus (HCV) infection presents a major global health burden, with the WHO estimating that 170 million chronic carriers are at risk of developing severe clinical outcomes such as cirrhosis and hepatic cellular carcinoma (56, 71). The virus belongs to the single-stranded positive-sense RNA virus family Flaviviridae and is characterized by considerable genetic diversity. HCV diversity is classified into six main genotypes (genotypes 1 to 6), each of which is further divided into numerous subtypes, and the virus exhibits nucleotide sequence divergences of 30 and 20% at the genotype and subtype levels, respectively (58). The high genomic heterogeneity of HCV is a result of both its high rate of evolution and its long-term association with human populations (60). Although there is no indication for a zoonotic virus reservoir, a related virus has recently been discovered in dogs (22).The greatest diversity of HCV is found in West and Central Africa and in Southeast Asia, where the virus appears to have persisted endemically for at least several centuries (49, 60). The current distribution of HCV genotypes and subtypes is geographically structured, reflecting differences in the rates and routes of transmission of the various subtypes and genotypes. Epidemic strains, exemplified by subtypes 1a, 1b, and 3a, are characterized by high prevalence, low genetic diversity, and a global distribution and are typically associated with transmission via infected blood products and injecting drug use (IDU) during the 20th century (13, 4...

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Section: Figmentioning

confidence: 99%

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

Raghwani

Thomas

Koekkoek

et al. 2012

J Virol

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“…Each of these NNIs targets four different binding pockets of the HCV polymerase, thumb-1 NNI-1 (10), thumb-2 NNI-2 (29,48), palm-1 NNI-3 (9), and palm-2 NNI-4 (19), respectively. Historically, the screen for novel NS5B inhibitors was limited to representatives of genotype 1b only (3,28) because the tools to target other genotypes were not yet available (16,38,40). Further assessment of these analogs, using enzyme isolates and intergenotypic chimeric replicons derived from clinical iso-lates, revealed that the genotypic coverage of the NNI-1 and -4 analogs extends beyond genotype 1, unlike the NNI-2 and -3 derivatives that typically inhibit genotype 1 only (16,38).…”

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confidence: 99%

“…Further assessment of these analogs, using enzyme isolates and intergenotypic chimeric replicons derived from clinical iso-lates, revealed that the genotypic coverage of the NNI-1 and -4 analogs extends beyond genotype 1, unlike the NNI-2 and -3 derivatives that typically inhibit genotype 1 only (16,38). An additional drawback stems from the lower genetic barrier of the NNI-2 and -3 analogs in genotype 1 (25) and the reduced susceptibility in subtype 1a of the NNI-3 series (7,16,34,38,43). This effect was mostly attributed to the Y415F polymorphism observed in the NNI-3 binding site in subtype 1a (38).…”

mentioning

confidence: 99%

“…Historically, the screen for novel NS5B inhibitors was limited to representatives of genotype 1b only (3,28) because the tools to target other genotypes were not yet available (16,38,40). Further assessment of these analogs, using enzyme isolates and intergenotypic chimeric replicons derived from clinical iso-lates, revealed that the genotypic coverage of the NNI-1 and -4 analogs extends beyond genotype 1, unlike the NNI-2 and -3 derivatives that typically inhibit genotype 1 only (16,38). An additional drawback stems from the lower genetic barrier of the NNI-2 and -3 analogs in genotype 1 (25) and the reduced susceptibility in subtype 1a of the NNI-3 series (7,16,34,38,43).…”

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confidence: 99%

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1a/1b Subtype Profiling of Nonnucleoside Polymerase Inhibitors of Hepatitis C Virus

Nyanguile¹,

Devogelaere²,

Vijgen³

et al. 2010

J Virol

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The RNA-dependent RNA polymerase (NS5B) of hepatitis C virus (HCV) is an unusually attractive target for drug discovery since it contains five distinct drugable sites. The success of novel antiviral therapies will require nonnucleoside inhibitors to be active in at least patients infected with HCV of subtypes 1a and 1b. Therefore, the genotypic assessment of these agents against clinical isolates derived from genotype 1-infected patients is an important prerequisite for the selection of suitable candidates for clinical development. Here we report the 1a/1b subtype profiling of polymerase inhibitors that bind at each of the four known nonnucleoside binding sites. We show that inhibition of all of the clinical isolates tested is maintained, except for inhibitors that bind at the palm-1 binding site. Subtype coverage varies across chemotypes within this class of inhibitors, and inhibition of genotype 1a improves when hydrophobic contact with the polymerase is increased. We investigated if the polymorphism of the palm-1 binding site is the sole cause of the reduced susceptibility of subtype 1a to inhibition by 1,5-benzodiazepines by using reverse genetics, X-ray crystallography, and surface plasmon resonance studies. We showed Y415F to be a key determinant in conferring resistance on subtype 1a, with this effect being mediated through an inhibitor-and enzyme-bound water molecule. Binding studies revealed that the mechanism of subtype 1a resistance is faster dissociation of the inhibitor from the enzyme.

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“…A recent study demonstrated the utility of chimeric replicons for broadspectrum activity determination of HCV inhibitors. Herlihy et al created a panel of intergenotypic chimeric replicons harboring NS5B sequences from different genotypes (2b, 3a, 4a, 5a, 6a) (Herlihy et al, 2008). Stable cell lines were generated with replicationcompetent chimeras in order to evaluate the antiviral activity of HCV nonnucleoside polymerase inhibitors (NNIs) that target different regions of the protein.…”

Section: Hcv Targeting By New Chemical Entitiesmentioning

confidence: 99%

Cellular models for the screening and development of anti-hepatitis C virus agents

Gondeau

Pichard-Garcia

Maurel

2009

Pharmacology & Therapeutics

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Investigations on the biology of hepatitis C virus (HCV) have been hampered by the lack of small animal models. Efforts have therefore been directed to designing practical and robust cellular models of human origin able to support HCV replication and production in a reproducible, reliable and consistent manner. Many different models based on different forms of virions and hepatoma or other cell types have been described including virus-like particles, pseudotyped particles, subgenomic and full length replicons, virion productive replicons, immortalised hepatocytes, fetal and adult primary human hepatocytes. This review focuses on these different cellular models, their advantages and disadvantages at the biological and experimental levels, and their respective use for evaluating the effect of antiviral molecules on different steps of HCV biology including virus entry, replication, particles generation and excretion, as well as on the modulation by the virus of the host cell response to infection.

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Development of Intergenotypic Chimeric Replicons To Determine the Broad-Spectrum Antiviral Activities of Hepatitis C Virus Polymerase Inhibitors

Cited by 48 publications

References 50 publications

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b

1a/1b Subtype Profiling of Nonnucleoside Polymerase Inhibitors of Hepatitis C Virus

Cellular models for the screening and development of anti-hepatitis C virus agents

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