Updateon different aspects of HCV variability: focus on NS5B polymerase

Marascio, Nadia; Torti, Carlo; Liberto, Maria Carla; Focà, Alfredo

doi:10.1186/1471-2334-14-s5-s1

Cited by 30 publications

(23 citation statements)

References 42 publications

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“…HCV exists as a quasispecies [ 32 , 33 ]. Its high replication rate, >1000 virions per day, and the absence of a proofreading activity in the NS5B polymerase are the main factors that contribute to the emergence of mutations in the viral genome.…”

Section: Discussionmentioning

confidence: 99%

HCV Genotyping from NGS Short Reads and Its Application in Genotype Detection from HCV Mixed Infected Plasma

et al. 2015

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Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

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Section: Discussionmentioning

confidence: 99%

HCV Genotyping from NGS Short Reads and Its Application in Genotype Detection from HCV Mixed Infected Plasma

et al. 2015

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“…These results compel us to conclude that ORF1 may be the region responsible for deciding the species barrier. ORF1 encodes non-structural proteins of the virus and viral nonstructural proteins are known to interact with host cell proteins and modulate host cell environment (Ayllon et al, 2015;Marascio et al, 2014). When PK-15 and HepG2/C3A cells were infected with virions generated from the above three constructs, only the HEV-4FG construct showed positive results (only nsRNA positive), while other constructs remained completely negative.…”

Section: Discussionmentioning

confidence: 99%

Hepatitis E virus (HEV)-1 harbouring HEV-4 non-structural protein (ORF1) replicates in transfected porcine kidney cells

Chatterjee

Devhare

Pingle

et al. 2016

Journal of General Virology

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Hepatitis E virus (HEV) is a causative agent of acute hepatitis and a major public health problem in India. There are four mammalian HEV genotypes worldwide. In India, genotype 1 (HEV-1) is restricted to humans whereas genotype 4 (HEV-4) circulates in pigs. Studies from our laboratory have shown that HEV-4 (swine) virus can establish experimental infection in rhesus monkeys; however, HEV-1 (human) virus cannot infect pigs. Viral and/or cellular factors responsible for this host specificity are not yet known. We developed 12 different genotype 1-4 chimeric full genome clones with pSK-HEV2 as the backbone and by replacing structural (ORF2 and ORF3), nonstructural (ORF1) and non-coding regions (NCR) with corresponding segments from the HEV-4 clone. S10-3 (human hepatoma) and PK-15 (pig kidney) cells were transfected with transcripts generated from the above clones to test their replication competence. Transfected cells were monitored for successful virus replication by detecting replicative intermediate RNA and capsid protein (immunofluorescence assay). All the chimeric constructs were able to replicate in S10-3 cells. However, only two chimeric clones, HEV-1 (HEV-4 5¢NCR-ORF1) and HEV-1 (HEV-4 ORF1), containing 5¢NCR-ORF1 and ORF1 regions from the HEV-4 clone, respectively, were able to replicate in PK-15 cells. We demonstrate for the first time the crucial role of ORF1 polyprotein in crossing the species barrier at the cellular level. These results indicate the importance of interactions between ORF1 protein domains and host cell specific factors during HEV replication and the critical role of cellular factors as post-entry barrier/s in virus establishment.

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“…Nucleoside inhibitors (NIs) bind to the catalytic site of the RNA polymerase causing chain termination. Nonnucleoside inhibitors bind to a less conserved site resulting in a conformational change that distorts the positioning of residues binding RNA resulting in inhibition of polymerization [59,60].…”

Section: Ns5b Nucleoside Polymerase Inhibitors (Npis)mentioning

confidence: 99%

Advances in Treatment of Hepatitis C

Kamal¹

2017

Advances in Treatment of Hepatitis C and B

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Hepatitis C infection (HCV) is a major cause of chronic hepatitis and cirrhosis worldwide. Interferon-based regimen has been the sole therapy to eradicate HCV infection for decades. However, this interferon and ribavirin combination is associated with several serious adverse events and the sustained virologic response rate was suboptimal. The recent discovery of oral direct-acting antiviral agents (DAAs) heralded a revolution in the treatment of chronic HCV. This breakthrough in HCV resulted in high rates of HCV eradication with sustained virologic response rates ranging between 90 and 100% across different genotypes. New therapies were administered orally for 12 or 24 months and this resulted in better compliance and few adverse events. DAAs are categorized into four major groups namely: NS5B nucleotide inhibitors, NS5B nonnucleoside inhibitors, NS5A replication complex inhibitors, and NS3/4A protease inhibitors (PI). Several interferonfree regimens have been approved and adequately assessed and several new regimens with high potencies, less cross-resistance, and better safety profile are in the process of approval. Thus, the era of HCV eradication and cure has begun.

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Updateon different aspects of HCV variability: focus on NS5B polymerase

Cited by 30 publications

References 42 publications

HCV Genotyping from NGS Short Reads and Its Application in Genotype Detection from HCV Mixed Infected Plasma

HCV Genotyping from NGS Short Reads and Its Application in Genotype Detection from HCV Mixed Infected Plasma

Hepatitis E virus (HEV)-1 harbouring HEV-4 non-structural protein (ORF1) replicates in transfected porcine kidney cells

Advances in Treatment of Hepatitis C

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