Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus

Background Reducing the burden of the hepatitis C virus (HCV) requires large-scale deployment of intervention programmes, which can be informed by the dynamic pattern of HCV spread. In Spain, ongoing transmission of HCV is mostly fuelled by people who inject drugs (PWID) infected with subtype 1a (HCV1a). Aim Our aim was to map how infections spread within and between populations, which could help formulate more effective intervention programmes to halt the HCV1a epidemic in Spain. Methods Epidemiological links between HCV1a viruses from a convenience sample of 283 patients in Spain, mostly PWID, collected between 2014 and 2016, and 1,317, 1,291 and 1,009 samples collected abroad between 1989 and 2016 were reconstructed using sequences covering the NS3, NS5A and NS5B genes. To efficiently do so, fast maximum likelihood-based tree estimation was coupled to a flexible Bayesian discrete phylogeographic inference method. Results The transmission network structure of the Spanish HCV1a epidemic was shaped by continuous seeding of HCV1a into Spain, almost exclusively from North America and European countries. The latter became increasingly relevant and have dominated in recent times. Export from Spain to other countries in Europe was also strongly supported, although Spain was a net sink for European HCV1a lineages. Spatial reconstructions showed that the epidemic in Spain is diffuse, without large, dominant within-country networks. Conclusion To boost the effectiveness of local intervention efforts, concerted supra-national strategies to control HCV1a transmission are needed, with a strong focus on the most important drivers of ongoing transmission, i.e. PWID and other high-risk populations.

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Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus

10.1101/2020.06.16.155150 ◽

2020 ◽

Cited By ~ 1

Author(s):

P. Simmonds ◽

L. Cuypers ◽

W.L. Irving ◽

J. McLauchlan ◽

G.S. Cooke ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Rna Structure ◽

Large Scale ◽

Rna Virus ◽

Energy Difference ◽

Folding Energy ◽

Stem Loop ◽

Coding Regions ◽

Progressive Liver Disease

ABSTRACTMechanisms underlying the ability of hepatitis C virus (HCV) to establish persistent infections and induce progressive liver disease remain poorly understood. HCV is one of several positive-stranded RNA viruses capable of establishing persistence in their immunocompetent vertebrate hosts, an attribute associated with formation of large scale RNA structure in their genomic RNA. We developed novel methods to analyse and visualise genome-scale ordered RNA structure (GORS) predicted from the increasingly large datasets of complete genome sequences of HCV. Structurally conserved RNA secondary structure in coding regions of HCV localised exclusively to polyprotein ends (core, NS5B). Coding regions elsewhere were also intensely structured based on elevated minimum folding energy difference (MFED) values, but the actual stem-loop elements involved in genome folding were structurally entirely distinct, even between subtypes 1a and 1b. Dynamic remodelling was further evident from comparison of HCV strains in different host genetic background. Significantly higher MFED values, greater suppression of UpA dinucleotide frequencies and restricted diversification were found in subjects with the TT genotype of the rs12979860 SNP in the IFNL4 gene compared to the CC (non-expressing) allele. These structural and compositional associations with expression of interferon-λ4 were recapitulated on a larger scale by higher MFED values and greater UpA suppression of genotype 1 compared to genotype 3a, associated with previously reported HCV genotype-associated differences in hepatic interferon-stimulated gene induction. Associations between innate cellular responses with HCV structure and further evolutionary constraints represents an important new element in RNA virus evolution and the adaptive interplay between virus and host.

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Enhanced virus translation enables miR-122-independent Hepatitis C Virus propagation

10.1101/2021.06.08.447644 ◽

2021 ◽

Author(s):

Mamata Panigrahi ◽

Michael Palmer ◽

Joyce A Wilson

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Virus Replication ◽

Rna Structure ◽

Genome Stability ◽

Internal Ribosomal Entry Site ◽

Terminal Region ◽

Translation Regulation ◽

Virus Propagation ◽

Entry Site

The 5’UTR of the Hepatitis C Virus genome forms RNA structures that regulate virus replication and translation. The region contains a viral internal ribosomal entry site and a 5’ terminal region. Binding of the liver specific miRNA, miR-122, to two conserved binding sites in the 5’ terminal region regulates viral replication, translation, and genome stability, and is essential for efficient virus replication, but its precise mechanism of its action is still under debate. A current hypothesis is that miR-122 binding stimulates viral translation by facilitating the viral 5’ UTR to form the translationally active HCV IRES RNA structure. While miR-122 is essential for detectable virus replication in cell culture, several viral variants with 5’ UTR mutations exhibit low level replication in the absence of miR-122. We show that HCV mutants capable of replicating independently of miR-122 also replicate independently of other microRNAs generated by the canonical miRNA synthesis pathway. Further, we also show that the mutant genomes display an enhanced translation phenotype that correlates with their ability to replicate independently of miR-122. Finally, we provide evidence that translation regulation is the major role for miR-122, and show that miR-122-independent HCV replication can be rescued to miR-122-dependent levels by the combined impacts of 5’ UTR mutations that stimulate translation, and by stabilizing the viral genome by knockdown of host exonucleases and phosphatases that degrade the genome. Thus, we provide a model suggesting that translation stimulation and genome stabilization are the primary roles for miR-122 in the virus life cycle.

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Chronic Infection with Hepatitis C Virus Subtype 1 g in a Japanese Patient Successfully Treated with Glecaprevir/Pibrentasvir

Internal Medicine ◽

10.2169/internalmedicine.8673-21 ◽

2022 ◽

Author(s):

Takeshi Hatanaka ◽

Satoru Kakizaki ◽

Takuya Kaburagi ◽

Naoto Saito ◽

Sachi Nakano ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Chronic Infection ◽

Japanese Patient ◽

Virus Subtype

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Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling

eLife ◽

10.7554/elife.21198 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 25

Author(s):

Zane A Jaafar ◽

Akihiro Oguro ◽

Yoshikazu Nakamura ◽

Jeffrey S Kieft

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Translation Initiation ◽

Rna Structure ◽

Initiation Factor ◽

Internal Ribosome Entry ◽

Eukaryotic Translation ◽

Eukaryotic Translation Initiation ◽

Hcv Ires ◽

Type 3

Internal ribosome entry sites (IRESs) are important RNA-based translation initiation signals, critical for infection by many pathogenic viruses. The hepatitis C virus (HCV) IRES is the prototype for the type 3 IRESs and is also invaluable for exploring principles of eukaryotic translation initiation, in general. Current mechanistic models for the type 3 IRESs are useful but they also present paradoxes, including how they can function both with and without eukaryotic initiation factor (eIF) 2. We discovered that eIF1A is necessary for efficient activity where it stabilizes tRNA binding and inspects the codon-anticodon interaction, especially important in the IRES’ eIF2-independent mode. These data support a model in which the IRES binds preassembled translation preinitiation complexes and remodels them to generate eukaryotic initiation complexes with bacterial-like features. This model explains previous data, reconciles eIF2-dependent and -independent pathways, and illustrates how RNA structure-based control can respond to changing cellular conditions.

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Sa1542 BIOINFORMATIC ANALYSIS OF CODON USAGE OF HEPATITIS C VIRUS SUBTYPE 6XA

Gastroenterology ◽

10.1016/s0016-5085(20)33987-1 ◽

2020 ◽

Vol 158 (6) ◽

pp. S-1327

Author(s):

Wei Hou

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Codon Usage ◽

Bioinformatic Analysis ◽

Virus Subtype

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The First Complete Genome Sequences of Hepatitis C Virus Subtype 2b from Latin America: Molecular Characterization and Phylogeographic Analysis

Proceedings ◽

10.3390/proceedings2020050121 ◽

2020 ◽

Vol 50 (1) ◽

pp. 121

Author(s):

Natália Spitz ◽

José J. Barros ◽

Kycia M. do Ó ◽

Carlos E. Brandão-Mello ◽

Natalia M. Araujo

Keyword(s):

Latin America ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Latin American ◽

Complete Genome ◽

Direct Sequencing ◽

Epidemiological Data ◽

National Prevalence ◽

Latin American Countries ◽

Virus Subtype

The hepatitis C virus (HCV) has remarkable genetic diversity and exists as eight genotypes (1 to 8) with distinct geographic distributions. No complete genome sequence of HCV subtype 2b (HCV-2b) is available from Latin American countries, and the factors underlying its emergence and spread within the continent remain unknown. The present study was conducted to determine the first full-length genomic sequences of HCV-2b isolates from Latin America and reconstruct the spatial and temporal diversification of this subtype in Brazil. Nearly complete HCV-2b genomes isolated from two Brazilian patients were obtained by direct sequencing of long PCR fragments and analyzed together with reference sequences using the Bayesian coalescent and phylogeographic framework approaches. The two HCV-2b genomes were 9318 nucleotides (nt) in length (nt 37–9354). Interestingly, the long RT-PCR technique was able to detect the co-circulation of viral variants that contained an in-frame deletion of 2022 nt, encompassing E1, E2, and p7 proteins. Spatiotemporal reconstruction analyses suggest that HCV-2b had a single introduction in Brazil during the early 1980s, displaying an epidemic history characterized by a low and virtually constant population size to date. These results coincide with epidemiological data in Brazil and may explain the low national prevalence of this subtype.

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Positively selected amino acid sites in the entire coding region of hepatitis C virus subtype 1b

Gene ◽

10.1016/s0378-1119(01)00640-0 ◽

2001 ◽

Vol 276 (1-2) ◽

pp. 83-87 ◽

Cited By ~ 15

Author(s):

Yoshiyuki Suzuki ◽

Takashi Gojobori

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Amino Acid ◽

Acid Sites ◽

Coding Region ◽

Subtype 1B ◽

Virus Subtype

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Enzymatic properties of hepatitis C virus NS3-associated helicase

Microbiology ◽

10.1099/0022-1317-81-5-1335 ◽

2000 ◽

Vol 81 (5) ◽

pp. 1335-1345 ◽

Cited By ~ 27

Author(s):

Chantal Paolini ◽

Raffaele De Francesco ◽

Paola Gallinari

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Rna Structure ◽

Structural Protein ◽

Single Cycle ◽

Detailed Characterization ◽

Stem Loop ◽

Hybrid Substrates ◽

Serine Protease Activity

The hepatitis C virus non-structural protein 3 (NS3) possesses a serine protease activity in the N-terminal one-third, whereas RNA-stimulated NTPase and helicase activities reside in the C-terminal portion. In this study, an N-terminal hexahistidine-tagged full-length NS3 polypeptide was expressed in Escherichia coli and purified to homogeneity by conventional chromatography. Detailed characterization of the helicase activity of NS3 is presented with regard to its binding and strand release activities on different RNA substrates. On RNA double-hybrid substrates, the enzyme was shown to perform unwinding activity starting from an internal ssRNA region of at least 3 nt and moving along the duplex in a 3′ to 5′ direction. In addition, data are presented suggesting that binding to ATP reduces the affinity of NS3 for ssRNA and increases its affinity for duplex RNA. Furthermore, we have ascertained the capacity of NS3 to specifically interact with and resolve the stem–loop RNA structure (SL I) within the 3′-terminal 46 bases of the viral genome. Finally, our analysis of NS3 processive unwinding under single cycle conditions by addition of heparin in both helicase and RNA-stimulated ATPase assays led to two conclusions: (i) NS3-associated helicase acts processively; (ii) most of the NS3 RNA-stimulated ATPase activity may not be directly coupled to translocation of the enzyme along the substrate RNA molecule.

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