Heterogeneous genomic locations within NS3, NS4A and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach

Sajid, Muhammad Imran; Javed, Aneela; Ali, Amjad; Mansoor, Atika

doi:10.1016/j.meegid.2016.06.031

Cited by 3 publications

(2 citation statements)

References 51 publications

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“…Thus our proposed protocol could be used to determine both genotype/subtype and NS5A polymorphism for any new HCV infected patient. Indeed, the NS4B-NS5A region has recently been described as a candidate to perform genotyping and subtyping for HCV [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

An NS5A single optimized method to determine genotype, subtype and resistance profiles of Hepatitis C strains

André-Garnier

Besse²,

Rodallec³

et al. 2017

PLoS ONE

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The objective was to develop a method of HCV genome sequencing that allowed simultaneous genotyping and NS5A inhibitor resistance profiling. In order to validate the use of a unique RT-PCR for genotypes 1–5, 142 plasma samples from patients infected with HCV were analysed. The NS4B-NS5A partial region was successfully amplified and sequenced in all samples. In parallel, partial NS3 sequences were analyzed obtained for genotyping. Phylogenetic analysis showed concordance of genotypes and subtypes with a bootstrap >95% for each type cluster. NS5A resistance mutations were analyzed using the Geno2pheno [hcv] v0.92 tool and compared to the list of known Resistant Associated Substitutions recently published. In conclusion, this tool allows determination of HCV genotypes, subtypes and identification of NS5A resistance mutations. This single method can be used to detect pre-existing resistance mutations in NS5A before treatment and to check the emergence of resistant viruses while undergoing treatment in major HCV genotypes (G1-5) in the EU and the US

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Section: Discussionmentioning

confidence: 99%

An NS5A single optimized method to determine genotype, subtype and resistance profiles of Hepatitis C strains

André-Garnier

Besse²,

Rodallec³

et al. 2017

PLoS ONE

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“…Since the whole genome analysis is expensive and highly complex, the sequencing of specific HCV genomic regions, like Core and/or NS5B, represented, and still represents a more convenient method to study HCV genetic diversity [34]. Furthermore, various studies have showed that performing the sequencing of NS3 and NS5A non-structural genes involved in DAA drug resistance also produces highly reliable genotype information and can therefore provide both resistance and evolutionary information for molecular epidemiology [9,10,34,35].…”

Section: Introductionmentioning

confidence: 99%

NS5A Gene Analysis by Next Generation Sequencing in HCV Nosocomial Transmission Clusters of HCV Genotype 1b Infected Patients

Bellocchi

Aragri

Carioti

et al. 2019

Cells

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Background: The aim of the study was to investigate the intra-host variability through next-generation-sequencing (NGS) of the NS5A-gene in nosocomial transmission-clusters observed in two Italian hospitals among hepatitis C virus (HCV)-genotype-1b infected patients. Methods: HCV-sequencing was performed by Sanger-sequencing (NS3 + NS5A + NS5B) and by NGS (NS5A, MiSeq-Illumina) in 15 HCV-1b infected patients [five acute with onco-hematologic-disease and 10 (4/6 acute/chronic) with β-thalassemia]. Resistance-associated-substitutions (RAS) were analysed by Geno2pheno-algorithm. Nucleotide-sequence-variability (NSV, at 1%, 2%, 5%, 10% and 15% NGS-cutoffs) and Shannon entropy were estimated. Phylogenetic analysis was performed by Mega6-software and Bayesian-analysis. Results: Phylogenetic analysis showed five transmission-clusters: one involving four HCV-acute onco-hematologic-patients; one involving three HCV-chronic β-thalassemia-patients and three involving both HCV-acute and chronic β-thalassemia-patients. The NS5A-RAS Y93H was found in seven patients, distributed differently among chronic/acute patients involved in the same transmission-clusters, independently from the host-genetic IL-28-polymorphism. The intra-host NSV was higher in chronic-patients versus acute-patients, at all cutoffs analyzed (p < 0.05). Even though Shannon-entropy was higher in chronic-patients, significantly higher values were observed only in chronic β-thalassemia-patients versus acute β-thalassemia-patients (p = 0.01). Conclusions: In nosocomial HCV transmission-clusters, the intra-host HCV quasispecies divergence in patients with acute-infection was very low in comparison to that in chronic-infection. The NS5A-RAS Y93H was often transmitted and distributed differently within the same transmission-clusters, independently from the IL-28-polymorphism.

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A pan-genotypic Hepatitis C Virus NS5A amplification method for reliable genotyping and resistance testing

Walker

Ennker

Kaiser

et al. 2019

Journal of Clinical Virology

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Heterogeneous genomic locations within NS3, NS4A and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach

Cited by 3 publications

References 51 publications

An NS5A single optimized method to determine genotype, subtype and resistance profiles of Hepatitis C strains

An NS5A single optimized method to determine genotype, subtype and resistance profiles of Hepatitis C strains

NS5A Gene Analysis by Next Generation Sequencing in HCV Nosocomial Transmission Clusters of HCV Genotype 1b Infected Patients

A pan-genotypic Hepatitis C Virus NS5A amplification method for reliable genotyping and resistance testing

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