Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience

Campo, J.A. Del; Parra-Sánchez, Manuel; Figueruela, Blanca; García-Rey, Silvia; Quer, Josep; Gregori, Josep; Bernal, Samuel; Grande, Lourdes; Palomares, J.C.; Romero‐Gómez, Manuel

doi:10.1016/j.ijid.2017.12.016

Cited by 26 publications

(27 citation statements)

References 21 publications

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“…The simple identification of subtype 4r, as discussed above, would provide sufficient information to reinforce treatment in patients infected with this subtype. However, HCV resistance testing can be used confidently in settings that have easy access to a reliable, quality‐controlled assay, as recently reported . Classically, three coding regions are analyzed, including NS3 protease, NS5A, and NS5B RNA polymerase, whereas in‐house databases or free‐access Internet tools are used for sequence interpretation.…”

Section: Discussionmentioning

confidence: 99%

“…However, HCV resistance testing can be used confidently in settings that have easy access to a reliable, quality-controlled assay, as recently reported. (33)(34)(35) Classically, three coding regions are analyzed, including NS3 protease, NS5A, and NS5B RNA polymerase, whereas in-house databases or free-access Internet tools are used for sequence interpretation. It is, however, important to note that NS5A RASs preexisting at treatment baseline were easily found by population or deep sequencing in our patients, but this was not the case for RASs at NS5B position S282, which appear to be the main drivers of sofosbuvir-based treatment failures in these patients and were present as minor, undetectable populations at baseline in our study (including when using deep sequencing).…”

Section: Discussionmentioning

confidence: 99%

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Frequent Antiviral Treatment Failures in Patients Infected With Hepatitis C Virus Genotype 4, Subtype 4r

et al. 2019

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Frequent Antiviral Treatment Failures in Patients Infected With Hepatitis C Virus Genotype 4, Subtype 4r

et al. 2019

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“…Sequencing is increasingly utilised in the clinical management of HBV infection to inform on prognosis, treatment choice, drug resistance and to provide insight into complex cases (39,40). Whilst progress in applying new sequencing technologies to HBV has been slow to date, we are now entering an era of rapid change.…”

Section: Resultsmentioning

confidence: 99%

Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

McNaughton

Revill

Matthews

et al. 2019

Preprint

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Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), thus far characterised. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. An alignment of these reference sequences and maximum-likelihood phylogenetic trees of the sequences are provided to simplify classification. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level.

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“…The application of NGS assays to analyse quasispecies HCV genomes has been increasing in recent years. Several laboratory-developed NGS assays had been previously described in the literature for phylogenetic studies [14], outbreak investigation [15,16], characterisation of HCV full genome [17,18] and identification of HCV GT and ST in clinical samples [19,20]. However, there are fewer reports of adoption of NGS assays in routine HCV genotyping.…”

Section: Discussionmentioning

confidence: 99%

HCV Genotyping with Concurrent Profiling of Resistance-Associated Variants by NGS Analysis

Poon¹,

Tang²,

Koay³

2019

Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations

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Determination of viral characteristics including genotype (GT), subtype (ST) and resistance-associated variants (RAVs) profile is important in assigning direct-acting antivirals regimes in HCV patients. To help achieve the best clinical management of HCV patients, a routine diagnostic laboratory should aim at reporting accurate viral GT/ST and RAVs using a reliable diagnostic platform of choice. A laboratory study was conducted to evaluate performance characteristics of a new commercial next-generation sequencing (NGS)-based HCV genotyping assay in comparison to another widely used commercial line probe assay for HCV genotyping. Information on RAVs from deeply sequenced NS3, NS5A and NS5B regions in samples classified as HCV 1a and 1b was harnessed from the fully automated software. Perfect (100%) concordance at HCV genotype level was achieved in GT2 (N = 13), GT3 (N = 55) and GT5 (N = 7). NGS refined the ST assignment in GTs 1, 4 and 6, and resolved previously indeterminate GTs reported by line probe assay. NGS was found to have consistent intra-and inter-run reproducibility in terms of genotyping, subtyping and RAVs identification. Detection of infections with multiple HCV GTs or STs is feasible by NGS. Deep sequencing allows sensitive identification of RAVs in the GT 1a and 1b NS3, NS5A and NS5B regions, but the list of target RAVs is not exhaustive.

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Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience

Cited by 26 publications

References 21 publications

Frequent Antiviral Treatment Failures in Patients Infected With Hepatitis C Virus Genotype 4, Subtype 4r

Frequent Antiviral Treatment Failures in Patients Infected With Hepatitis C Virus Genotype 4, Subtype 4r

Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

HCV Genotyping with Concurrent Profiling of Resistance-Associated Variants by NGS Analysis

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