Forskning
Udskriv Udskriv
Switch language
Region Hovedstaden - en del af Københavns Universitetshospital
Udgivet

A near full-length open reading frame next generation sequencing assay for genotyping and identification of resistance-associated variants in hepatitis C virus

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  1. Aseptic meningitis outbreak associated with echovirus 4 in Northern Europe in 2013-2014

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  2. Clinical validation of the Cobas 4800 HPV assay using cervical samples in SurePath medium under the VALGENT4 framework

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  3. Clinical performance of the HPV-Risk assay on cervical samples in SurePath medium using the VALGENT-4 panel

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  4. Taking gastro-surveillance into the 21st century

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  1. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  2. Global and local envelope protein dynamics of hepatitis C virus determine broad antibody sensitivity

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  3. An alternate conformation of HCV E2 neutralizing face as an additional vaccine target

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  4. Association between vancomycin-resistant Enterococcus faecium colonization and subsequent infection: a retrospective WGS study

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

  5. Equine pegiviruses cause persistent infection of bone marrow and are not associated with hepatitis

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Vis graf over relationer
BACKGROUND The current treatment options for hepatitis C virus (HCV), based on direct acting antivirals (DAA), are dependent on virus genotype and previous treatment experience. Treatment failures have been associated with detection of resistance-associated substitutions (RASs) in the DAA targets of HCV, the NS3, NS5A and NS5 B proteins. OBJECTIVE To develop a next generation sequencing based method that provides genotype and detection of HCV NS3, NS5A, and NS5 B RASs without prior knowledge of sample genotype. STUDY DESIGN In total, 101 residual plasma samples from patients with HCV covering 10 different viral subtypes across 4 genotypes with viral loads of 3.84-7.61 Log IU/mL were included. All samples were de-identified and consequently prior treatment status for patients was unknown. Almost full open reading frame amplicons (∼ 9 kb) were generated using RT-PCR with a single primer set. The resulting amplicons were sequenced with high throughput sequencing and analysed using an in-house developed script for detecting RASs. RESULTS The method successfully amplified and sequenced 94% (95/101) of samples with an average coverage of 14,035; four of six failed samples were genotype 4a. Samples analysed twice yielded reproducible nucleotide frequencies across all sites. RASs were detected in 21/95 (22%) samples at a 15% threshold. The method identified one patient infected with two genotype 2b variants, and the presence of subgenomic deletion variants in 8 (8.4%) of 95 successfully sequenced samples. CONCLUSIONS The presented method may provide identification of HCV genotype, RASs detection, and detect multiple HCV infection without prior knowledge of sample genotype.
OriginalsprogEngelsk
TidsskriftJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology
Vol/bind105
Sider (fra-til)49-56
Antal sider8
ISSN1386-6532
DOI
StatusUdgivet - 1 aug. 2018

ID: 54603922