6533b830fe1ef96bd1296609
RESEARCH PRODUCT
HCV NS3 sequencing as a reliable and clinically useful tool for the assessment of genotype and resistance mutations for clinical samples with different HCV-RNA levels
V C Di MaioV CentoD Di PaoloM AragriF De LeonardisM TontodonatiV MicheliM C BellocchiF P AntonucciA BertoliI LenciM MilanaL GianserraM MelisA Di BiagioC SarrecchiaL SarmatiS LandonioS FranciosoL LambiaseL A NicoliniS MarencoL NosottiV GiannelliM SicilianoD RomagnoliA PellicelliJ VecchietC F MagniS BabudieriM S MuraG TalianiC MastroianniU Vespasiani-gentilucciM RomanoF MoriscoA GasbarriniV VulloS BrunoC BaigueraC PasquazziG TisoneA PicciottoM AndreoniG ParrutiG RizzardiniM AngelicoC F PernoF Ceccherini-silbersteinHcv Italian Resistance Network Study Group. Collaborators (129) Mariani RM PaoloniN IapadreA GrimaldiB MenzaghiT QuirinoJ VecchietB BruzzoneA De MariaA Di BiagioS MarencoLa NicoliniA PicciottoC ViscoliK CasinelliMd MonacheM LichtnerC MastroianniA AghemoS BrunoM CerroneM ColomboAd MonforteE DanieliF DonatoG GubertiniS LandonioCf MagniA ManconV MicheliS MonicoF NieroM PuotiG RizzardiniMl RussoR AlfieriM GnocchiA OrroL MilanesiE BaldelliM BertolottiV BorghiC MussiniD RomagnoliG BrancaccioN CaporasoGb GaetaV LemboF MoriscoV CalvarusoA CraxìV Di MarcoA MazzolaS PettaE D'amicoP CacciatoreA ConsorteVp PalittiG ParrutiA PieriE PolilliM TontodonatiM AndreoniM AngelicoF AntenucciFp AntonucciM AragriD ArmeniaL BaiocchiM BellocchiA BertoliE BiliottiM BiolatoL CariotiF Ceccherini-silbersteinV CentoG CerasariC CervaM CiottiC D'ambrosioG D'ettorreF De LeonardisA De Sanctis Di Maio VcD Di PaoloS FranciosoC FurlanP GalloA GasbarriniV GiannelliL GianserraA GriecoS GriecoL LambiaseB LattanziI LenciV MalagninoM ManuelliM MerliL MiglioresiM MilanaL NosottiD PalazzoC PasquazziA PellicelliCf PernoM RomanoF SantopaoloMm SantoroL SarmatiC SarrecchiaD SforzaM SicilianoMc SorboM SpazianteV SvicherG TalianiE TetiG TisoneU Vespasiani-gentilucciV VulloA MangiaS BabudieriI MaidaM MelisMs MuraL FalconiD Di GiammartinoP. Tarquinisubject
0301 basic medicinens3Genotyping TechniquesvirusesDrug ResistanceHepacivirusViral Nonstructural Proteinsmedicine.disease_causeGastroenterologyTelaprevirchemistry.chemical_compoundgenotype; genotyping techniques; hepacivirus; hepatitis C; humans; RNA viral; retrospective studies; sequence analysis; DNA; viral nonstructural proteins; drug resistance viral; mutation; pharmacology; infectious diseases0302 clinical medicineRetrospective StudieGenotypePharmacology (medical)ViralGenotype; Genotyping Techniques; Hepacivirus; Hepatitis C; Humans; RNA Viral; Retrospective Studies; Sequence Analysis DNA; Viral Nonstructural Proteins; Drug Resistance Viral; MutationProteolytic enzymesvirus diseasesSettore MED/07 - Microbiologia e Microbiologia ClinicaHepatitis Chcv-rna levelsInfectious DiseasesHCV-RNARNA Viral030211 gastroenterology & hepatologySequence Analysismedicine.drugHumanMicrobiology (medical)medicine.medical_specialtyGenotypeHepatitis C virusConcordanceSettore MED/12 - GASTROENTEROLOGIAGenotype; Genotyping Techniques; Hepacivirus; Hepatitis C; Humans; RNA Viral; Retrospective Studies; Sequence Analysis DNA; Viral Nonstructural Proteins; Drug Resistance Viral; Mutation; Pharmacology; Pharmacology (medical); Infectious DiseasesBiology03 medical and health sciencesBoceprevirInternal medicineDrug Resistance ViralmedicinehcvHumansGenotypingGenotyping TechniquesRetrospective StudiesPharmacologyHepaciviruViral Nonstructural ProteinSettore MED/09 - MEDICINA INTERNASequence Analysis DNADNAVirologydigestive system diseases030104 developmental biologychemistrySequence AnalysiMutationRNAGenotyping TechniqueRNA viraldescription
OBJECTIVES: This study aims to evaluate the reliability and clinical utility of NS3 sequencing in hepatitis C virus (HCV) 1-infected patients who were candidates to start a PI-containing regimen. METHODS: NS3 protease sequencing was performed by in-house-developed HCV-1 subtype-specific protocols. Phylogenetic analysis was used to test sequencing reliability and concordance with previous genotype/subtype assignment by commercial genotyping assays. RESULTS: Five hundred and sixty-seven HCV plasma samples with quantifiable HCV-RNA from 326 HCV-infected patients were collected between 2011 and 2014. Overall, the success rate of NS3 sequencing was 88.9%. The success rate between the two subtype protocols (HCV-1a/HCV-1b) was similarly high for samples with HCV-RNA >3 log IU/mL (>92% success rate), while it was slightly lower for HCV-1a samples with HCV-RNA ≤3 log IU/mL compared with HCV-1b samples. Phylogenetic analysis confirmed the genotype/subtype given by commercial genotyping assays in 92.9% (303/326) of cases analysed. In the remaining 23 cases (7.1%), 1 was HCV-1g (previously defined as subtype 1a), 1 was HCV-4d (previously defined as genotype 1b) and 1 was HCV-1b (previously defined as genotype 2a/2c). In the other cases, NS3 sequencing precisely resolved the either previous undetermined/discordant subtype 1 or double genotype/subtype assignment by commercial genotyping assays. Resistance-associated variants (RAVs) to PI were detected in 31.0% of samples. This prevalence changed according to PI experience (17.1% in PI-naive patients versus 79.2% in boceprevir/telaprevir/simeprevir-failing patients). Among 96 patients with available virological outcome following boceprevir/telaprevir treatment, a trend of association between baseline NS3 RAVs and virological failure was observed (particularly for HCV-1a-infected patients: 3/21 failing patients versus 0/22 achieving sustained virological response; P = 0.11). CONCLUSIONS: HCV-NS3 sequencing provides reliable results and at the same time gives two clinically relevant pieces of information: a correct subtype/genotype assignment and the detection of variants that may interfere with the efficacy of PI.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2016-01-01 |