Cells (Jul 2019)

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

  • Maria Concetta Bellocchi,
  • Marianna Aragri,
  • Luca Carioti,
  • Lavinia Fabeni,
  • Rosaria Maria Pipitone,
  • Giuseppina Brancaccio,
  • Maria Chiara Sorbo,
  • Silvia Barbaliscia,
  • Velia Chiara Di Maio,
  • Fabrizio Bronte,
  • Stefania Grimaudo,
  • Walter Mazzucco,
  • Ferdinando Frigeri,
  • Marco Cantone,
  • Antonio Pinto,
  • Carlo Federico Perno,
  • Antonio Craxì,
  • Giovanni Battista Gaeta,
  • Vito Di Marco,
  • Francesca Ceccherini-Silberstein

DOI
https://doi.org/10.3390/cells8070666
Journal volume & issue
Vol. 8, no. 7
p. 666

Abstract

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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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