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

• Published in: Cells (Basel, Switzerland) Vol. 8; no. 7; p. 666
• Main Authors: Bellocchi, Maria Concetta, Aragri, Marianna, Carioti, Luca, Fabeni, Lavinia, Pipitone, Rosaria Maria, Brancaccio, Giuseppina, Sorbo, Maria Chiara, Barbaliscia, Silvia, Di Maio, Velia Chiara, Bronte, Fabrizio, Grimaudo, Stefania, Mazzucco, Walter, Frigeri, Ferdinando, Cantone, Marco, Pinto, Antonio, Perno, Carlo Federico, Craxì, Antonio, Gaeta, Giovanni Battista, Di Marco, Vito, Ceccherini-Silberstein, Francesca
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 02.07.2019; MDPI
• Subjects: Acute Disease; acute infection; Adult; Amino Acid Substitution; Antiviral Agents - pharmacology; Antiviral Agents - therapeutic use; Asymptomatic; Bayesian analysis; beta-Thalassemia - genetics; beta-Thalassemia - immunology; beta-Thalassemia - therapy; Blood diseases; Blood Transfusion; Chronic Disease; Chronic infection; Cross Infection - drug therapy; Cross Infection - transmission; Cross Infection - virology; Disease transmission; Drug resistance; Drug Resistance, Viral - genetics; Epidemics; Epidemiology; Female; Gene polymorphism; Genes; Genetic diversity; Genotype; Genotype & phenotype; Haplotypes; HCV; Hematological diseases; Hepacivirus - genetics; Hepacivirus - pathogenicity; Hepatitis C; Hepatitis C - drug therapy; Hepatitis C - transmission; Hepatitis C - virology; High-Throughput Nucleotide Sequencing; HIV; Hospitals; Host-Pathogen Interactions - genetics; Host-Pathogen Interactions - immunology; Human immunodeficiency virus; Humans; Infections; Interferons - genetics; Interferons - immunology; Male; Middle Aged; Next-generation sequencing; NGS; nosocomial transmission; Patients; Phylogenetics; Phylogeny; Polymorphism, Single Nucleotide; sequencing; Thalassemia; Viral Nonstructural Proteins - genetics; Viruses; Central Africa; United States > US; Italy; HCV; nosocomial transmission; NGS; acute infection; chronic infection; sequencing
• ISSN: 2073-4409; 2073-4409
• DOI: 10.3390/cells8070666

: 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. : 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. : 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). : 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.