{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:41:26Z","timestamp":1760240486280,"version":"build-2065373602"},"reference-count":63,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2019,7,2]],"date-time":"2019-07-02T00:00:00Z","timestamp":1562025600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003407","name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["Bandiera InterOmics Protocollo PB05 1\u00b0"],"award-info":[{"award-number":["Bandiera InterOmics Protocollo PB05 1\u00b0"]}],"id":[{"id":"10.13039\/501100003407","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Italian Ministry of Health","award":["RF-2016-02362422"],"award-info":[{"award-number":["RF-2016-02362422"]}]},{"DOI":"10.13039\/100016726","name":"Aviralia Foundation","doi-asserted-by":"publisher","award":["free contribution"],"award-info":[{"award-number":["free contribution"]}],"id":[{"id":"10.13039\/100016726","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Vironet C Foundation","award":["free contribution"],"award-info":[{"award-number":["free contribution"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>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 \u03b2-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 \u03b2-thalassemia-patients and three involving both HCV-acute and chronic \u03b2-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 &lt; 0.05). Even though Shannon-entropy was higher in chronic-patients, significantly higher values were observed only in chronic \u03b2-thalassemia-patients versus acute \u03b2-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.<\/jats:p>","DOI":"10.3390\/cells8070666","type":"journal-article","created":{"date-parts":[[2019,7,2]],"date-time":"2019-07-02T12:11:17Z","timestamp":1562069477000},"page":"666","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["NS5A Gene Analysis by Next Generation Sequencing in HCV Nosocomial Transmission Clusters of HCV Genotype 1b Infected Patients"],"prefix":"10.3390","volume":"8","author":[{"given":"Maria Concetta","family":"Bellocchi","sequence":"first","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marianna","family":"Aragri","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luca","family":"Carioti","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lavinia","family":"Fabeni","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosaria Maria","family":"Pipitone","sequence":"additional","affiliation":[{"name":"Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giuseppina","family":"Brancaccio","sequence":"additional","affiliation":[{"name":"Infectious Diseases, Department of Mental and Physical Health and Preventive Medicine, Campania University \u201cLuigi Vanvitelli\u201d, 80138 Naples, Italy"},{"name":"Department of Molecular Medicine, University of Padua, 35121 Padua, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9146-4892","authenticated-orcid":false,"given":"Maria Chiara","family":"Sorbo","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Barbaliscia","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Velia Chiara","family":"Di Maio","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabrizio","family":"Bronte","sequence":"additional","affiliation":[{"name":"Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3225-4112","authenticated-orcid":false,"given":"Stefania","family":"Grimaudo","sequence":"additional","affiliation":[{"name":"Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5090-1366","authenticated-orcid":false,"given":"Walter","family":"Mazzucco","sequence":"additional","affiliation":[{"name":"Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ferdinando","family":"Frigeri","sequence":"additional","affiliation":[{"name":"Hematology Division, \u201cSan Sebastiano\u201d Hospital, 81100 Caserta, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Cantone","sequence":"additional","affiliation":[{"name":"Infectious Diseases, Department of Mental and Physical Health and Preventive Medicine, Campania University \u201cLuigi Vanvitelli\u201d, 80138 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio","family":"Pinto","sequence":"additional","affiliation":[{"name":"Hematology Department, National Cancer Institute \u201cFondazione Pascale\u201d, IRCCS, 80131 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlo Federico","family":"Perno","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Clinic Microbiology, University of Milan, 20162 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio","family":"Crax\u00ec","sequence":"additional","affiliation":[{"name":"Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1573-6224","authenticated-orcid":false,"given":"Giovanni Battista","family":"Gaeta","sequence":"additional","affiliation":[{"name":"Infectious Diseases, Department of Mental and Physical Health and Preventive Medicine, Campania University \u201cLuigi Vanvitelli\u201d, 80138 Naples, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6397-4206","authenticated-orcid":false,"given":"Vito","family":"Di Marco","sequence":"additional","affiliation":[{"name":"Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE) Department, University of Palermo, 90127 Palermo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Ceccherini-Silberstein","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,7,2]]},"reference":[{"key":"ref_1","unstructured":"(2019, February 01). 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