Browsing by Author "Benvenuto, Domenico"

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Citation - WoS: 4
Citation - Scopus: 5
Analysis of Three Mutations in Italian Strains of Sars-Cov Implications for Pathogenesis
(Karger, 2021) Benvenuto, Domenico; Benedetti, Francesca; Demir, Ayse Banu; Ciccozzi, Massimo; Zella, Davide
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus initially detected in Wuhan in December 2019, responsible for coronavirus disease 2019 (COVID-19), a respiratory syndrome currently affecting >220 countries around the world, with >80 million cases registered and >1.8 million deaths. Objective: As several vaccines are still being developed and 2 have been approved, it is particularly important to perform evolutionary surveillance to identify mutations potentially affecting vaccine efficacy. Methods: DynaMut server has been used to evaluate the impact of the mutation found on SARS-CoV-2 isolates available on GISAID. Results: In this article, we analyze whole genomes sequenced from Italian patients, and we report the characterization of 3 mutations, one of which presents in the spike protein. Conclusion: The mutations analyzed in this article can be useful to evaluate the evolution of SARS-CoV-2.
Citation - WoS: 17
Citation - Scopus: 18
Evidence for Mutations in Sars-Cov Italian Isolates Potentially Affecting Virus Transmission
(Wiley, 2020) Benvenuto, Domenico; Demir, Ayse Banu; Giovanetti, Marta; Bianchi, Martina; Angeletti, Silvia; Pascarella, Stefano; Cauda, Roberto; Cassone, Antonio
Italy is the first western country suffering heavy severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and disease impact after coronavirus disease-2019 pandemia started in China. Even though the presence of mutations on spike glycoprotein and nucleocapsid in Italian isolates has been reported, the potential impact of these mutations on viral transmission has not been evaluated. We have compared SARS-CoV-2 genome sequences from Italian patients with virus sequences from Chinese patients. We focussed upon three nonsynonymous mutations of genes coding for S(one) and N (two) viral proteins present in Italian isolates and absent in Chinese ones, using various bioinformatics tools. Amino acid analysis and changes in three-dimensional protein structure suggests the mutations reduce protein stability and, particularly for S1 mutation, the enhanced torsional ability of the molecule could favor virus binding to cell receptor(s). This theoretical interpretation awaits experimental and clinical confirmation.
Citation - WoS: 15
Citation - Scopus: 17
Identification of the Nucleotide Substitutions in 62 Sars-Cov Sequences From Turkey
(Tubitak Scientific & Technical Research Council Turkey, 2020) Demir, Ayse Banu; Benvenuto, Domenico; Abacioglu, Hakan; Angeletti, Silvia; Ciccozzi, Massimo
A previously unknown coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to cause coronavirus disease 2019 (COVID-19) pandemic. The first case of COVID-19 in Turkey has been declared in March 11th, 2020 and from there on, more than 150,000 people in the country have been diagnosed with the disease. In this study, 62 viral sequences from Turkey, which have been uploaded to GISAID database, were analyzed by means of their nucleotide substitutions in comparison to the reference SARS-CoV-2 genome from Wuhan. Our results indicate that the viral isolates from Turkey harbor some common mutations with the viral strains from Europe, Oceania, North America and Asia. When the mutations were evaluated, C3037T, C14408T and A23403G were found to be the most common nucleotide substitutions among the viral isolates in Turkey, which are mostly seen as linked mutations and are part of a haplotype observed high in Europe.
Implications of Possible Hbv-Driven Regulation of Gene Expression in Stem Cell-Like Subpopulation of Huh-7 Hepatocellular Carcinoma Cell Line
(Mdpi, 2022) Demir, Ayse Banu; Benvenuto, Domenico; Karacicek, Bilge; Erac, Yasemin; Spoto, Silvia; Angeletti, Silvia; Ciccozzi, Massimo; Tosun, Metiner
Elevated levels of STIM1, an endoplasmic reticulum Ca2+ sensor/buffering protein, appear to be correlated with poor cancer prognosis in which microRNAs are also known to play critical roles. The purpose of this study is to investigate possible HBV origins of specific microRNAs we identified in a stem cell-like subpopulation of Huh-7 hepatocellular carcinoma (HCC) cell lines with enhanced STIM1 and/or Orai1 expression that mimicked poor cancer prognosis. Computational strategies including phylogenetic analyses were performed on miRNome data we obtained from an EpCAM- and CD133-expressing Huh-7 HCC stem cell-like subpopulation with enhanced STIM1 and/or Orai1 expression originally cultured in the present work. Results revealed two putative regions in the HBV genome based on the apparent clustering pattern of stem loop sequences of microRNAs, including miR3653. Reciprocal analysis of these regions identified critical human genes, of which their transcripts are among the predicted targets of miR3653, which was increased significantly by STIM1 or Orai1 enhancement. Briefly, this study provides phylogenetic evidence for a possible HBV-driven epigenetic remodeling that alters the expression pattern of Ca2+ homeostasis-associated genes in STIM1- or Orai1 overexpressing liver cancer stem-like cells for a possible mutual survival outcome. A novel region on HBV-X protein may affect liver carcinogenesis in a genotype-dependent manner. Therefore, detection of the viral genotype would have a clinical impact on prognosis of HBV-induced liver cancers.