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Article Citation - WoS: 10Citation - Scopus: 12Detection of Viruses by Probe-Gated Silica Nanoparticles Directly From Swab Samples(Elsevier, 2022) Tuna, Bilge Guvenc; Durdabak, Dilara Buse; Ercan, Meltem Kazak; Dogan, Soner; Kavruk, Murat; Dursun, Ali Dogan; Ozalp, Veli CengizViral infection has been one of the major health issues for human life. The real-time reverse transcription polymerase chain reaction (RT-PCR)-based detection has primarily been used for virus detection as a highly reliable procedure. However, it is a relatively long and multi-stage process. In addition, required skilled personnel and complex instrumentation presents difficulties in large scale monitoring efforts. Therefore, we report here a direct and fast detection method for CoV-2 genome as applied in the nose-throat swab samples without any further processing. The detection principle is based on fluorescein-loaded mesoporous silica nanoparticles capped by specific gene sequences probes immobilized on the surface of the nanoparticles. Upon hybridization with the target viral genome, the fluorescein molecules were released from the mesopores. Testing with synthetic oligonucleotides, the NSP12 gene-based detection resulted in a strong signal. Target detection time could be optimized to 15 min and the limit of detection was 1.4 RFU with 84% sensitivity with clinical samples (n = 43).Article Biotechnological Preparedness for Novel Pandemics: Diagnostic Performance of IVDS Against SARS-CoV(Wiley, 2025) Kavruk, Murat; Ercan, Meltem; Borsa, Baris Ata; Ozalp, Veli Cengiz; Hernandez, Frank J.Although the COVID-19 pandemic has created many challenges and negative impacts around the world, some of which will persist into the future, its technological challenge has created a unique opportunity in a globalized world. It is a rare event that almost all of humanity to be directed towards a single goal and to try to produce solutions, but the necessity of a similar global action in the future has begun to enter the agenda again. The predictions made on the basis of countries and institutions against the possibility of a pandemic, which is defined as Disease X, are shaped by the experience of the COVID-19 pandemic. Technologically, one of the know-how we have gained in this pandemic is the performance of IVD and test systems in terms of quality and quantity. A comprehensive analysis of the products produced by combining biotechnology with different strategies has not been conducted. In this context, we have analyzed the technical preferences, limitations, and other performance parameters of IVDs and test kits that could be developed against a future Disease X. The performance parameters of 2,882 biotechnological products listed for use in the European Union have been analyzed, and areas that could be targeted for increased effectiveness have been identified. Our study is the first of its kind in this field and can serve as a guide for those who want to work on detection methods, diagnostics, and novel technologies for deployment in future pandemics.Article Citation - WoS: 3Citation - Scopus: 3Shared 6mer Peptides of Human and Omicron (21k and 21l) at Sars-Cov Mutation Sites(Mdpi, 2022) Adiguzel, Yekbun; Shoenfeld, YehudaWe investigated the short sequences involving Omicron 21K and Omicron 21L variants to reveal any possible molecular mimicry-associated autoimmunity risks and changes in those. We first identified common 6mers of the viral and human protein sequences present for both the mutant (Omicron) and nonmutant (SARS-CoV-2) versions of the same viral sequence and then predicted the binding affinities of those sequences to the HLA supertype representatives. We evaluated change in the potential autoimmunity risk, through comparative assessment of the nonmutant and mutant viral sequences and their similar human peptides with common 6mers and affinities to the same HLA allele. This change is the lost and the new, or de novo, autoimmunity risk, associated with the mutations in the Omicron 21K and Omicron 21L variants. Accordingly, e.g., the affinity of virus-similar sequences of the Ig heavy chain junction regions shifted from the HLA-B*15:01 to the HLA-A*01:01 allele at the mutant sequences. Additionally, peptides of different human proteins sharing 6mers with SARS-CoV-2 proteins at the mutation sites of interest and with affinities to the HLA-B*07:02 allele, such as the respective SARS-CoV-2 sequences, were lost. Among all, any possible molecular mimicry-associated novel risk appeared to be prominent in HLA-A*24:02 and HLA-B*27:05 serotypes upon infection with Omicron 21L. Associated disease, pathway, and tissue expression data supported possible new risks for the HLA-B*27:05 and HLA-A*01:01 serotypes, while the risks for the HLA-B*07:02 serotypes could have been lost or diminished, and those for the HLA-A*03:01 serotypes could have been retained, for the individuals infected with Omicron variants under study. These are likely to affect the complications related to cross-reactions influencing the relevant HLA serotypes upon infection with Omicron 21K and Omicron 21L.Editorial Citation - Scopus: 1Safety and Feasibility of Surgery for Oropharyngeal Cancers During the Sars-Cov(Frontiers Media Sa, 2021) Gorphe, Philippe; Grandbastien, Bruno; Dietz, Andreas; Duvvuri, Umamaheswar; Ferris, Robert L.; Golusinski, Wojciech; Simon, Christian[No Abstract Available]Article Citation - WoS: 4Citation - Scopus: 7Real-Time Learning and Monitoring System in Fighting Against Sars-Cov in a Private Indoor Environment(Mdpi, 2022) Erisen, SerdarThe SARS-CoV-2 virus has posed formidable challenges that must be tackled through scientific and technological investigations on each environmental scale. This research aims to learn and report about the current state of user activities, in real-time, in a specially designed private indoor environment with sensors in infection transmission control of SARS-CoV-2. Thus, a real-time learning system that evolves and updates with each incoming piece of data from the environment is developed to predict user activities categorized for remote monitoring. Accordingly, various experiments are conducted in the private indoor space. Multiple sensors, with their inputs, are analyzed through the experiments. The experiment environment, installed with microgrids and Internet of Things (IoT) devices, has provided correlating data of various sensors from that special care context during the pandemic. The data is applied to classify user activities and develop a real-time learning and monitoring system to predict the IoT data. The microgrids were operated with the real-time learning system developed by comprehensive experiments on classification learning, regression learning, Error-Correcting Output Codes (ECOC), and deep learning models. With the help of machine learning experiments, data optimization, and the multilayered-tandem organization of the developed neural networks, the efficiency of this real-time monitoring system increases in learning the activity of users and predicting their actions, which are reported as feedback on the monitoring interfaces. The developed learning system predicts the real-time IoT data, accurately, in less than 5 milliseconds and generates big data that can be deployed for different usages in larger-scale facilities, networks, and e-health services.Article Citation - WoS: 11Citation - Scopus: 11Impact of Vaccination on the Presence and Severity of Symptoms in Hospitalized Patients With an Infection of the Omicron Variant (b.1.1.529) of the Sars-Cov (subvariant Ba.1)(Elsevier Sci Ltd, 2023) Beraud, Guillaume; Bouetard, Laura; Civljak, Rok; Michon, Jocelyn; Tulek, Necla; Lejeune, Sophie; Epaulard, OlivierObjectives: The emergence of SARS-CoV-2 variants raised questions about the extent to which vaccines designed in 2020 have remained effective. We aimed to assess whether vaccine status was associated with the severity of Omicron SARS-CoV-2 infection in hospitalized patients.Methods: We conducted an international, multi-centric, retrospective study in 14 centres (Bulgaria, Croatia, France, and Turkey). We collected data on patients hospitalized for >= 24 hours between 1 December 2021 and 3 March 2022 with PCR-confirmed infection at a time of exclusive Omicron circu-lation and hospitalization related or not related to the infection. Patients who had received prophylaxis by monoclonal antibodies were excluded. Patients were considered fully vaccinated if they had received at least two injections of either mRNA and/or ChAdOx1-S or one injection of Ad26.CoV2-S vaccines. Results: Among 1215 patients (median age, 73.0 years; interquartile range, 57.0-84.0; 51.3% men), 746 (61.4%) were fully vaccinated. In multivariate analysis, being vaccinated was associated with lower 28 -day mortality (Odds Ratio [95% Confidence Interval] (OR [95CI]) = 0.50 [0.32-0.77]), intensive care unit admission (OR [95CI] = 0.40 [0.26-0.62]), and oxygen requirement (OR [95CI] = 0.34 [0.25-0.46]), independent of age and comorbidities. When co-analysing these patients with Omicron infection with 948 patients with Delta infection from a study we recently conducted, Omicron infection was associated with lower 28-day mortality (OR [95CI] = 0.53 [0.37-0.76]), intensive care unit admission (OR [95CI] = 0.19 [0.12-0.28]), and oxygen requirements (OR [95CI] = 0.50 [0.38-0.67]), independent of age, comorbidities, and vaccination status.Discussion: Originally designed vaccines have remained effective on the severity of Omicron SARS-CoV-2 infection. Omicron is associated with a lower risk of severe forms, independent of vaccination and pa-tient characteristics. Guillaume Beraud, Clin Microbiol Infect 2023;29:642 (c) 2022 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).Article Comparison of SARS-CoV IgG Responses in Hemodialysis Patients and Healthcare Workers After COVID-19 Vaccination(Frontiers Media S.A., 2025) Ozturk, Hakki; Ozsoy, Metin; Tuna, Aysegul; Varlibas, Artuner; Cesur, Salih; Aksoy, Altan; Demir, Mehmet EminAim: This study aimed to compare SARS-CoV-2 IgG antibody levels in hemodialysis (HD) patients and healthcare workers (HCWs) after COVID-19 vaccination and to identify factors influencing these levels. Materials and methods: A total of 193 participants were included: 104 HD patients and 89 age- and sex-matched HCWs as controls. All had completed a primary COVID-19 vaccination series (two doses of CoronaVac or BNT162b2) and a booster dose. SARS-CoV-2 anti-spike IgG was measured at least one month after the last vaccine dose using a commercial immunoassay (Abbott SARS-CoV-2 IgG II Quant, CMIA). Results in Arbitrary Units (AU/mL) were converted to WHO standard Binding Antibody Units (BAU/mL) (1 AU/mL = 0.142 BAU/mL). IgG titers >= 7.1 BAU/mL (equivalent to 50 AU/mL) were considered positive. Results: All participants had positive SARS-CoV-2 IgG antibodies. There were no statistically significant differences in IgG levels between HD patients and HCWs at any individual time interval (<3 months, 3-6 months, or >6 months) or in the overall mean titers (HD: 1259 +/- 1112 BAU/mL; HCW: 1002 +/- 765 BAU/mL; p = 0.216). No individual in either group had an IgG titer below 7.1 BAU/mL. Vaccine type, dialysis vintage, and presence of comorbidities did not significantly impact antibody levels. In the HCWs group, those vaccinated only with CoronaVac had significantly lower IgG levels than those receiving only BNT162b2 or a heterologous regimen (CoronaVac followed by BNT162b2). However, among HD patients, IgG levels did not differ by vaccine regimen. Conclusion: HD patients mounted a SARS-CoV-2 IgG antibody response comparable to that of healthy HCWs, with no participant falling below the positivity threshold. Dialysis duration and comorbid conditions did not significantly affect post-vaccination IgG levels. While HCWs who received only CoronaVac showed lower antibody titers than those who received BNT162b2 or a heterologous schedule, this difference was not observed in HD patients. These results suggest that COVID-19 vaccination elicits a robust humoral immune response in the HD population, underscoring the benefit of vaccination in this high-risk group.Article Citation - WoS: 3Citation - Scopus: 3Predicted Sars-Cov Mirnas Associated With Epigenetic Viral Pathoge-Nesis and the Detection of New Possible Drugs for Covid-19(Bentham Science Publ Ltd, 2021) Cetin, Zafer; Bayrak, Tuncay; Ogul, Hasan; Saygili, Eyup Ilker; Akkol, Esra KupeliObjective: The outbreak of COVID-19 caused by SARS-CoV-2 has promptly spread worldwide. This study aimed to predict mature miRNA sequences in the SARS-CoV-2 genome, their effects on protein-protein interactions in the affected cells, and gene-drug relationships to detect possible drug candidates. Methods: Viral hairpin structure prediction, classification of hairpins, mutational examination of precursor miRNA candidate sequences, Minimum Free Energy (MFE) and regional entropy analysis, mature miRNA sequences, target gene prediction, gene ontology enrichment, and Protein-Protein Interaction (PPI) analysis, and gene-drug interactions were performed. Results: A total of 62 candidate hairpins were detected by VMir analysis. Three hairpin structures were classified as true precursor miRNAs by miRBoost. Five different mutations were detected in precursor miRNA sequences in 100 SARS-CoV-2 viral genomes. Mutations slightly elevated MFE values and entropy in precursor miRNAs. Gene ontology terms associated with fibrotic pathways and immune system were found to be enriched in PANTHER, KEGG and Wiki pathway analysis. PPI analysis showed a network between 60 genes. CytoHubba analysis showed SMAD1 as a hub gene in the network. The targets of the predicted miRNAs, FAM214A, PPM1E, NUFIP2 and FAT4, were downregulated in SARS-CoV-2 infected A549 cells. Conclusion: miRNAs in the SARS-CoV-2 virus genome may contribute to the emergence of the Covid-19 infection by activating pathways associated with fibrosis in the cells infected by the virus and modulating the innate immune system. The hub protein between these pathways may be the SMAD1, which has an effective role in TGF signal transduction.Book Part In Silico Study of Molecular Mimicry Between Sars-Cov and Neutrophil Extracellular Traps Composition in Granulocyte-Rich Supernatants of Patients With Systemic Lupus Erythematosus and Lupus Nephritis(Elsevier, 2022) Adiguzel,Y.; Shoenfeld,Y.Neutrophil extracellular traps (NETs) are detected in both COVID-19 and autoimmune disorders. Molecular mimicry between NETs-related proteins and SARS-CoV-2 proteins may be the mechanism that can lead to an autoimmune response. Accordingly, similar sequences were searched with blastp, between SARS-CoV-2 proteins and 148 proteins that were reported in the NETs composition induced in neutrophils of supernatants from patients with systemic lupus erythematosus and lupus nephritis. Query-subject epitope pairs with strong-binding affinities to 12 HLA supertype representative alleles were predicted for the aligned sequences with at least 50% identities. According to the prediction results, all HLA alleles under study have affinities to the similar SARS-CoV-2 and NETs' proteins. These affinities can bring molecular mimicry-based autoimmunity risk with NETs-pathology, in susceptible individuals, upon infection with SARS-CoV-2. However, HLA-A∗01:01 carriers can be at a higher risk due to the association of this allele with the highest number of NETs-related human proteins, and similar (unique) query-subject epitope pairs of those proteins and SARS-CoV-2. Additionally, HLA-A∗02:01 carriers may specifically be prone to higher risk than expected, if infected with SARS-CoV-2. Furthermore, HLA-A∗24:02 was predicted to bind strongly to an elevated number of unique SARS-CoV-2 subject sequences while the number of both associated human proteins, and unique queries of those, are rather low. It may be indicative of a pertaining pathology despite viral evolution. © 2023 Elsevier Inc. All rights reserved.
