Fakülteler / Faculties
Permanent URI for this communityhttps://hdl.handle.net/11727/1395
Browse
12 results
Search Results
Item Evaluation of the COVID-19 Rapid Antigen Test(2023) Sanli, Ozlem Oguc; Kuscu, Ozlem Ozkan; Incekas, Caner; 0000-0001-7899-0233; 0000-0001-9019-423XIntroduction: Coronavirus disease, is an infectious disease caused by the SARS-CoV-2. The gold standard method to diagnose is the reverse transcriptase polymerase chain reaction test. Rapid antigen tests can also be used for diagnosis. This study aims to compare the results of these two methods.Materials and Methods: Between November 2021 and July 2022, the study included 1811 patients who visited the emergency depart-ment with coronavirus-related symptoms and signs. Respiratory samples from these patients were simultaneously evaluated using both reverse transcriptase polymerase chain reaction and rapid antigen tests. The reverse transcriptase polymerase chain reaction tests were conducted using the BioSpeedy SARS-CoV-2 reverse transcriptase polymerase chain reaction kit (Bioeksen-Turkiye), while the rapid antigen tests were performed using the RapidForTM SARS-CoV-2 Ag (Vitrosens-Germany).Results: The comparison of the reverse transcriptase polymerase chain reaction test and rapid antigen test results showed a 90.67% sensitivity, 98.28% specificity, 91.27% positive predictive value, 98.15% negative predictive value, and 97.02% (1757/1811) accuracy. Qualitative results of both tests exhibited a very good agreement (Kappa= 0.892, p< 0.001). According to the reverse transcriptase polymerase chain reaction test, the sensitivity of the rapid antigen test was found to be 100% in 28 samples with a cycle threshold <17, 100% in 78 samples with a cycle threshold <20, 98.33% in 120 samples with a cycle threshold <22, and 96.28% in 215 samples with a cycle threshold <25.Conclusion: When the results of the study are evaluated, it is seen that the use of the rapid antigen test for screening purposes and confirmation of patients with negative test results by Reverse transcriptase polymerase chain reaction will provide advantages in terms of both time and cost. Due to the low sensitivity and high positive predictive value of the vitrosens rapid antigen test, we think that this test can be used in the first stage to accelerate the diagnosis of patients with high viral load, who are more likely to be infectious, to prevent transmission and to start their treatment quickly.Item Assessment of Endodontic Emergency Care in a COVID-19 Pandemic(2022) Sisli, Selen Nihal; Koc, Cemre; Sayin, Ceren Efe; Gulsahi, Kamran; https://orcid.org/0000-0003-3510-7265Objective: This study compared the aerosol-generating and non-aerosol -generating endodontic emergency procedures' success and assessed the outcome of endodontic treatments initiated before a pandemic but could not be completed in the targeted time. Materials and Methods: Emergency treatments were performed according to symptoms of teeth. Treatment success or failure was determined according to patients whether not re-referral with untimely pain. Short-term outcome and complications arising from teeth, which endodontic treatments were prolonged were also recorded. A chi-square test was used in the statistical analysis, and p<0.05 was considered significant. Results: The aerosol-generating procedure group's success rate was 86.2%, while it was 70.0% in the non-aerosol generating procedure group (p=0.050). The short-term survival rate of teeth was 83.7% in patients whose endodontic treatment had been prolonged. Conclusion: Considering the pros and cons, each emergency patient should be evaluated case-by-case.Item The Impacts of 13 Novel Mutations of SARS-Cov-2 on Protein Dynamics: in Silico Analysis From Turkey(2022) Unlu, Sezin; Uskudar-Guclu, Aylin; Cela, Isli; 37520163SARS-CoV-2 inherits a high rate of mutations making it better suited to the host since its fundamental role in evolution is to provide diversity into the genome. This research aims to identify variations in Turkish isolates and predict their impacts on proteins. To identify novel variations and predict their impacts on protein dynamics, in silico methodology was used. The 411 sequences from Turkey were analysed. Secondary structure prediction by Garnier-Osguthorpe-Robson (GOR) was used. To find the effects of identified Spike mutations on protein dynamics, the SARS-CoV-2 structures (PDB:6VYB, 6M0J) were uploaded and predicted by Cutoff Scanning Matrix (mCSM), DynaMut and MutaBind2. To understand the effects of these mutations on Spike protein molecular dynamics (MD) simulation was employed. Turkish sequences were aligned with sequences worldwide by MUSCLE, and phylogenetic analysis was performed via MegaX. The 13 novel mutations were identified, and six of them belong to spike glycoprotein. Ten of these variations revealed alteration in the secondary structure of the protein. Differences of free energy between the reference sequence and six mutants were found below zero for each of six isolates, demonstrating these variations have stabilizing effects on protein structure. Differences in vibrational entropy calculation revealed that three variants have rigidification, while the other three have a flexibility effect. MD simulation revealed that point mutations in spike glycoprotein and RBD:ACE-2 complex cause changes in protein dynamics compared to the wild-type, suggesting possible alterations in binding affinity. The phylogenetic analysis showed Turkish sequences distributed throughout the tree, revealing multiple entrances to Turkey.Item COVID-19 Infections in Pediatric Renal Transplant Recipients(2022) Yilmaz, Aysun Caltik; Baskin, Esra; Gulleroglu, Kaan; Karakaya, Deniz; Akdur, Aydincan; Moray, Gokhan; Haberal, Mehmet; https://orcid.org/0000-0003-0774-4419; https://orcid.org/0000-0003-1434-3824; https://orcid.org/0000-0002-3462-7632; 35384829; AAD-1877-2021; AAJ-8833-2021; AAJ-8097-2021Objectives: The new coronavirus SARS-CoV-2 (COVID-19) first appeared in Turkey in March 2020, spread rapidly, and caused many deaths. Although COVID-19 is mostly a respiratory disease, it can cause kidney and multiorgan failure in some cases. We believe that by sharing information about the course and effects of COVID-19 infection in kidney transplant recipients receiving long-term immunosuppressive therapy our understanding will improve. Materials and Methods: Between March 2020 and October 2021, COVID-19 was researched in kidney transplant recipients under the age of 20 years who were followed at the Baskent University Transplantation Center. We documented the clinical characteristics and prognosis of pediatric kidney transplant recipients with COVID-19 disease. Results: Our study group included 23 patients with COVID-19 infection from 215 pediatric kidney transplant recipients. The mean age of the patients was 14.6 +/- 4.7 years; there were 9 female patients. The mean follow-up time posttransplant was 62.3 +/- 43.2 months. In 13 patients (56.5%), fever was the most frequent symptom. Most patients (n = 18, 78%) had minor symptoms and recovered completely after receiving supportive treatment. Four patients (17%) required hospitalization. One was diagnosed with COVID-19 infection 1 week after being treated with rituximab for acute antibody-mediated rejection. That patient died because of significant lung disease and multiorgan failure. Conclusions: Despite the fact that most of our pediatric transplant recipients had mild symptoms of COVID-19, we believe that particular caution should be observed in patients who have recently received intensive immunosuppressive medications. As a result of potential new vaccines, national immunization programs, and the emergence of novel virus strains, the clinical picture may change in the future. We believe that, as information sharing increases, we will learn more about COVID-19 in renal transplant recipients.Item SARS-Cov-2 Infection Might Be A Predictor of Mortality in Intracerebral Hemorrhage(2023) Mowla, Ashkan; Shakibajahromi, Banafsheh; Shahjouei, Shima; Baharvahdat, Humain; Harandi, Ali Amini; Rahmani, Farzad; Mondello, Stefania; Rahimian, Nasrin; Cernigliaro, Achille; Hokmabadij, Elyar Sadeghi; Ebrahimzadeh, Seyed Amir; Ramezani, Mahtab; Mehrvar, Kaveh; Farhoudi, Mehdi; Naderi, Soheil; Fenderi, Shahab Mahmoudnejad; Pishjoo, Masoud; Alizada, Orkhan; Purroy, Francisco; Requena, Manuel; Tsivgoulis, Georgios; Zand, Ramin; 36455388Background: SARS-CoV-2 infection may be associated with uncommon complications such as intracerebral hemorrhage (ICH), with a high mortality rate. We compared a series of hospitalized ICH cases infected with SARS-CoV-2 with a non-SARS-CoV-2 infected control group and evaluated if the SARS-CoV-2 infection is a predictor of mortality in ICH patients.Methods: In a multinational retrospective study, 63 cases of ICH in SARS-CoV-2 infected patients admitted to 13 tertiary centers from the beginning of the pandemic were collected. We compared the clinical and radiological characteristics and in-hospital mortality of these patients with a control group of non-SARS-CoV-2 infected ICH patients of a previous cohort from the country where the majority of cases were recruited.Results: Among 63 ICH patients with SARS-CoV-2 infection, 23 (36.5%) were women. Compared to the non-SARS-CoV-2 infected control group, in SARS-CoV-2 infected patients, ICH occurred at a younger age (61.4 +/- 18.1 years versus 66.8 +/- 16.2 years, P = 0.044). These patients had higher median ICH scores ([3 (IQR 2-4)] versus [2 (IQR 1-3)], P = 0.025), a more frequent history of diabetes (34% versus 16%, P = 0.007), and lower platelet counts (177.8 +/- 77.8 x 109/L versus 240.5 +/- 79.3 x 109/L, P < 0.001). The in-hospital mortality was not significantly different between cases and controls (65% versus 62%, P = 0.658) in univariate analysis; however, SARS-CoV-2 infection was significantly associated with in-hospital mortality (aOR = 4.3, 95% CI: 1.28-14.52) in multivariable analysis adjusting for potential confounders.Conclusion: Infection with SARS-CoV-2 may be associated with increased odds of in-hospital mortality in ICH patients.Item IgG Neutralizing Antibodies to SARS-CoV-2 Among Healthcare Workers Who Frequently Encountered Patients with COVID-19(2022) Yesilagac, Hasan; Aliskan, Hikmet Eda; Gumus, Hatice Hale; Odemis, Ilker; Unsal, Zuhal Ekici; 0000-0003-2638-0163; 0000-0001-9071-9606; AAD-1638-2019; AAJ-2108-2021Introduction: Since the Severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) first emerged in Wuhan, on 12 December 2019, it has spread rapidly across the world and developed into a pandemic. As healthcare workers are frequently in contact with Coronavirus disease-2019 (COVID-19) patients, they can be affected more often than the general population. In this study we aimed to investigate the SARS-CoV-2 seroprevalence and the IgG antibody levels among healthcare workers who frequently encountered COVID-19 patients in our hospital.Materials and Methods: In total, 182 healthcare workers were identified from database and their data was retrospectively analyzed. Participants with previous PCR positivity, pregnant, autoimmune disease history or immunosuppressive treatment history were excluded. Participants were grouped depending on their frequency of contact with COVID-19 patients (high and medium risk). All the samples were tested simultaneously for anti-SARS-CoV-2-IgG antibodies by the ELISA method. A chi-square test was used to compare categorical variables. A t-test and an ANOVA test were carried out to where appropriate.Results: Serological testing of 182 HCWs exposed to SARS-CoV-2 patients illustrated that 13.2% of them (24 out of 182) might have experienced an asymptomatic or subclinical SARS-CoV-2 infection. High risk participants, anosmia, and ageusia were statistically significant risk factors. The rate of detection of antibody positivity among doctors (p=0.030) and patients with anosmia, and ageusia (p=0.047) were found significantly higher than the others. In addition, SARS-CoV-2 antibody ratio results were found significantly higher in the groups of high risk participants (p=0.046), patients with clinical signs (p=0.008), myalgia (p=0.039), anosmia, and ageusia (p=0.025), respectively.Conclusion: Our study showed that serological testing is useful for determining asymptomatic or subclinical infections prevelance of SARS-CoV-2 among those with close contact with COVID-19 patients. Serological tests can be helpful determining the prevelance COVID-19 infection, especially among the HCWs.Item Comparison Of Clinical Characteristics Of Second And Third Peaks Of COVID-19 Pandemic: Effects Of Vaccination And Preventive Measures(2022) Ozdemir, Ozer; Arslan, Atakan; Bulbul, Hande M.; Ozdemir, PelinBACKGROUND: Understanding the differences in consequent peaks of COVID-19 may guide us for better predicting future disease characteristics. In this study, we aimed to compare clinical and radiological characteristics as well as out-comes of hospitalized patients with the diagnosis of COVID-19 in second and third peaks of disease.METHODS: We retrospectively included 303 hospitalized patients with COVID-19. The study population was examined in two groups: patients hospitalized between October 2020 and January 2021 during second peak and patients hospital-ized between March and June 2021 during third peak.RESULTS: There were 171 patients in group 1 and 132 patients in group 2. The patients in group 2 were younger (64 +/- 13.27 vs. 56.02 +/- 15.39, respectively; P<0.001) and female proportion was higher (64.9% and 48.5% males; P=0.005). Smoking history and presence of comorbidities were less in group 2 (41.5% vs. 25.7%, P=0.008; and 78.5% vs. 59.1%, P<0.001) and symptom duration was shorter (median 7 days vs. 6 days, P=0.039). CT severity scores, LDH, CRP, D-di-mer, Ferritin, and creatinine levels were lower in group 2 (P=0.003, P=0.008, P<0.001, P<0.001, P<0.001, respectively), and mortality ratio was lower (N.=39 [28%] vs. N.=15 [11.4%], P=0.01). Duration of hospital stay and need for intensive unit care were similar across groups (median 8 days vs. 7 days, P=0.673 and N.=39 [22.8%] vs. N.=33 [25.2%], P=0.683).CONCLUSIONS: Although duration of hospital stay was lower in third peak, clinical severity scores and prognostic markers were lower compared with second peak. These may reflect the increased proportion of immunized people, and the effect of preventive measures.Item Promising Drug Fondaparinux for the Treatment of COVID-19: an In Silico Analysis of Low Molecular Weight Heparin, Direct Oral Anticoagulant, and Antiplatelet Drug Interactions with Host Protease Furin(2022) Ertan-Bolelli, Tugba; Bolelli, Kayhan; Elci, Sitki Doga; Belen-Apak, F. Burcu; 0000-0002-2179-997X; 0000-0002-9278-6703; 36401727; G-5289-2013Purpose As of July 2022, the COVID-19 pandemic has affected over 555 million worldwide confirmed cases and caused more than 6.3 million deaths. The studies showed that the D-dimer levels were increased in non-survivors compared to survivors and heparin treatment has begun to be administered to the patients in severe clinics. As we knew that the entrance of SARS-CoV-2 to the host cell needs to be facilitated by host proteases; we published our hypothesis that heparin as a serine protease inhibitor may block the interaction between spike protein receptor-binding domain and host proteases. In our study, we aimed to investigate the interactions between not only heparins but also other antiplatelet and anticoagulant drugs including fondaparinux. Methods In this study, docking studies were carried out to evaluate the interactions between low molecular weight heparins (LMWHs) (enoxaparin, dalteparin, tinzaparin), direct oral anticoagulant, and antiplatelet drugs with host proteases. Molecular docking studies were performed by using Schrodinger molecular modeling software. 3D structures of the ligands were obtained from the 2D structures by assigning the OPLS-2005 force field using the Maestro 12.7. The 3D crystal structure of the furin complexed with an inhibitor, 2,5-dideoksistreptamin derivative, was extracted from the Protein Data Bank (PDB ID: 5MIM). Docking studies were carried out using the Grid-based Ligand Docking with Energetics module of the Schrodinger Software. Results The docking studies revealed that fondaparinux was the most relevant molecule to interact with furin with a docking score of - 12.74. It showed better interaction than the natural ligand of furin with an increased score compared to the docking score of - 8.155 of the natural ligand. AnaGA*IsA structure representing LMWH structure has shown a docking score of - 11.562 which was also better than the score of the natural ligand of furin. Conclusion Our findings have shown that LMWHs and fondaparinux can be used for their possible antiviral effects in COVID-19 patients. Our results have shown that in accordance with heparin and LMWH, fondaparinux can also be a candidate for "drug repurposing" in COVID-19 therapy, not only because of their anticoagulant but also possible antiviral effects.Item Comparison Of Confirmed And Probable COVID-19 Patients In The Intensive Care Unit During The Normalization Period(2022) Yesiler, Fatma Irem; Capras, Mesher; Kandemir, Emre; Sahinturk, Helin; Gedik, Ender; Zeyneloglu, Pinar; https://orcid.org/0000-0002-0612-8481; https://orcid.org/0000-0003-0159-4771; 34812130; AAJ-4212-2021; AAJ-1419-2021The decrease in social distance together with the normalization period as of June 1, 2020, in our country caused an increase in the number of coronavirus disease 2019 (COVID-19) patients. Our aim was to compare the demographic features, clinical courses, and outcomes of confirmed and probable COVID-19 patients admitted to our intensive care unit (ICU) during the normalization period. Critically ill 128 COVID-19 patients between June 1, 2020, and December 2, 2020, were analyzed retrospectively. The mean age was 69.7 +/- 15.5 y (61.7% male). Sixty-one patients (47.7%) were confirmed. Dyspnea (75.0%) was the most common symptom and hypertension (71.1%) was the most common comorbidity. The mean Acute Physiology and Chronic Health Evaluation System (APACHE II) score; Glasgow Coma Score; Sequential Organ Failure Assessment scores on ICU admission were 17.4 +/- 8.2,12.3 +/- 3.9, and 5.9 +/- 3.4, respectively. One hundred and one patients (78.1%) received low-flow oxygen, 48 had high-flow oxygen therapy (37.5%), and 59 (46.1%) had invasive mechanical ventilation. Fifty-three patients (41.496) had vasopressor therapy and 30 (23.4%) patients had renal replacement therapy due to acute kidney injury (AKI). Confirmed patients were more tachypneic (p= 0.005) and more hypoxemic than probable patients (p < 0.001). Acute respiratory distress syndrome and AKI were more common in confirmed patients than probable (both p < 0.001). Confirmed patients had higher values of hemoglobin, C- reactive protein, fibrinogen, and D-dimer than probables (respectively, p = 0.028. 0.006, 0.000. and 0.019). The overall mortality was higher in confirmed patients (p = 0.209, 52.6% vs. 47.4%). Complications are more common among confirmed COVID-19 patients admitted to ICU. The mortality rate of confirmed COVID-19 patients admitted to the ICU was found to be higher than probable patients. Mortality of confirmed cases was higher than prediction of APACHE-II scoring system.Item SARS-CoV-2 Mutations and their Viral Variants(2022) Cosar, Begum; Karagulleoglu, Zeynep Yagmur; Unal, Sinan; Ince, Ahmet Turan; Uncuoglu, Dilruba Beyza; Tuncer, Gizem; Kilinc, Bugrahan Regaip; Ozkan, Yunus Emre; Ozkoc, Hikmet Ceyda; Demir, Ibrahim Naki; Eker, Ali; Karagoz, Feyzanur; Simsek, Said Yasin; Yasar, Bunyamin; Pala, Mehmetcan; Demir, Aysegul; Atak, Irem Naz; Mendi, Aysegul Hanife; Bengi, Vehdi Umut; Sevel, Guldane Cengiz; Altuntas, Evrim Gunes; Kilic, Pelin; Demir-Dora, Devrim; https://orcid.org/0000-0003-0359-6308; 34580015Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occur spontaneously during replication. Thousands of mutations have accumulated and continue to since the emergence of the virus. As novel mutations continue appearing at the scene, naturally, new variants are increasingly observed.Since the first occurrence of the SARS-CoV-2 infection, a wide variety of drug compounds affecting the binding sites of the virus have begun to be studied. As the drug and vaccine trials are continuing, it is of utmost importance to take into consideration the SARS-CoV-2 mutations and their respective frequencies since these data could lead the way to multi-drug combinations. The lack of effective therapeutic and preventive strategies against human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications.The reason why the mutations in glycoprotein S lead to vaccine escape is related to the location of the mutation and the affinity of the protein. At the same time, it can be said that variations should occur in areas such as the receptor-binding domain (RBD), and vaccines and antiviral drugs should be formulated by targeting more than one viral protein.