Tıp Fakültesi / Faculty of Medicine
Permanent URI for this collectionhttps://hdl.handle.net/11727/1403
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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 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 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.Item The Changing Dynamics Of Neutralizing Antibody Response Within 10 Months Of SARS-Cov-2 Infections(2022) Bastug, Aliye; Bodur, Hurrem; Aydos, Omer; Filazi, Nazlican; Oksuz, Ergun; https://orcid.org/0000-0002-5723-5965; 34967013; K-8238-2012There are limited data on how long neutralizing antibody (NAb) response elicited via primary SARS-CoV-2 infection will last. Eighty-four serum samples were obtained from a prospective cohort of 42 laboratory-confirmed COVID-19 inpatients at the time of discharge from the hospital and in the late convalescent phase. A virus neutralization assay was performed to determine the presence and titers of NAbs with authentic SARS-CoV-2. Long-term dynamics of NAbs and factors that may have an impact on humoral immunity were investigated. Mild and moderate/severe patients were compared. The mean sampling time was 11.12 +/- 5.02 days (4-28) for the discharge test and 268.12 +/- 11.65 days (247-296) for the follow-up test. NAb response was present in 83.3% of the patients about 10 months after infection. The detectable long-term NAb rate was significantly higher in mild patients when compared to moderate/severe patients (95.7% vs. 68.4%, p = 0.025). In the follow-up, NAb-positive and -negative patients were compared to determine the predictors of the presence of long-term humoral immunity. The only significant factor was disease severity. Patients with mild infections have more chance to have NAbs for a longer time. Age, gender, and comorbidity did not affect long-term NAb response. NAb titers decreased significantly over time, with an average rank of 24.0 versus 19.1 (p = 0.002). Multivariate generalized estimating equation analysis revealed that no parameter has an impact on the change of NAb titers over time. The majority of the late convalescent patients still had detectable low levels of neutralizing antibodies. The protective effect of these titers of NAbs from re-infections needs further studies.Item Cross-Sectional Analysis Of Tobacco Addiction In Hospitalized COVID-19 Patients(2022) Darilmaz Yuce, Gulbahar; Torun, Serife; Hekimoglu, Koray; Tuna, Derin; Sozbilici, Betul Rana; Cetin, Hikmet Oguz; Narlioglu, Mehmet Emin; Balli, Murat; Ozyesil, Ahmet Suheyl; Yavuz Colak, Meric; Ulubay, Gaye; Akcay, Muserref Sule; https://orcid.org/0000-0002-0805-0841; 36164949; AAD-9097-2021Introduction: The COVID-19 pandemic has become an important health issue with consequences for special populations since 2019. Tobacco use is an important public health issue and tobacco users are a risk group for lung infections.Materials and Methods: The aim of this study is to obtain information about disease prevalence and severity, laboratory parameters, and changes in radio-logical findings between smokers and non-smokers who were hospitalized, followed up, and treated for COVID-19, and to find answers to critical questi-ons regarding the response to antiviral and supportive therapy. Two hundred eighty-six patients who were hospitalized and treated between March 2020-February 2021 in the COVID-19 Isolation Ward of Baskent University Hospital were included in the study. The patients were grouped as current smokers, non-smokers, and ex-smokers. The groups were compared in terms of symptoms, laboratory findings, radiological findings, and treatment respon-se.Results: The median age of the patients included in the study was 59 (IQR= 32). Of the patients, 40.6% were female and 59.4% were male. In our study, we discovered that there were fewer female smokers (p< 0.001). When the current smokers (n= 56), non-smokers (n= 159), and ex-smokers (n= 71) were compared based on their findings, it was found that dyspnea was more common in current smokers (p= 0.009). Lung involvement was found to be more common (p= 0.002) and multifocal in the current smokers group (p= 0.038). The levels of oxygen saturation at the times of admission and discharge were lower in current smokers (p= 0.002 and p= 0.038). The need for nasal oxygen and noninvasive mechanical ventilation was also found to be higher in current smokers (p= 0.008 and p= 0.039). Systemic steroid requirement was higher in current smokers (p= 0.013). There was no statistically significant differen-ce in terms of mortality between current smokers, ex-smokers, and non-smokers (p= 0.662).Conclusion: The analysis of the findings of the patients hospitalized in the COVID-19 isolation ward indicated that COVID-19 leads to a more serious course in patients with a history of smoking.Item Allergen fragrance molecules: a potential relief for COVID-19(2021) Aydin, Asli Deniz; Altinel, Faruk; Erdogmus, Hueseyin; Son, Cagdas Devrim; 0000-0002-8326-3900; 33478471; AAJ-5382-2021BackgroundThe latest coronavirus SARS-CoV-2, discovered in China and rapidly spread Worldwide. COVID-19 affected millions of people and killed hundreds of thousands worldwide. There are many ongoing studies investigating drug(s) suitable for preventing and/or treating this pandemic; however, there are no specific drugs or vaccines available to treat or prevent SARS-CoV-2 as of today.MethodsFifty-eight fragrance materials, which are classified as allergen fragrance molecules, were selected and used in this study. Docking simulations were carried out using four functional proteins; the Covid19 Main Protase (MPro), Receptor binding domain (RBD) of spike protein, Nucleocapsid, and host Bromodomain protein (BRD2), as target macromolecules. Three different software, AutoDock, AutoDock Vina (Vina), and Molegro Virtual Docker (MVD), running a total of four different docking protocol with optimized energy functions were used. Results were compared with the five molecules reported in the literature as potential drugs against COVID-19. Virtual screening was carried out using Vina, molecules satisfying our cut-off (-6.5kcal/mol) binding affinity was confirmed by MVD. Selected molecules were analyzed using the flexible docking protocol of Vina and AutoDock default settings.ResultsTen out of 58 allergen fragrance molecules were selected for further docking studies. MPro and BRD2 are potential targets for the tested allergen fragrance molecules, while RBD and Nucleocapsid showed weak binding energies. According to AutoDock results, three molecules, Benzyl Cinnamate, Dihydroambrettolide, and Galaxolide, had good binding affinities to BRD2. While Dihydroambrettolide and Galaxolide showed the potential to bind to MPro, Sclareol and Vertofix had the best calculated binding affinities to this target. When the flexible docking results analyzed, all the molecules tested had better calculated binding affinities as expected. Benzyl Benzoate and Benzyl Salicylate showed good binding affinities to BRD2. In the case of MPro, Sclareol had the lowest binding affinity among all the tested allergen fragrance molecules.ConclusionAllergen fragrance molecules are readily available, cost-efficient, and shown to be safe for human use. Results showed that several of these molecules had comparable binding affinities as the potential drug molecules reported in the literature to target proteins. Thus, these allergen molecules at correct doses could have significant health benefits.Item Predominant Mutations of SARS-CoV-2: Their Geographical Distribution and Potential Consequences(2021) Unlu, Sezin; Uskudar Guclu, Aylin; Basustaoglu, Ahmet; 0000-0001-7490-7981; 0000-0002-1872-028X; AAQ-4702-2021; AAU-6196-2020Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged in late December 2019 in Wuhan, China. More than 83 million people have been infected, and more than 1.8 million people have died, as reported to the World Health Organization on the 3rd of January, 2021. Analysis of genetic variations is critical for understanding the spreading pattern of SARS-CoV-2 across several countries. This review aimed to gather information about the prominent mutations of SARS-CoV-2 by analyzing the origin, viral pathogenesis, and mutation rate. Moreover, we concluded their potential impacts on SARS-CoV-2 therapeutics. Mutations in the spike protein (D614G, N501Y, E484K, A222V, S477N, and G485R), ORF1ab (P323L, N628N, Y455Y, A97V, and F106F), nucleocapsid protein (R203K and G204R), ORF8 (L84S), and ORF3a (Q57H and G251V) were examined in this review by analyzing relevant articles from the beginning of the current pandemic to the most recent date. A detailed analysis of articles demonstrates that D614G is the major variation distributed globally, and its frequency increased rapidly from early in March, followed by several other variations in either spike or different proteins. In addition, it was seen that the currently circulating N501Y and E484K variants revealed a public concern regarding vaccines' efficacy. Investigation of variations of SARS-CoV-2 would lead to understanding their potential mechanism of action against SARS-CoV-2, thereby suggesting suitable therapeutics. Several mechanisms were suggested to have a role in SARS-CoV-2 mutation rate and evolution. Possible therapeutics and vaccines against SARS-CoV-2 were proposed.