TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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Article Analysis of Nucleotide Changes in Rt-Pcr Primer/Probe Binding Regions in Sars-Cov-2 Isolates Reported from Turkey(Ankara Microbiology Society, 2021-07-16) Sayıner, Ayça Arzu; Appak, Özgür; Demir, Ayse Banu; Bulgurcu, AlihanThe SARS-CoV-2 virus, which caused the COVID-19 epidemic, caused more than 55 million cases and nearly 1.5 million deaths worldwide. For the microbiological diagnosis of the disease, the most valid method is detecting the presence of the viral genome by real-time reverse transcription polymerase chain reaction (rRT-PCR). However, due to the nature of the RNA viruses, frequent mutations may affect the sensitivity of the analyses made on the genetic material of the virus, such as PCR. In this study, we aimed to investigate the mutations in the primer-probe binding regions of the rRT-PCR panels used in COVID-19 diagnosis. SARS-CoV-2 whole genome sequence data (n= 194) isolated from COVID-19 cases in Turkey and uploaded on GISAID database from the centers in Istanbul (n= 78), Ankara (n= 58), Kars (n= 47), Bursa (n= 2), Adiyaman (n= 2), Erciyes (n= 1) and Kocaeli (n= 1) between March 17-September 14, 2020 were analyzed. In order to determine the nucleotide changes, SARS-CoV-2 sequences from Turkey were compared to the reference genome sequence (NC_045512.1) present in GenBank website. The constructed data set was aligned using the MAFFT program and was checked manually if the sequences were in the same frame by using the AliView program. Primer-probe binding sites of the thirteen SARS-CoV-2 rRT-PCR panels from seven different institutes (US CDC, China CDC, Charite CDC, Pasteur, HKU, Thailand, NIID) that are being used in COVID-19 diagnosis were evaluated in terms of nucleotide changes within the corresponding regions compared to the reference genome. Sequence diversities in the viral genomes were determined via positional nucleotide numerical calculator and entropy calculator modules and nucleotide and entropy changes in primer-probe binding regions for each rRT-PCR panel were examined. Among thirteen different primer-probe panels, nucleotide changes in the target regions of the seven primer-probe panels were determined. When viral sequences with nucleotide changes in the primer-probe binding regions were examined, the most common changes were observed in the China CDC N-forward primer and US CDC N3-forward primer binding regions. It is important that the kits to be used as diagnostic tests are designed specific to the regions with less nucleotide changes. Nucleotide changes may not be critical for DNA amplification for most PCR panels, but should be carefully monitored as they may affect the sensitivity of the assay. If the risk of alteration of the designed region is high, the primer - probe binding sites should be checked frequently and updated when necessary.Article An Incidental Study of the Effects of COVID-19 Lockdowns on the Muscle Strength of Patients With Postpolio Syndrome: Do These Patients Need a Break(Wolters Kluwer Medknow Publications, 2024-04) Tanigor, Goksel; Cinar, Ece; Darilgen, Atinc; Kancay, Mustafa Sedat; On, Arzu YagizIntroduction: This study was designed before the emergence of the COVID 19 pandemic, to assess the annual changes in muscle strength in relatively young Turkish people with postpolio syndrome (PPS). After we completed the baseline measurements, the COVID 19 pandemic emerged and lockdowns followed right after. Thus, the purpose of the study turned to how these lockdowns, which induced a sedentary lifestyle, have affected muscle strength in participants with PPS compared to healthy controls. Materials and Methods: This study included 49 hip joints (21 PPS vs. 28 healthy controls) and 51 knee joints (23 PPS vs. 28 healthy controls). Concentric isokinetic testing of bilateral hip and knee muscles was performed in all participants with PPS and controls just before the outbreak of the COVID 19 pandemic. The measurements were repeated after 1 year of lockdowns. Results: Perceived physical activities were reported to be decreased by 35.9% and 32.2% in participants with PPS and controls, respectively. No significant changes were observed in muscle strengths, and these changes did not differ between PPS and healthy controls. Conclusion: This is the first and possibly the only study to show that the muscle strengths of participants with PPS did not change significantly during 1 year of physical restraints due to the COVID 19 pandemic. These findings may support the basic principle in the rehabilitation of participants with PPS, which includes conserving energy and avoiding the overuse of muscles. However, more data from studies with a larger number of participants and longer follow ups, which will hopefully never happen again in a situation like this, are required to draw a conclusion.Article Strengthening Primary Health Care Through Moocs (massive Open Online Courses): a Cross-Sectional Study(Duzce Univ, FAC Medicine, 2023-10-20) Gökdemir, Özden; Hoedbecke, Kyle; Bojaj, Gazmend; Küçükerdem, Halime Seda; Bhattacharya, Sudip; Bakola, Maria; Jelastopulu, Eleni; Hoedebecke, KyleObjective: After the increased number of COVID-19-positive patients, a plateau phase and a decrease in the numbers were expected, followed by a second phase which could lead to an increased health system workload. The importance of training well-educated and qualified healthcare professionals (HPs) has been reconsidered. The rapid spread of the epidemic revealed the limitations of traditional method education. Massive online courses (MOOCs) were offered as a solution to keep the information up-to-date and accessible. The aim of our study was to evaluate the perceptions and experiences of healthcare professionals on strengthening the health system during the COVID-19 pandemic. Methods: In this descriptive cross-sectional multi-centered study, an online survey was applied to HPs between February-May 2021. There were 28 participating countries. Due to international participation, the survey was conducted in English. Results: There were 88 female and 87 male participants. Most of the participants were from Europe and Euroasia. Most of them reported their income as $501-$1500 US Dollars). The duration of job experience was between 5-15 years. 111 of them have completed a postdoctoral degree. Conclusion: According to the survey, all the groups reported as the effect of strengthening primary care by MOOC was positive.Article Citation - Scopus: 1Operating Room Nurses’ Metaphorical Perceptions of Coronavirus Disease 2019, Quarantine, and Mask Concepts: A Qualitative Study(AVES, 2023-09-04) Savsar, Adile; Damar, Hale Turhan; Ogce, Filiz; Turhan Damar, Hale; Öğce Aktaş, FilizAmaç: Bu çalışmanın amacı ameliyathane hemşirelerinin COVID-19, maske kullanımı ve karantina sürecine ilişkin algılarını, metaforlar aracılığıyla ortaya çıkarmaktır. Yöntemler: Bu tanımlayıcı kalitatif çalışma ameliyathane hemşireleri ile yapılmıştır (n = 96). Çalışma verileri tanıtıcı özellikler formu ve yarı yapılandırılmış form kullanılarak Eylül 2020-Mart 2021 tarihleri arasında toplanmıştır. Ameliyathane hemşirelerinden “COVID-19”, “maske kullanımı” ve “karantina süreci” kavramlarını neye benzettiklerini, benzetme nedeniyle birlikte yazması istenmiştir. Veriler, “içerik analizi” yöntemiyle incelenmiştir. Bulgular: Araştırmadaki üç farklı kavrama ilişkin toplam 181 metafor üretilmiştir. “COVID-19” kavramına ilişkin benzetmeler “Kontaminasyon ve mutasyon,” “Zarar verici” ve “Başetme ve uyum süreci” olarak üç kategoride toplanmıştır. “Karantina süreci” kavramına ilişkin benzetmeler “Özgürlüğün Kısıtlaması” ve “Değişim Süreci” olarak iki kategoride toplanmıştır. “Maske kullanımı” kavramına ilişkin benzetmeler ise “olumlu yönleri,” “olumsuz yönleri” ve “hem olumlu hem de olumsuz” olarak üç kategoride toplanmıştır. Sonuç: Bu çalışma ameliyathanelerde çalışan hemşirelerin pandemide yaşadıkları zorlukların yansıra bu sürecin olumlu yönlerine de odaklandığını göstermektedir.Article Citation - WoS: 1Citation - Scopus: 1Comparison of Facial Palsy Cases Before and During the Pandemic Coronavirus Disease-2019(Galenos Publ House, 2023-06-23) Uysal, Hasan Armağan; Güllüoğlu, HalilObjective: The pandemic coronavirus disease-2019 (COVID-19) is caused by a novel type of coronavirus named severe acute respiratory syndrome coronavirus-2 and is rapidly spreading all over the world. In addition to various neurological symptoms, acute facial palsy was diagnosed as the main neurological symptom in some COVID-19 patients. The current study aimed to analyze the variation and any possible association in the case numbers or medical symptoms of patients with facial palsy before and during the COVID-19 pandemic.Methods: The clinical files of patients who were diagnosed with facial palsy in the Neurology Department of Medicalpoint Hospital, University of Economics Faculty of Medicine, Izmir were retrospectively investigated. To compare the facial palsy cases according to different periods, two patient groups were formed: before the COVID-19 pandemic and during the COVID-19 pandemic. The pandemic group was further divided into two subgroups as COVID-19-positive and COVID-19-negative patients to compare the effects of COVID-19 on facial palsy.Results: During the specified COVID-19 period (May 2020-January 2021) of the study, 38 patients were admitted to the hospital for facial palsy; 34 facial palsy patients were admitted in the same calendar period as the two previous years (May 2018-January 2019). There was no significant difference in the frequency of facial palsy between these two time periods. There were significant differences between before and during the COVID-19 pandemic groups regarding response to cortisone therapy (p<0.001), facial palsy grade (p<0.001), electromyography findings (p=0.005), denervation (p<0.001), and 6 months recovery (p<0.001) data. There were also significant differences between the COVID-19-positive and COVID-19-negative subgroups regarding response to cortisone therapy (p=0.015) and facial palsy grade (p=0.001).Conclusion: The current study findings support the possible association between the severity of the clinical course of facial palsy and COVID-19. Further studies are needed to prove a direct association between facial palsy and COVID-19.Article The Experience of Women Infected by the Covid-19 During Pregnancy: a Qualitative Study(Galenos Publ House, 2023-03-23) Ugurlu, Meltem; Kıratlı, Didem; Yavan, TülayObjective: To gain deeper understanding of experiences of pregnant women infected with coronavirus disease-2019 (COVID-19) during the Methods: This study, which was planned as a descriptive qualitative study, was performed out with 15 pregnant women infected with COVID-19. The data were collected between January 5th and March 15th, 2021 using a semi-structured interview form and in-depth interview method. Content analysis, one of the qualitative research method, was used to evaluate the data. The research was planned based on the Qualitative Research Reporting Consolidated Criteria checklist, which is a guide for qualitative research. Results: Four main themes were found in experiences of pregnant women infected with COVID-19: (1) psychosocial health; (2) change in daily routines on quarantine days, (3) coping and (4) perinatal period changes. Pregnant women experienced both psychological and physical difficulties. They used the expression closed box to describe the anxiety and anxious state experienced due to the uncertainty of the perinatal outcomes brought about by COVID-19 during pregnancy. Conclusion: Understanding the experiences of pregnant women infected with COVID-19 is the first step in determining treatment and care management for nurses and healthcare professionals. During the pandemic period, pregnant women need to reach prenatal care services on time, to support them physically and psychosocially, to provide information with e-health services, and to provide remote follow-up support to cope with the process.Article Citation - WoS: 2Citation - Scopus: 2Analysis of Nucleotide Changes in Rt-Pcr Primer/Probe Binding Regions in Sars-Cov Isolates Reported From Turkey(Ankara Microbiology Soc, 2021-07-16) Demir, Ayse Banu; Bulgurcu, Alihan; Appak, Ozgur; Sayiner, Ayca ArzuThe SARS-CoV-2 virus, which caused the COVID-19 epidemic, caused more than 55 million cases and nearly 1.5 million deaths worldwide. For the microbiological diagnosis of the disease, the most valid method is detecting the presence of the viral genome by real-time reverse transcription polymerase chain reaction (rRT-PCR). However, due to the nature of the RNA viruses, frequent mutations may affect the sensitivity of the analyses made on the genetic material of the virus, such as PCR. In this study, we aimed to investigate the mutations in the primer-probe binding regions of the rRT-PCR panels used in COVID-19 diagnosis. SARS-CoV-2 whole genome sequence data (n= 194) isolated from COVID-19 cases in Turkey and uploaded on GISAID database from the centers in Istanbul (n= 78), Ankara (n= 58), Kars (n= 47), Bursa (n= 2), Adiyaman (n= 2), Erciyes (n= 1) and Kocaeli (n= 1) between March 17-September 14, 2020 were analyzed. In order to determine the nucleotide changes, SARS-CoV-2 sequences from Turkey were compared to the reference genome sequence (NC_045512.1) present in GenBank website. The constructed data set was aligned using the MAFFT program and was checked manually if the sequences were in the same frame by using the AliView program. Primer-probe binding sites of the thirteen SARS-CoV-2 rRT-PCR panels from seven different institutes (US CDC, China CDC, Charite CDC, Pasteur, HKU, Thailand, NIID) that are being used in COVID-19 diagnosis were evaluated in terms of nucleotide changes within the corresponding regions compared to the reference genome. Sequence diversities in the viral genomes were determined via positional nucleotide numerical calculator and entropy calculator modules and nucleotide and entropy changes in primer-probe binding regions for each rRT-PCR panel were examined. Among thirteen different primer-probe panels, nucleotide changes in the target regions of the seven primer-probe panels were determined. When viral sequences with nucleotide changes in the primer-probe binding regions were examined, the most common changes were observed in the China CDC N-forward primer and US CDC N3-forward primer binding regions. It is important that the kits to be used as diagnostic tests are designed specific to the regions with less nucleotide changes. Nucleotide changes may not be critical for DNA amplification for most PCR panels, but should be carefully monitored as they may affect the sensitivity of the assay. If the risk of alteration of the designed region is high, the primer - probe binding sites should be checked frequently and updated when necessary.Review Article Effects of Coronavirus Disease-2019 Pandemic and New Normal on the Orthopedic Outpatient Clinic Practice(Galenos Yayincilik, 2021-12-28) Biçen, Ahmet Çağdaş; Turken, Mehmet Aykut; Bicen, CagdasObjective: This study aimed to evaluate the effects of the coronavirus disease-2019 pandemic on the orthopedic outpatient clinic, including an investigation of the number, changes in complaints, and demographics of patients. Materials and Methods: Data of patients who visited the orthopedic outpatient clinic at our hospital within four periods were evaluated. Period 1 was between March and May 2019, period 2 was between June and August 2019, period 3 was between March and May 2020, and period 4 was between June and August 2020. Data of patients were recorded for each period including age, gender, number, and International Classification of Diseases 10th Revision codes for comparative analysis. Results: This study included 7,120 patients who were admitted to the orthopedic outpatient clinic within the four periods. The lowest number of patients (1,119) who visited the outpatient clinic was observed in the three months following the pandemic declaration (period 3), in March 2020, whereas the highest number (2,149) was observed in the three months following the lifting of restrictions, in June 2020 (period 4). No significant difference was observed in the age between the four periods (p=0.945). However, a difference was found between the periods for patients aged >= 65 years. Reasons for admission were also different between the periods. In period 3, admissions due to traumatic reasons were statistically higher compared with the other three periods (p<0.001, p=0.003, p<0.001). Conclusion: It was observed that the number of patients visiting the orthopedic outpatient clinic increased after the restrictions were lifted. Outpatient clinic management must be organized in a way that prevents contamination and preserves efficient outpatient support.Article Citation - WoS: 32Citation - Scopus: 32Covid-19 Anxiety in People Living With Hiv: an Online Cross-Sectional Study(Tubitak Scientific & Technical Research Council Turkey, 2020-12-17) Kuman Tuncel, Ozlem; Pullukcu, Husnu; Erdem, Huseyin Aytac; Kurtaran, Behice; Tasbakan, Selin Ece; Isikgoz Tasbakan, Meltem; Tuncel, Ozlem KumanBackground/aim: The emergence of the coronavirus disease 2019 (COVID-19) outbreak has had an enormous emotional impact on sonic vulnerable groups, such as people living with human immunodeficiency virus (HIV) (PLHIV). This study was planned with the aim of assessing the anxiety levels of PLHIV and the sources of their anxiety. Materials and methods: A web-based questionnaire was sent to PLHIV using the virtual snowball sampling method. The questionnaire included questions about sociodemographic status, information about HIV infection, and the Beck Anxiety Inventory (BAI). Additionally, some opinions of the participants about COVID-19 were asked. Results: A total of 307 respondents, with a median age of 33 years, from 32 different cities, participated in the study. More than half of the respondents reported the belief that COVID-19 was not sufficiently well-known by the medical community and nearly 45% believed that they would have snore complications if they contracted COVID-19. One-fourth of the participants had anxiety. Having a preexisting psychiatric disorder, perceiving that they were practicing insufficient preventive measures, not being sure about the presence of any individuals with COVID-19 in their environment, and living with a household member with a chronic disease were found to be the risk factors of PLHIV for having anxiety during this pandemic. The BAI scores were correlated with the patient-reported anxiety levels about the spread of COVID-19 in Turkey, acquiring COVID-19, transmitting COVID-19 to another person, and transmitting HIV to another person. Among the stated conditions, the most common concern was the spread of COVID-19 all over the country, while the least common was transmitting HIV to someone else. Conclusion: The results revealed that a significant proportion of the sample had anxiety, and the findings were essential for developing evidence-based strategies for decreasing the anxiety of PLHIV, especially for those who had risk factors and to provide them with better health care during this pandemic or other pandemic-like crises.Article Citation - WoS: 15Citation - Scopus: 17Identification of the Nucleotide Substitutions in 62 Sars-Cov Sequences From Turkey(Tubitak Scientific & Technical Research Council Turkey, 2020-06-21) Demir, Ayse Banu; Benvenuto, Domenico; Abacioglu, Hakan; Angeletti, Silvia; Ciccozzi, MassimoA 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.