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, Alihan
    The 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 Yagiz
    Introduction: 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.