Browsing by Author "Kulah, Canan"

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Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection
(SPRINGER HEIDELBERG, 2022-01-01) Cirit, Osman Sezer; Mutlu, Esvet; Sancak, Banu; Kocagoz, Tanil; Can, Ozge; Cicek, Candan; Sayiner, Ayca Arzu; Appak, Ozgur; Uyar, Neval Yurttutan; Kulah, Canan; Cicek, Aysegul Copur; Ozgumus, Osman Birol; Altintop, Yasemin Ay; Saatci, Esma; Karsligil, Tekin; Zer, Yasemin; Ozen, Nevgun Sepin; Cekin, Yesim; Karahan, Zeynep Ceren; Evren, Ebru; Karakoc, Ayse Esra; Orhan, Sultan Gulbahce; Mutlu, Derya; Bozdemir, Tugba; Cayci, Yeliz Tanriverdi; Cinar, Canberk; Tasbakan, Meltem; Mert, Merve; Cinar, Ece; Kutsoylu, Oya Ozlem Eren; Kocagoz, Sesin; Erturk, Ayse; Celik, Ilhami; Mete, Ayse Ozlem; Eneyli, Muge Gunalp; Akdemir, Irem; Karakok, Taliha; Inan, Dilara; Atilla, Aynur; Taflan, Sevket Onur; Yoruk, Kagan Etka
Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor (TM) Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor (TM) SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9\%) were positive and 98 (22.1\%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor (TM). Antigen Rapid Test Kit was 80.3\% whereas specificity was found to be 87.8\%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7\%, while it increased to 95.7\% in samples 20 <= Ct < 25 and reached 100\% in samples with Ct values below 20. RapidFor (TM) SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.
Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients
(PUBLIC LIBRARY SCIENCE, 2020-01-01) Akgun, Emel; Tuzuner, Mete Bora; Sahin, Betul; Kilercik, Meltem; Kulah, Canan; Cakiroglu, Hacer Nur; Serteser, Mustafa; Unsal, Ibrahim; Baykal, Ahmet Tarik
COVID-19 or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared throughout the World and currently affected more than 9 million people and caused the death of around 470,000 patients. The novel strain of the coronavirus disease is transmittable at a devastating rate with a high rate of severe hospitalization even more so for the elderly population. Naso-oro-pharyngeal swab samples as the first step towards detecting suspected infection of SARS-CoV-2 provides a non-invasive method for PCR testing at a high confidence rate. Furthermore, proteomics analysis of PCR positive and negative naso-oropharyngeal samples provides information on the molecular level which highlights disease pathology. Samples from 15 PCR positive cases and 15 PCR negative cases were analyzed with nanoLC-MS/MS to identify the differentially expressed proteins. Proteomic analyses identified 207 proteins across the sample set and 17 of them were statistically significant. Protein-protein interaction analyses emphasized pathways like Neutrophil degranulation, Innate Immune System, Antimicrobial Peptides. Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified proteins are linked to alteration in the innate immune system specifically via neutrophil degranulation and NETosis.
Six-year distribution pattern of hepatitis C virus in Turkey: a multicentre study
(TAYLOR \& FRANCIS LTD, 2016-01-01) Altindis, Mustafa; Dal, Tuba; Akyar, Isin; Karatuna, Onur; Gokahmetoglu, Selma; Ulger, Seda Tezcan; Kulah, Canan; Uzun, Berrin; Sener, Asli Gamze; Ozdemir, Mehmet; Aydogan, Sibel; Kuskucu, Mert Ahmet; Midilli, Kenan; Otlu, Baris; Celen, Mustafa Kemal; Buruk, Kurtulus; Guducuoglu, Huseyin
Hepatitis C infection is a public health problem. The aim of this retrospective study was to determine the distribution of hepatitis C virus (HCV) genotypes in seven regions of Turkey, by evaluating 7002 patients with chronic HCV in a six-year period. During the 2009-2014 period, serum/plasma samples from 7002 new consecutive HCV RNA positive patients were collected. The female patients were 3867 (55.2\%). The genotype distribution of HCV patiens was evaluated by ages and years. Statistical analysis was performed by using the Mann-Whitney test and the chi(2) analysis. During the six-year period, genotype 1b was the most common genotype (67.7\%) followed by untypeable genotype 1 (7.7\%), genotype 4 (7.3\%) and genotype 3 (6.7\%). In 2014, genotype 3 was the second most common one (11.3\%) and genotype 4 was the third most common one (9.8\%). In the group with <25 years old patients, genotype 1b was most common (78.48\%, 62/79) between the years of 2009 and 2011, whereas genotype 3 (34.8\%, 86/247), between the years of 2012 and 2014. Genotype 1b was the most common in the groups between 26 and 35 years, 36 and 45 years, 46 and 55 years, 56 and 65 years. The rate of genotype 3 was increased from 4.78\% to 10.06\% and the rate of genotype 4 was increased from 1.3\% to 3.84\%, from 2009-2011 to 2012-2014. In recent years, genotypes 3 and 4 have gained importance. New therapeutic strategies and survey studies may be required for the modified HCV genotype pattern.