Browsing by Author "Sayiner, Ayca Arzu"

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Citation - WoS: 2
Citation - Scopus: 2
Analysis of Nucleotide Changes in Rt-Pcr Primer/Probe Binding Regions in Sars-Cov Isolates Reported From Turkey
(Ankara Microbiology Soc, 2021) Demir, Ayse Banu; Bulgurcu, Alihan; Appak, Ozgur; Sayiner, Ayca Arzu
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.
Citation - WoS: 15
Citation - Scopus: 14
Changes on Hepatitis C Virus Genotype Distribution in Western Turkey: Evaluation of Twelve-Year Data
(Aves, 2020) Duran, Alev Cetin; Cetinkaya, Ozgul Kaya; Sayiner, Ayca Arzu; Seydaoglu, Gulsah; Ozkaratas, Emre; Abacioglu, Hakan
Background/Aims: Hepatitis C virus (HCV) prevalence is 1% in Turkey with genotype 1 being the predominant type traditionally. However unique geographical location of Turkey and increasing human migration in the region influences the epidemiology of the infection. The aim of this study was to determine the changes in distribution of HCV genotypes and risk factors. Materials and Methods: In this retrospective single-center study, HCV genotyping results of 558 patients were evaluated in between 2005 and 2016.Three different HCV genotyping assays were used during the 12-year study period;restriction fragment length polymorphism (RFLP), Abbott Real Time HCV Genotype II and Bosphore HCV genotyping kit. Results: The most prevalent HCV genotype was genotype 1 detected in 88.4% of the patients followed by genotype 3 (5.2%),genotype 4 (2.9%),genotype 2 (2.1%), mixed genotypes (1.1%) and genotype 5 (0.3%). Genotype 1a showed an increasing prevalence. There were 19 patients (3.4%) either of foreign nationalities or Turkish citizens living abroad. Genotype 3 was the most common type among these patients which 10.3% had intravenous drug use history. Syrian migrant population differed in terms of HCV genotypes. Genotype 5 detected in two Syrian patients, which is the first report of HCV type 5 in Western Turkey. Among the HCV genotype 4 infected patients, 31.3% were Syrians. Conclusion: Our study showed that although genotype 1b dominance continues, the distribution and prevalence of HCV genotypes are changing in our region mainly due to migration and increase in the frequency of patients with non-traditional risk factors such as intravenous drug use. Monitoring the epidemiology of HCV genotypes may provide guidance in treatment decisions.
Validation of a Multiplex Qrt-PCR Assay for the Detection of RSV, Influenza A/B Virus and SARS-CoV
(BMC, 2026) Bulgurcu, Alihan; Sayiner, Ayca Arzu
The significant burden of viral respiratory diseases necessitates rapid detection of key pathogens. Simultaneous testing for SARS-CoV-2, RSV, and influenza A/B as an initial step, followed by broader panels as needed, offers a cost-effective diagnostic strategy. This study aimed to validate a new commercial multiplex qRT-PCR assay (Diagnovital (R) RTA Laboratories, Turkey) for the simultaneous detection of these viruses. Analytical sensitivity was determined using Probit regression analysis on serial dilutions (10(5)-10(1) copies/ml) for each target virus. Specificity was evaluated with 120 negative samples and 32 positive samples for non-target respiratory viruses. External quality control panels and clinical specimens positive for RSV (n = 39), influenza A/B (n = 71), SARS-CoV-2 (n = 64) were used for accuracy testing. Intra- and inter-assay precision were analyzed using samples near the limit of detection. The performance was compared to routine diagnostic tests. The assay's analytical sensitivity was 420.7, 296.7, 368.6, 1362.6, and 1459.7 copies/ml for SARS-CoV-2 Alpha and Omicron variants, influenza A, influenza B, and RSV, respectively. Analytical specificity was 100%, and precision showed CV% < 5. Detection rates for SARS-CoV-2, influenza A, influenza B, and RSV were 100%, 95.1%, 97.5%, and 94.8%, respectively, with false negatives occurring in samples with Ct > 33. Comparative analysis showed high correlations between assays, with strong agreement (Cohen's kappa ranging from 0.861 to 1). These findings demonstrate the clinical applicability of the Diagnovital (R) assay, though false negatives may occur in low-concentration samples.