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 Citation - Scopus: 3Clinical Impact of Hepatitis C Virus Genomic Variations(Ankara Microbiology Society, 2015-10-08) Ergünay K.; Abacioglu H.; Ergünay, Koray; Abacioglu, HakanHepatitis C virus (HCV) is a globally-dispersed agent of chronic hepatitis with a significant public health threat, affecting over 110 million individuals throughout the world. The increased risk for chronicity after exposure and the lack of a protective vaccine make HCV is a leading infectious cause of cirrhosis, liver failure requiring transplantation and hepatocellular carcinoma. The replicative process and infection dynamics in the host enable HCV to generate an array of closely-related but non-identical genetic variants known as quasispecies in the infected individuals. Pathogenesis and outcome in HCV infections are directly affected by the virus genetic heterogeneity, reflected as the emergence of quasispecies in infected individuals. The evolution of these highly-diverse viral populations in the host directly influences the disease course, via providing a pool of variants capable of resuming viral replication under extrinsic and/or intrinsic selective pressures. Viral quasispecies go through several alterations during the course of the infection, and provide a background for the selection of escape mutants from the host humoral and cell-mediated immune responses and antiviral treatment. Supported by the robust next generation sequencing techniques, recent studies have provided significant insights on the genomic diversity and progression as well as on the origin and the epidemiology of HCV. This review provides an overview of the mechanisms of HCV genetic variability, and the interactions with the host, that affects clinical disease, covering viral and host determinants of humoral and cell-mediated immune responses, alterations during the early and late stages of the infection and disease progression leading to chronicity. In addition, current findings in virus evolution and epidemiology were briefly interpreted from the inter-species and population perspectives. The impact of viral genomic heterogeneity on antiviral treatment in the era of direct-acting agents is also discussed, along with an overview of current methods employed for the characterization of viral diversity.