Browsing by Author "Bozdayi, Gulendam"

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Detection of HPV DNA in Esophageal Lesions: a Cross-Sectional Study
(2020) Dinc, Bedia; Altay-Kocak, Aylin; Aydog, Gulden; Kuran, Sedef; Akoglu, Musa; Ozkan, Secil; Bozdayi, Gulendam; 32162873
Background: Several studies have documented human papillomavirus (HPV) in extra-cervical tumors. We aimed to detect HPV type 16 and HPV other than type 16 (OT-16) DNA in esophageal papilloma and esophagus squamous cell carcinoma (ESCC) samples and to compare clinicopathological features of HPV positive and negative patients. Methods: Materials were obtained from a tertiary care public hospital and studied in an university hospital for this cross-sectional study. Seventy-six tissue samples (50 papilloma and 26 ESCC) were included. After deparaf-finization by xylene and DNA extraction by phenol chloroform-isoamyl-alcohol, 76 samples were studied with a G6PDH control kit. Forty-four papilloma and 21 ESCC samples with enough tissues were studied for HPV DNA. HPV OT-16 DNA and HPV type 16 were detected by real time-polymerase chain reaction. Results: Twelve (27.3%) and one (2.3%) of the papilloma samples were HPV type 16 and other than type 16 positive, respectively. Eleven (52.4%) and one (4.8%) of ESCC samples were HPV type 16 and mixed type positive, respectively. Conclusions: We suggest that HPV infection is common in esophageal papilloma and ESCC. Due to the wellknown association of HPV with premalignant and malignant conditions, follow-up of these patients accompanied by HPV should be implemented.
Emergence of rotavirus G9 in 2012, as the dominant genotype in Turkish children with diarrhea, in a university hospital in Ankara
(2019) Kocak, Aylin Altay; Aydin, Merve; Matsumoto, Takashi; Yahiro, Takaaki; Dalgic, Buket; Bozdayi, Gulendam; Ahmed, Kamruddin
Introduction: Rotavirus infection is a major cause of morbidity and mortality in infants and young children with diarrhea throughout the world. Material and Methods: In this study, we aimed to determine the detection rate of rotavirus infection in 181 children less than 5 years of age presenting with acute gastroenteritis and admitted to a tertiary care hospital in Ankara, Turkey, from April to November 2012. We documented the epidemiological data by elucidating the prevalent genotypes. Stool specimens were collected, and rotavirus antigen in the samples was detected using ELISA. G and P genotypes were determined by RT-PCR via type specific primers. The nucleotide sequence of the concerned genes was determined by Sanger sequencing and phylogenetic analysis was performed by neighbor-joining method. Results: Of the 181 samples, 28 (15.5%) were positive for the rotavirus antigen. Twenty-seven samples were positive for G genotypes and 21 were positive for P genotypes. Genotypes G1 (7.1%), G2 (7.1%), G3 (7.1%), G4 (3.6%), G9 (71.5%) and P4 (3.6%), P8 (71.4%) were identified. Genotype G9P[8] (50%) was predominant in the combination of G and P genotypes. Most of the G9 strains of this study formed an independent cluster in Lineage III, except two strains which clustered with an Ethiopian G9 strain of 2012. Conclusions: It seems that during 2012 season, genotype G9P[8] increased significantly in Ankara due to a new circulating strain of G9.
Investigation of Group A Rotavirus G10, G12 Genotypes Emerging in Patients with Acute Gastroenteritis in a Tertiary Care Hospital
(2021) Kahraman, Hande; Kocak, Aylin Altay; Albakkour, Katren; Muftah, Hager; Dalgic, Buket; Caglar, Kayhan; Ahmed, Kamruddin; Bozdayi, Gulendam; 34666655
Rotaviruses are the most common cause of viral gastroenteritis with the highest mortality and morbidity rates in children aged 0-5 years. The aim of this study was to determine the frequency of rotavirus infection in patients whose stool samples were sent to microbiology laboratory to investigate the etiology of diarrhea, to investigate the rotavirus genotypes that are common in our region and G10, G12 genotypes that have recently become common in the world. Fecal samples of 476 patients aged between 0-92 years who applied between November 2016 and February 2018 were studied via immunochromatographic rapid test and enzyme-linked immunosorbent assay (ELISA) methods. ELISA positive samples were studied by nested reverse transcriptase chain reaction (RT-PCR) and genotyped by agarose gel electrophoresis. Rotavirus was found positive in 18.3% and 17% of stool samples by immunochromatographic test and ELISA, respectively. All ELISA positive samples were also detected as positive by RT-PCR. 18.5% of female patients and 15.7% of male patients were found to be positive and rotavirus positivity was not statistically significant between genders. The frequency of rotavirus in different age groups was 23.5% (6-12 years), 17.3% (13-24 months) and 16% (25-36 months). It was determined that rotavirus cases were most common in the spring. G1, G2, G3, G4, G9, G10, and G12 were detected in 37%, 7.4%, 16.1%, 6.2%, 9.9%, 2.5%, 26% of the samples, respectively. G12 was the most common genotype after G1. The most common G and P genotype combination was G1P[8] (17.2%). This was followed by G12P[8] (11.11%) and G3P[8] (11.11%). P[8] (53%) was found to be the dominant P genotype. In this study, it was observed that rotavirus, which is the cause of childhood diarrhea, can also be encountered in advanced ages and even new genotypes that infect humans worldwide may also be the causative agents. Therefore, we concluded that it is important to investigate new genotypes such as G10 and G12 in molecular epidemiological studies.
Investigation of JC Virus Positivity By Real-time Polymerase Chain Reaction in Patients with Hematopoietic Stem Cell Transplant
(2020) Colak, Meryem; Kocak, Aylin Altay; Kaynar, Lale Aydin; Ozkurt, Zubeyde Nur; Yegin, Zeynep Arzu; Bozdayi, Gulendam; 0000-0002-0451-0142; AAI-8012-2021
Introduction: In immunocompromised hosts, JC virus (JCV) can reactivate and cause a lytic infection of oligodendrocytes, resulting in progressive multifocal leukoencephalopathy (PML). Bone marrow is an important reservoir and possible site of neurotropic transformation for JCV. The aim of this retrospective study was to investigate the prevalance of JCV infection by real-time polymerase chain reaction (PCR) in patients sent from bone marrow transplant service to the laboratory in our hospital. Materials and Methods: A total of 153 clinical samples obtained from 62 patients with hematopoietic stem cell transplant between December 2013 and April 2018 were included into the study. Viral nucleic acids were extracted from the samples with QIAamp DSP Virus Kit in EZ1 Advanced (Qiagen, Germany) device. Isolated viral DNA was amplified with Real Star (R) JCV PCR Kit in Rotor-GeneQ (Altona, Germany) and JCV DNA was detected with qualitative method. Results: Sixty-two patients, 35 (56.5%) males and 27 (43.5%) females, between 18 years and 71 years of age were included into the study. Total JCV DNA positivity rate was found as 11.1% (17/153). Patients' diagnosis was respectively as follows: 45.2% acute myeloid leukemia, 19.4% acute lymphoblastic leukemia, 9.7% multiple myeloma. 6.4% myeloblastic sendrome, 6.4% non-Hodgkin lymphoma, 6.4% Hodgkin lymphoma, and 6.4% anemia. The distribution of JCV DNA positivity rates was found respectively as 40% acute myeloid leukemia, 30% multiple myeloma, 10% Hodgkin lymphoma, 10% acute lymphoblastic leukemia and 10% Non-hodgkin lymphoma. It was observed that 50% of JCV DNA positive patients died in the follow-up period after hematopoietic stem cell transplantation. Conclusion: It is not possible to diagnose JCV infections clinically because they are usually asymptomatic. However, up to 90% of those diagnosed with PML die within the first six months receiving a diagnosis. Detection and clinical surveillance JCV DNA by real-time PCR for hematopoietic stem cell transplantation patients is important for early diagnosis and treatment.
Multi-assay investigation of viral etiology in pediatric central nervous system infections
(2020) Altay-Kocak, Aylin; Bozdayi, Gulendam; Michel, Janine; Polat, Meltem; Kanik-Yuksek, Saliha; Tezer, Hasan; Ozkul, Aykut; Ahmed, Kamruddin; Nitsche, Andreas; Ergunay, Koray; 32683347
Introduction: In an attempt to identify a wide spectrum of viral infections, cerebrospinal fluid (CSF) specimens were collected from pediatric cases with the preliminary diagnosis of viral encephalitis/meningoencephalitis in two reference hospitals, from October 2011 to December 2015. Methodology: A combination of nucleic acid-based assays, including in house generic polymerase chain reaction (PCR) assays for enteroviruses, flaviviruses and phleboviruses, a commercial real-time PCR assay for herpesviruses and a commercial real time multiplex PCR, enabling detection of frequently-observed viral, bacterial and fungal agents were employed for screening. Results: The microbial agent could be characterized in 10 (10%) of the 100 specimens. Viral etiology could be demonstrated in 7 (70%) specimens, which comprises Human Herpesvirus 6 (4/7), Herpes Simplex virus type1 (2/7) and Enteroviruses (1/7). In 3 specimens (30%), Streptococcus pneumoniae, Listeria monocytogenes and Staphylococcus aureus were detected via the multiplex PCR, which were also isolated in bacteriological media. All specimens with detectable viral nucleic acids, as well as unreactive specimens via nucleic acid testing remained negative in bacteriological cultures. Conclusions: Herpes and enteroviruses were identified as the primary causative agents of central nervous system infections in children. Enterovirus testing must be included in the diagnostic work-up of relevant cases.
The prevalence and distribution of human papillomavirus in 4267 Turkish women with or without cervical lesions: A hospital-based study
(2022) Altay-Kocak, Aylin; Kazanci, Ferah; Dogu-Tok, Canan; Onan, Anil; Erdem, Ozlem; Ozkan, Secil; Bozdayi, Gulendam; 0000-0002-0451-0142; 35676203; AAI-8012-2021
In the present study, it was aimed to screen the genotypes of human papillomavirus (HPV) retrospectively in women with gynecological symptoms who were admitted to a tertiary care university hospital in Ankara, Turkey. A total of 4267 cervical swab samples of women aged 18-79 years were sent to Medical Virology Laboratory from January 2017 to November 2020. Nucleic acid extraction and amplification of samples were done by an automated system. The test can detect 14 high-risk HPV (HR-HPV) types in a single analysis that performs a real-time polymerase chain reaction, by providing individual results on the highest-risk genotypes HPV 16 and HPV 18 and pooled results on other high-risk genotypes (OHR-HPV) (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68). HPV DNA positivity was detected in 14.2% (605/4267) of the samples. HPV type 16 and type 18 were detected in 2.4% and 0.7% of the samples, respectively. OHR-HPV types were found in 8.8% of the samples. Of the 1.9% and 0.4% samples had mixed types with type 16+ OHR-HPV and type 18+ OHR-HPV, respectively. The results of this study presented the rates of HR-HPV genotypes of a university hospital in Ankara, over a 4-year period. It was observed that the positivity rate of type 18 is decreasing and some OHR-HPV types are increasing. HPV vaccination is not in the national immunization program in Turkey yet, however, HPV vaccines are available and the vaccination rates for women are increasing.
Relationship between chest computed tomography findings and clinical conditions of coronavirus disease (COVID-19): A multicentre experience
(2021) Yilmaz Demirci, Nilgun; Ugras Dikmen, Asiye; Tasci, Canturk; Dogan, Deniz; Arslan, Yakup; Ocal, Nesrin; Tasar, Mustafa; Bozlar, Ugur; Artuk, Cumhur; Yilmaz, Gulden; Karacaer, Zehra; Avci, Ismail Yasar; Tuncer Ertem, Gunay; Erdinc, Fatma Sebnem; Kinikli, Sami; Altun Demircan, Serife; Ergun, Elif; Nercis Kosar, Pinar; Karakoc, Ayse Esra; Gokcek, Atila; Aloglu, Melike; Gulgosteren, Sevtap; Atikcan, Sukran; Akcay, Sule; Erol, Cigdem; Hekimoglu, Koray; Cerit, Mahi Nur; Erbas, Gonca; Ozger, Hasan Selcuk; Bozdayi, Gulendam; Senol, Esin; Yurdakul, Ahmet Selim; Yilmaz, Aydin; 0000-0002-2535-2534; 0000-0002-0805-0841; 34105857; AAJ-1219-2021; AAD-9097-2021
Aims This study aimed to investigate the clinical and chest computed tomography (CT) features associated with clinical parameters for coronavirus disease (COVID-19) in the capital of Turkey, Ankara. Materials and methods Epidemiological, clinical features, laboratory findings and radiological characteristics of 1563 hospitalised patients with COVID-19 in Ankara were collected, reviewed and analysed in this study. The risk factors associated with disease severity were investigated. Results Non-severe (1214; 77.7%) and severe cases (349; 22.3%) were enrolled in the study. Compared with the non-severe group, the severe group were significantly older and had more comorbidities (ie, hypertension, diabetes mellitus, cardiovascular disease and chronic kidney disease). Smoking was more common in the severe group. Severe patients had higher respiratory rates and higher incidences of cough and dyspnoea compared with non-severe patients. Compared with the non-severe patients, the severe patients had increased C-reactive protein (CRP), procalcitonin, neutrophil to lymphocyte ratio (NLR) and CRP/albumin ratio and decreased albumin. The occurrence rates of consolidation, subpleural sparing, crazy-paving pattern, cavity, halo sign, reversed halo sign, air bronchogram, pleural thickening, micronodule, subpleural curvilinear line and multilobar and bilateral involvement in the CT finding of the severe patients were significantly higher than those of the non-severe patients. Conclusions Many factors are related to the severity of COVID-19, which can help clinicians judge the severity of the patient and evaluate the prognosis. This cohort study revealed that male sex, age (>= 55 years), patients with any comorbidities, especially those with cardiovascular disease, dyspnoea, increased CRP, D-dimer and NLR, and decreased lymphocyte count and CT findings of consolidation and multilobar involvement were predictors of severe COVID-19.
Retrospective evaluation of viral respiratory tract infections in a university hospital in Ankara, Turkey (2016-2019)
(2022) Altay-Kocak, Aylin; Sarzhanova, Shakhnoza; Tapisiz, Anil; Dizbay, Murat; Basustaoglu, Ahmet; Bozdayi, Gulendam; 0000-0002-0451-0142; 35656958; AAI-8012-2021
Introduction: Viruses are responsible for two-thirds of all acute respiratory tract infections. This study aims to retrospectively detect respiratory tract viruses in patients from all age groups who visited the hospital. Methodology: A total of 1592 samples from 1416 patients with respiratory tract symptoms were sent from several clinics to the Molecular Microbiology Laboratory at Gazi University Hospital from February 2016 to January 2019. Nucleic acid extraction from nasopharyngeal swabs, throat swabs or bronchoalveolar lavage (BAL) samples sent to our laboratory was done using a commercial automated system. Extracted nucleic acids were amplified by a commercial multiplex-real time Polymerase Chain Reaction (PCR) method, which can detect 18 viral respiratory pathogens. Results: Among 1592 samples, 914 (57.4%) were positive for respiratory viruses. The most prevalent were rhinovirus (25.2%) and influenza A virus (12.1%), the least prevalent was the bocavirus (2.6%). Rhinovirus was the most detected as a single agent (21.2%, 194/914) among all positive cases, followed by coronavirus (9.3%, 85/914). The detection rates of coronavirus, human adenovirus, respiratory syncytial virus A/B, human parainfluenza viruses, human metapneumovirus-A/B, human parechovirus, enterovirus and influenza B virus were 9.9%, 8%, 7.7%, 5%, 3.4%, 3.1%, 3%, and 2.8%, respectively. Conclusions: The most detected viral agents in our study were influenza A virus and rhinovirus. Laboratory diagnosis of respiratory viruses is helpful to prevent unnecessary antibiotic use and is essential in routine diagnostics for antiviral treatment. Multiplex Real-time PCR method is fast and useful for the diagnosis of viral respiratory infections.
The Role of Human Parvovirus B19 in the Pediatric Patients with Pancytopenia?
(2019) Colak, Meryem; Kocak, Aylin A.; Dinc, Bedia; Kaya, Zuhre; Kocak, Ulker; Yenicesu, Idil; Bozdayi, Gulendam; https://orcid.org/0000-0002-0451-0142; 31850715; AAI-8012-2021
Background: Parvoviruses are small DNA viruses causing erythema infectiosum, which is known as the fifth disease. The aim of this study was to investigate the presence of Parvovirus B19 DNA by Real-Time-PCR retrospectively in clinical samples of children diagnosed as acute leukemia and aplastic anemia when investigating the cause of pancytopenia and to investigate its relationship with the clinical manifestations. Methods: The study samples were collected between March 2014 and March 2018 in Gazi University, Faculty of Medicine, Department of Pediatric Hematology. Sixty pediatric patients; 37 males and 23 females, were included in the study. Nucleic acid isolation was performed by using MagNA-Pure Compact Nucleic Acid Isolation Kit (Roche, Germany). Extracted DNA was studied with LightCycler (R) 2.0 using the Real-Time PCR method and LightCycler (R) Parvovirus B19 Quantification Kit (Roche, Germany), and the results were evaluated quantitatively. Parvovirus B19 DNA detection interval of the kit was 10(1) - 10(6) copies/mL. Results: Sixty serum samples were investigated and 8.3% (5/60) Parvovirus B19 DNA positivity was determined. Of the five patients with Parvovirus B19 DNA positivity, three had acute lymphoblastic leukemia and two were diagnosed as aplastic anemia. Regarding viral load; 2/5, 1/5, 1/5, and 1/5 of the samples had a viral load of 10(2), 10(3), 104, and 105 copies/mL, respectively. Parvovirus B19 DNA positivity was detected in samples from March (2/5), April (2/5), and August (1/5). Conclusions: Patients with acute leukemia and aplastic anemia in childhood using immunosuppressive drugs, blood, and blood products during chemotherapy, encounter Parvovirus B19 infections in the follow-up period and are diagnosed by serological and molecular methods. As a result of the study, we suggest that the detection of Parvovirus B19 DNA by Real-Time PCR method in children being admitted with pancytopenia and diagnosed as acute leukemia and aplastic anemia is useful in the follow-up and treatment.
Should We Accept the HPV Type 66 into a Probable High-Risk Group? The Prevalence, Clinical and Histopathological Evaluation of HPV Type 66 in Gazi University, Ankara
(2021) Kazanci, Ferah; Kocak, Aylin Altay; Colak, Meryem; Erdem, Ozlem; Onan, M. Anil; Bozdayi, Gulendam; 0000-0002-0451-0142; AAI-8012-2021
Introduction: The prevalence of infection by different genotypes of human papillomavirus (HPV) varies among different geographic areas. The objective of the study is to determine the prevalence and distribution of HPV66 genotype among women with normal or abnormal Pap smear tests. Methods: This retrospective study was conducted in a tertiary care university hospital between January 2017 and February 2018, in central Anatolia of Turkey. This study included 288 women, 66 (%22.9) of whom had HPV DNA positive. HPV DNA screening was done by an automatized system using real time PCR method (Cobas 4800 System, Roche Diagnostics Ltd, Switzerland) and this method distinguishes types 16 and 18, while the other 12 oncogene types are reported as high-risk HPV (HR-HPV: 31,33,35,39,45,51,52,56,58,59,66,68). For the genotyping of other oncogene types, a commercial real time PCR method (NLM Genotypes 14 Real-TM Quant, NLM Diagnostic, Italy) was used. Results: The most common identified HPV types were HPV16 (%6.3), HPV 56 (%3.8), HPV 18(%3.1), HPV 66 (%3.1), HPV 51 (%2.8), HPV 52(%2.1). HPV type 66 which has admitted recently other-subtypes with their unclear oncogenicity is the third most identified type in our study. In our study 9 (%3.1) women had type 66 and 2 (%0.7) of whom had abnormal Pap smear results. One patient with syphilis whose pap smear test results was ASC-H/HSIL was evaluated by colposcopic examination and LEEP (Loop Electrosurgical Excision Procedure) and ECC (Endocervical Curettage) were performed. The result of histopatological report was benign. The other patient whose Pap smear test result was LSIL evaluated by colposcopic examination and found no pathological finding. Conclusion: The frequency of HPV 66 infection was found to be higher in our study compared to previous reports. In 2 patients out of 9 cases (% 2.4) who were detected HPV 66 had normal pap test results.