Diagnostic Utility of Cytomegalovirus (CMV) DNA Quantitation in Ulcerative Colitis.

Cytomegalovirus (CMV) colitis is a critical condition associated with severe complications in ulcerative colitis (UC). This study aimed to investigate the diagnostic value of the presence of CMV DNA in intestinal mucosa tissue and blood samples in patients with active UC. This study included 81 patients with exacerbated symptoms of UC. Patient data were obtained from the Hospital Information Management System. CMV DNA in colorectal tissue and plasma samples were analyzed using a real-time quantitative PCR assay. CMV markers were detected using immunohistochemistry and hematoxylin-eosin staining. Immunohistochemistry positivity was observed in tissue samples from eight (9.9%) patients. Only one (1.2%) patient showed CMV-specific intranuclear inclusion bodies. CMV DNA was detected in 63.0% of the tissues (median: 113 copies/mg) and in 58.5% of the plasma samples (median: 102 copies/mL). For tissues, sensitivity and the negative predictive value (NPV) for qPCR were excellent (100.0%), whereas specificity and the positive predictive value (PPV) were low (41.9% and 15.7%, respectively). For plasma, sensitivity and NPV were high (100.0%) for qPCR, whereas specificity and PPV were low (48.6% and 24.0%, respectively). CMV DNA ≥392 copies/mg in tissue samples (sensitivity 100.0% and specificity 83.6%) and ≥578 copies/mL (895 IU/mL) in plasma samples (sensitivity 66.7% and specificity 100.0%) provided an optimal diagnosis for this test. The qPCR method improved patient management through the early detection of CMV colitis in patients with UC. However, reliance on qPCR positivity alone can lead to overdiagnosis. Quantification of CMV DNA can improve diagnostic specificity, although standardization is warranted.

Development and validation of a simple risk scoring system for a COVID-19 diagnostic prediction mode.

Introduction: In a resource-constrained situation, a clinical risk stratification system can assist in identifying individuals who are at higher risk and should be tested for COVID-19. This study aims to find a predictive scoring model to estimate the COVID-19 diagnosis." Materials: Patients who applied to the emergency pandemic clinic between April 2020 and March 2021 were enrolled in this retrospective study. At admission, demographic characteristics, symptoms, comorbid diseases, chest computed tomography (CT), and laboratory findings were all recorded. Development and validation datasets were created. The scoring system was performed using the coefficients of the odds ratios obtained from the multivariable logistic regression analysis." Result: Among 1187 patients admitted to the hospital, the median age was 58 years old (22-96), and 52.7% were male. In a multivariable analysis, typical radiological findings (OR= 8.47, CI= 5.48-13.10, p< 0.001) and dyspnea (OR= 2.85, CI= 1.71-4.74, p< 0.001) were found to be the two important risk actors for COVID-19 diagnosis, followed by myalgia (OR= 1.80, CI= 1.08- 2.99, p= 0.023), cough (OR= 1.65, CI= 1.16-2.26, p= 0.006) and fatigue symptoms (OR= 1.57, CI= 1.06-2.30, p= 0.023). In our scoring system, dyspnea was scored as 2 points, cough as 1 point, fatigue as 1 point, myalgia as 1 point, and typical radiological findings were scored as 5 points. This scoring system had a sensitivity of 71% and a specificity of 76.3% for a cut-off value of >2, with a total score of 10 (p< 0.001). Conclusions: The predictive scoring system could accurately predict the diagnosis of COVID-19 infection, which gave clinicians a theoretical basis for devising immediate treatment options. An evaluation of the predictive efficacy of the scoring system necessitates a multi-center investigation.

[Investigation of Ganciclovir Resistance in Cytomegalovirus Isolates by Phenotypic and Genotypic Methods]. / Sitomegalovirüs Izolatlarinda Gansiklovir Direncinin Fenotipik ve Genotipik Yöntemlerle Arastirilmasi.

Ganciclovir-resistant cytomegalovirus (CMV) strains are reported following long-term antiviral agent use, especially for immune-suppressive patients. In this study, it was aimed to investigate the mutations in the UL97 gene of CMV, which causes ganciclovir (GCV) resistance by genotypic and phenotypic methods in patients who developed CMV infection following hematopoietic cell (HCT) or solid organ transplantation (SOT). Thirty patients who had HCT or SOT in Mediterranean University Hospital and developed CMV infection during routine follow-up with a viral load of CMV over 1000 copies/mL were included in the study. CMV DNA was analyzed by an automated system (Cobas Ampliprep/COBAS TaqMan CMV Test, Roche Diagnostics, Germany) quantitatively. DNA sequence analysis of the regions including codons 420-664 in the UL97 gene region was done by the Sanger sequencing method to detect mutations causing antiviral resistance and compared with defined mutations. In order to investigate antiviral resistance by phenotypic methods, heparinized blood samples of the patients were collected, 'buffy coat (leukocyte layer)' was inoculated into MRC-5 cells by centrifugation method and CMV growth in these cells was controlled with monoclonal antibodies when growth was detected, virus titer was determined and plaque reduction test was applied as recommended. It was determined that 22 of the 30 patients were HCT recipients and eight were SOT (five kidney, three liver) recipients. When the CMV serology pattern of the patients was evaluated before transplantation, 29 (96.7%) patients were found to be seropositive and one (3.3%) patient was found to be seronegative. Totally, nine CMV UL97 mutations were detected in seven (23.3%) pediatric patients who had HCT, including six seropositive and one seronegative case. In addition, one mutation (D605E) not known to cause GCV resistance was detected in a seronegative recipient and three previously unidentified mutations were detected (1474T, F499S, V559A) in a seronegative recipient. Five of the mutations defined were UL97 mutations with a defined clinical resistance against GCV in each of the five recipients (C603W, C592G, H520Q, M460V, A594T). In the plaque reduction test using 3 µM, 12 µM, 48 µM and 96 µM concentrations of GCV in CMV strains, the IC50 value was determined to be ≥ 8 µM for the five CMV strains, and the phenotypic presence of GCV resistance was shown. Clinical resistance associated with CMV UL97 mutation was detected in five (22.7%) of 22 patients who had HCT. GCV resistance was also demonstrated in these patients by phenotypic methods. No UL97 mutation was detected in the patients who had SOT.

Is There a Role for Dark Field Microscopy in the Diagnosis of Lyme Disease?A Narrative Review.

The diagnosis of Lyme disease is becoming more common in Turkey. Nonetheless, some physicians are not aware of the diagnostic principles that should be followed when faced with a suspected patient and could use tests that are not recommended, such as darkfield microscopy. Dark field microscopy is a diagnostic technique to visualize the spirochetes that cause Lyme disease; however, it is not recommended for the diagnosis of Lyme disease. One of the main limitations of dark field microscopy is its low sensitivity. Another limitation is its high false-positivity rate, as other microorganisms and cellular debris can be mistaken for spirochetes, leading to a misdiagnosis thatmay result in unnecessary treatment. Therefore, this study aimed to review the literature on the role of dark field microscopy as a diagnostic method for Lyme disease and inform physicians about recommended approaches in line with the recommendations of national or international guidelines. An electronic search of Pubmed, Scopus, and Web of Science was performed using the following medical subject headings (MeSH) search terms: Lyme borreliosis, Lyme disease, Borrelia burgdorferi, diagnosis, and microscopy. With this narrative review, we aimed to inform physicians better and improve patient care for patients with suspected Lyme disease.

Tocilizumab treatment in COVID-19: A prognostic study using propensity score matching.

BACKGROUND: The potential role of interleukin-6 (IL-6) in coronavirus disease 2019 (COVID-19) pneumonia provides the rationale for investigating IL-6 signaling inhibitors. OBJECTIVES: To evaluate and report treatment responses to tocilizumab (TCZ) in COVID-19 patients and compare mortality outcomes with those of standard care. MATERIAL AND METHODS: Patients hospitalized with a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, diagnosed with reverse transcription polymerase chain reaction (RT-PCR) between March 2020 and April 2021, were enrolled in this single-center retrospective cohort study. Propensity score matching was performed in order to reduce confounding effects secondary to imbalances in receiving TCZ treatment. RESULTS: A total of 364 patients were included in this study. Two hundred thirty-six patients received standard care, while 128 patients were treated with TCZ in addition to standard care (26 (20.3%) patients received a dose of 400 mg intravenously once, while 102 (79.7%) patients received a total dose of 800 mg intravenously). In the propensity score-matched population, less noninvasive mechanical ventilation (p = 0.041) and mechanical ventilation support (p = 0.015), and fewer deaths (p = 0.008) were observed among the TCZ-treated patients. The multivariate adjusted Cox regression model showed a significantly higher survival rate among TCZ patients compared to controls (hazard ratio (HR): 0.157, 95% confidence interval (95% CI): 0.026-0.951; p = 0.044). The hazard ratio for mortality in the TCZ group was 0.098 (95% CI: 0.030-0.318; p = 0.0001 using log-rank test). CONCLUSIONS: This study determined that TCZ treatment in COVID-19 patients was associated with better survival, reduced need for mechanical ventilation and reduced hospital-associated mortality.

Effect of oral antiseptics on the viral load of SARS-CoV-2: A randomized controlled trial.

BACKGROUND: In the oral cavity, which plays an important role in the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is possible to reduce the viral load of SARS-CoV-2 with antiseptics, thereby minimizing the transmission of the virus during dental procedures. OBJECTIVES: The aim of this study was to clinically evaluate the effect of the hypochlorous acid (HClO) and povidone-iodine (PVP-I) solutions on the oral viral load of SARS-CoV-2. MATERIAL AND METHODS: This randomized controlled trial was conducted on 75 patients hospitalized in the COVID-19 ward of a local hospital. All the patients included in the study were within the first 24 h of hospitalization and the first 5 days of coronavirus disease 2019 (COVID-19) symptoms. The viral load of mouthwash samples was measured with the cycle threshold (Ct) value of SARS-CoV-2 through a realtime reverse transcription polymerase chain reaction (RT-PCR). The patients were divided into 3 groups. The effect on the patient's SARS-CoV-2 viral load was investigated after gargling the mouths and throats for 30 s with HClO, PVP-I and isotonic saline. First, a sample was taken after gargling with isotonic saline, then another sample was taken after gargling for 30 s with a particular antiseptic to determine the viral load of SARS-CoV-2. RESULTS: Comparing the before and after mouthwash samples from all 3 groups, there were no statistically significant differences in the Ct values before and after gargling (p > 0.05). However, there were statistically significant differences in the number of negative samples after the use of HClO and PVP-I, which were positive before gargling (p < 0.05). CONCLUSIONS: In the light of the data obtained in this study, there is insufficient evidence that gargling with HClO or PVP-I reduces viral load. Taken together, these findings imply no role for antiseptics in the transmission of SARS-CoV-2 by the aerosol generated during dental procedures, or more generally, SARS-CoV-2 infection control.

Prognostic factors for COVID-19 patients.

INTRODUCTION: Determining prognostic factors in patients with coronavirus disease (COVID-19) can have great impact on treatment planning and follow-up strategies. Herein, we aimed to evaluate prognostic factors and clinical scores for confirmed COVID-19 patients in a tertiary-care hospital in the Bursa region of Turkey. METHODOLOGY: Patients who had been diagnosed with COVID-19 microbiologically and/or radiologically between March and October 2020 in a tertiary-care university hospital were enrolled retrospectively. Adult patients (≥ 18 years) with a clinical spectrum of moderate, severe, or critical illness were included. The dependent variable was 30-day mortality and logistic regression analysis was used to evaluate any variables with a significant p value (< 0.05) in univariate analysis. RESULTS: A total of 257 patients were included in the study. The mortality rate (30-day) was 14.4%. In logistic regression analysis, higher scores on sequential organ failure assessment (SOFA) (p < 0.001, odds ratio (OR) = 1.86, 95% CI = 1.42-2.45) and CURB-65 pneumonia severity criteria (p = 0.001, OR = 2.60, 95% CI = 1.47-4.57) were found to be significant in predicting mortality at admission. In deceased patients, there were also significant differences between the baseline, day-3, day-7, and day-14 results of D-dimer (p = 0.01), ferritin (p = 0.042), leukocyte (p = 0.019), and neutrophil (p = 0.007) counts. CONCLUSIONS: In our study of COVID-19 patients, we found that high SOFA and CURB-65 scores on admission were associated with increased mortality. In addition, D-dimer, ferritin, leukocyte and neutrophil counts significantly increased after admission in patients who died.

Association of SARS-CoV-2 cycle threshold (Ct) values with clinical course and serum biomarkers in COVID-19 patients.

INTRODUCTION: Our knowledge has gaps regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication levels and its association to severity of Coronavirus disease 2019 (COVID-19). The aim of this study was to investigate the association of SARS-CoV-2 viral load with disease severity and serum biomarkers in COVID-19 patients. METHODOLOGY: Viral load was determined via cycle threshold (Ct) values of SARS-CoV-2 real-time reverse transcriptase-polymerase chain reaction (RT-PCR) in 214 adult patients. Ct values were compared with clinical severity, biochemical and hematological biomarkers. RESULTS: Clinical course of the disease was mild (49.1%), moderate (40.2%), and severe (10.7%). Median Ct value was 28.2 (IQR: 22.2-33.8) during the first week of the disease. Ct values were lower within five days after symptom onset [lowest Ct value on the third day (median: 24, IQR: 20.6-32.3)], but they increased significantly during the second and third weeks. No association was detected between admission Ct values and disease severity. Gender, age, co-morbidity, and mortality did not differ significantly in patients with low (≤ 25) and high (> 25) Ct values. White blood cell, neutrophil, platelet, and especially lymphocyte counts, were significantly lower in patients with low Ct values. CONCLUSIONS: No definitive/clear correlation between SARS-CoV-2 viral load and severity and mortality was found in the studied COVID-19 patients. However, neutrophil, platelet, and especially lymphocyte count were significantly lower in patients with a high viral load.

Comparison of SARS-CoV-2 Antibodies and Six Immunoassays in Pediatric and Adult Patients 12 Weeks After COVID-19.

Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific humoral immune persistence has been proposed to be affected by patients' characteristics. Moreover, available conflicting assay results are needed to be settled through comparative research with defined clinical specimens. Methods This prospective study investigated SARS-CoV-2-specific antibodies among 43 adults and 34 children at a mean of 12 weeks after the onset of COVID-19 symptoms using six serological assays and compared their performance. We used two Euroimmun (Euroimmun, Luebeck, Germany), two automated Roche Elecsys (Basel, Switzerland), and two rapid immuno-chromatographic Ecotest (Matrix Diagnostics, Assure Tech. (Hangzhou) Co., L, China) assays to investigate SARS-CoV-2 antibodies. Results The findings showed that the Roche Elecsys anti-S total test yielded the best positivity/sensitivity (children 94.1% and adults 93.0%; p = 0.877) while five immunoglobulin IgG targeting assays had similar positivity/sensitivity between children (88.2% to 94.1%) and adults (88.4% to 93.0%) (p > 0.05). Although IgM positivity was relatively low (p < 0.001), it was found in the majority of our pediatric and adult patients (67.6% and 86.0%, respectively; p = 0.098). SARS-CoV-2 S IgG titers were found to be higher among males in pediatric and adult groups compared to females (p = 0.027 and p = 0.041, respectively). Furthermore, we observed significantly higher antibody titers among pneumonia patients (p = 0.001). Conclusion Overall, we concluded SARS-CoV-2 antibody persistence over an average of 12 weeks after the onset of COVID-19 symptoms. While automated Roche Elecsys total antibody assays yielded the best sensitivity (> 90%) and five assays targeting IgG had acceptable performance. Patients with pneumonia and males have higher antibody titers. The effect of antibody persistence on re-infections should be monitored in longitudinal studies.

Nine-month course of SARS-CoV-2 antibodies in individuals with COVID-19 infection.

BACKGROUND: The continual course of the pandemic points to the importance of studies on the rate and durability of protective immunity after infection or vaccination. AIMS: In this study, we aimed to monitor anti-nucleocapsid (N) and anti-spike (S) antibodies against SARS-CoV-2 nearly 9 months duration after infection. METHODS: Anti-nucleocapsid (N) (at 11-15-20-29-38 weeks) and anti-spike antibodies (at 11 and 38 weeks) against SARS-CoV-2 were monitored during 38 weeks after the initial symptoms of COVID-19. RESULTS: Of 37 cases between 18 and 57 years old, 54% were women. The findings showed that anti-N antibodies decreased significantly after the 15th week (between 15 and 20 weeks, p = 0.016; 20-29 weeks, p = 0.0009; and 29-38 weeks, p = 0.049). At the 38th week, mean antibody levels decreased 35% compared to the 11th week, and 8% of the cases turned negative results. Anti-N antibody average level was 56.48 on the 11th week (the cut-off index threshold ≥ 1). It was estimated statistically that it would decrease to an average of 20.48 in weeks 53-62. In females, average antibody levels of all measurements were lower than males (p > 0.05). Anti-S antibody levels 14% increased at 38th week compared to 11th week (quantitative positivity threshold ≥ 0.8 U/ml), and no cases were negative at 38th week. CONCLUSIONS: Patients had ≥ 90% positivity after at least 9 months of symptoms, both anti-N and anti-S antibodies. In all samples, both anti-N and anti-S antibody levels were lower in females. The findings suggest that the quantitative values of anti-S antibodies remained high for at least 9 months and could provide protection.

Serological Prevalence of Toxoplasma gondii in Faculty of Medicine of Bursa Uludag University During 2016-2018

Objective: This study aimed to retrospectively investigate Toxoplasma gondii IgG and IgM distribution and IgG avidity in serum samples with suspected toxoplasmosis in the medical microbiology serology laboratory of Faculty of Medicine Hospital at Bursa Uludag University over a 24-month period (January 2016 to December 2018). Methods: An enzyme-linked fluorescent assay using the VIDAS automated analyzer (BioMérieux, France) was used to determine T. gondii IgM antibodies, T. gondii IgG antibodies, and T. gondii IgG avidity. Results: The T. gondii IgM antibody positivity was found to be 1.7% (101/6104), whereas the T. gondii IgG antibody positivity was 37.9% (1.149/3024). The seropositivity of T. gondii IgG was 31.5% in women belonging to the childbearing age group. In this group, T. gondii IgG high and low avidity rates were 70.1% (134/191) and 15.2% (29/191), respectively. Conclusion: Screening and diagnosis of toxoplasma serology in women of childbearing age is important. The results of this study may be useful for designing optimal control and preventive measures against T. gondii infection.

Changing epidemiology of influenza and other respiratory viruses in the first year of COVID-19 pandemic.

INTRODUCTION: We aimed to determine the epidemiological change in influenza and other respiratory tract viruses isolated from patients with nasopharyngeal swab samples in our hospital during the COVID-19 period. METHODS: We investigated nasopharyngeal swabs for respiratory viruses between March 2020 and February 2021 during the first year of pandemic in Turkey. We used QIAStat Dx Respiratory panel (Qiagen, Germany) in QIAStat Dx (Qiagen, Germany) for detection of respiratory viruses between March 2020 and February 2021. Respiratory panel kit included influenza A, B, influenza A H1N1, rhinovirus/enterovirus, parainfluenza (PIV) 1,2,3,4, coronaviruses (CoVs) NL 63, 229E, OC43 and HKU1, human metapneumovirus (MPV) A/B, bocavirus, respiratory syncytial virus (RSV) A/B and adenovirus. RESULTS: We retrospectively analyzed the results of 319 nasopharyngeal swab samples. The average age of 199 (62.4%) male and 120 (37.6%) female patients between the ages of 0-92 was 16 years. We found that 101 (31.7%) samples were positive for viruses. Rhino/enteroviruses were the most common viruses in all age groups. Influenza positivity rate during the first year of pandemic declined to 2.3% from 17.3% among the previous year. MPV infection activity did not change during the pandemic. DISCUSSION: According to our findings we argue that epidemiology of respiratory viruses has changed during the pandemic period. Despite the current clinical focus on the COVID-19 pandemic, clinicians should keep in mind that rhino/enterovirus and MPV infections may mimic COVID-19 and respiratory infections should be differentially diagnosed with rapid multiplex kits containing SARS-CoV-2, rhino/enterovirus and MPV.

[Distribution of Hepatitis C Virus (HCV) Genotypes Among Intravenous Drug and Non-Drug User Patients]. / Damar Içi Madde Bagimliligi Olan ve Madde Bagimlisi Olmayan Hastalar Arasinda Hepatit C Virus (HCV) Genotiplerinin Dagilimi.

Genotype distribution of hepatitis C virus (HCV) can vary over the years between different patient groups and regions. The prevalence of intravenous drug users (IVDU) is known to increase in our country, yet there are a limited number of studies investigating the distribution of HCV genotypes in this group. These data are essential for monitorization of the changes in HCV epidemiology. The present study aimed to evaluate the five-year results of HCV genotyping among patients infected with HCV related to IVDU and unrelated to drug use. Plasma samples of 720 patients (HCV antibody, HCV RNA positive), which were sent to our laboratory for HCV genotyping between January 2014-March 2019 were analyzed. HCV RNA extraction from plasma samples was performed in the automated-extraction system of EZ1 advanced (Qiagen, Germany) using the EZ1 virus mini kit v2.0 (Qiagen, Germany). Amplicons were obtained by amplifying the 5'NCR and core gene region in the Rotorgene 6000 real-time PCR (Qiagen, Germany) device with the HCV RNA real-time quantitative 2.0 (NLM, Italy) kit. For the genotyping, a commercial line probe assay (LIPA) based on in vitro reverse hybridization GEN-C2.0 kit (NLM, Italy) which can distinguish 1, 2, 3, 4, 6 genotypes and 1a, 1b, 2a/c, 2b, 3a, 3b, 3c, 3k, 4a, 4b, 4c/d, 4e, 4f, 4h, 5a, 6a/b, 6g, 6f/q, 6m, 7a subtypes of HCV, based on variations in the 5'-NCR and core regions was used. HCV genotype distribution of 266 IVDU (93.2%: male; median age: 25 ± 6.82) and 454 non-drug users (51.3%: male; median age: 56.5 ± 16.06) were examined. In order of frequency in the group with IVDU; genotype 1a, 3a, 1b, 4c/d, 2b, 4, 3 were observed and genotype 1, 2a/c and mixed genotype (1+3a) were detected in one patient. In the group without IVDU, in order of frequency; genotype 1b, 1a, 3a, 1, 2a/c, 4 were observed and genotype 2b, 4c/d, 5a, 6a/b, 6 and mixed genotype (3+4) were detected in one patient. Genotypes 1a and 3a were significantly higher in the IVDU group (p< 0.00001, p< 0.00001), while 1b was significantly higher in patients without IVDU (p< 0.00001). Genotypes 1a and 3a were more common in young men (p< 0.00001, p= 0.000163), while 1b was higher in middleaged women (p< 0.00001). The incidence of genotypes 1b (p= 0.021) and 3a (p= 0.012) was higher in foreign nationals than the Turkish patients. When the HCV genotype distribution was examined by years, it was observed that the percentages of genotype 1b and 1a were decreasing, while the percentage of genotype 3a was increasing. As a result, in this study, HCV genotype distribution among IVDU was observed to be different from the general population without IVDU. It was found that genotypes 1a and 3a were more common in the IVDU group. As in the other regions of our country, genotype 1b was found most frequently in the general population. Genotype 3a increases significantly compared to years. In our study, the determination of genotypes existing in different parts of the world may be due to the foreign nationals living in our city and our region is a tourism center. It is also necessary to investigate whether there is an increase in IVDU over the years.

Follow-up of human adenovirus viral load in pediatric hematopoietic stem cell transplant recipients.

BACKGROUND: The spectrum of human adenovirus (HAdV)-related disease is broad, and the virus acts on many organs and systems in hematopoietic stem cell transplantation (HSCT) recipients. We aimed to evaluate the effect of HAdV-DNA positivity with clinical and laboratory findings 4 months after HSCT. METHODS AND RESULTS: We retrospectively investigated HAdV-DNA in 153 HSCT recipients (≤18 years) by quantitative real-time polymerase chain reaction (RealStar; Altona Diagnostics). The results of samples from January 2014 to December 2017 are included. HAdV-DNA was positive for at least one sample type in 50 (32.67%) patients. HAdV-DNA positivity rate was 8.92% (N: 145/1625), 40.25% (N: 64/159), and 25% (N: 2/8) for plasma, stool, and urine samples, respectively. HAdV-DNA was positive in the plasma of 38 (24.83%) patients at a median 16 (range: 1-58 days) days after HSCT. The mortality rate was 23.68% and 6.95% in plasma HAdV-positive and HAdV-negative patients (p = .014). Moreover, HAdV-DNA positivity had an impact on overall survival for allogeneic-HSCT (p = .013), with the cumulative effect including graft-versus-host disease state in multivariate analysis (p = .014). CONCLUSIONS: Plasma HAdV-DNA positivity is a potential influencer that decreases survival in the early post-transplant period. Due to the high mortality rates, close monitoring is required of HAdV infections after HSCT with sensitive methods, especially at the early stage.

[Comparison of Two Commercial Quantitative Cytomegalovirus (CMV) Polymerase Chain Reaction Tests Calibrated by World Health Organization International CMV Standard]. / Dünya Saglik Örgütü Uluslararasi Sitomegalovirüs (CMV) Standardi ile Kalibre Edilmis Iki Ticari Kantitatif CMV Polimeraz Zincir Reaksiyonu Testinin Karsilastirilmasi.

Cytomegalovirus (CMV) viral load quantitation is important in diagnosis, follow-up, and monitoring of antiviral therapy in transplanted patients. In this study, it was aimed to compare the results of the two commercial World Health Organization (WHO) International CMV standard calibrated polymerase chain reaction tests, CMV Cobas Ampliprep/Cobas Taqman (CMV-CAP/CTM) (Roche, Germany) and Artus CMV QIASymphony-Rotorgene (CMV-QS-RGQ) (Qiagen, Germany). Both tests were performed simultaneously on 244 plasma samples. The results were measured in copies/ml and converted to IU/ml by multiplying with 0.91 for CMV-CAP/CTM and 1.64 for CMV-QS-RGQ, as specified by the manufacturers. CMV DNA was detected in 174 (71.3%) and was not detected in 52 (21.3%) of the samples and eighteen (7.4%) samples had discordant results by both of the tests. In 16 out of 18 samples with discordance, the viral load was below the dynamic measuring ranges of both tests. In one sample, CMV DNA could not be detected by CMV-CAP/CTM but detected by CMV-QS-RGQ with 497 copies/ml, and 334 copies/ml CMV DNA was detected by CMV-CAP/CTM in another sample where it could not be detected by CMV-QS-RGQ. A high degree of agreement was found between the qualitative results of the both tests (kappa= 0.80, p< 0.001). For quantitative results in the dynamic measuring range of both assays (n= 129), the median viral load values measured by CMV-CAP/CTM and CMV-QS-RGQ were 1140 copies/ml (range: 151-254000) and 1826 copies/ml (range: 189-551521). When the results were converted to IU/ ml, the median viral load values measured by CMV-CAP/CTM and CMV-QS-RGQ were 1037 IU/ml (range: 137-231140) and 2993 IU/ml (range: 310-904133), respectively. There was a very strong correlation (r= 0.94, p< 0.001; r= 0.94, p< 0.001, respectively) between the log10 values of the quantitative results in the dynamic measuring ranges (n= 129) as copies/ml and IU/ml of both tests. CMV-QS-RGQ values corresponding to 150, 1000, 3000 copies/ml in CMV-CAP/CTM were as 94.5, 1571, 323.5 copies/ml and CMV-QS-RGQ values corresponding to 137, 910, 2730 IU/ml in CMV CAP/CTM were as 154, 2557.6, 6965.9 IU/ml, respectively. A variation of 0.45 log10 was determined between these values. In a total of 131 samples; 129 of them with the result of both tests in the dynamic measuring range and two of them which CMV DNA was not detected in one of the tests; it was found that 112 (85.5%) results for copy/ ml, 73 (56%) results for IU/ml were within the measurement difference of ± 0.5 log10 and 19 (14.5%) results for copy/ml and 58 (44%) results for IU/ml were greater than ± 0.5 log10. Bland-Altman analysis showed that CMV-CAP/CTM test made lower measurements than CMV-QS-RGQ and the average difference for copy/ml and IU/ml results were 0.22 log10 copies/ml and 0.47 log10 IU/ml. In conclusion; when the results were converted to IU/ml, the number of samples with an acceptable measurement difference between the two test results (≤ 0.5 log10) decreased and the number of samples with a measurement difference > 0.5 log10 increased and the difference was found as statistically significant (p< 0.001). Calibrating the Roche CMV CAP/CTM and Artus CMV-QS-RGQ tests with the WHO international CMV standard did not increase comparability between quantitative results in plasma samples, on the contrary, it was found that when the results were converted to IU/ml, a measurement difference indicating biologically significant viral replication was detected between the two test results.

Viral seroprevalence in pediatric kidney transplant recipients.

AIM: Viral infections commonly affect kidney transplant recipients and may lead to graft failure and death. The aim of this study was to evaluate the antibody seroprevalence against viral agents in kidney transplant recipients. MATERIAL AND METHODS: The records of children who underwent kidney transplantation between 2008 and 2018 in Akdeniz University Faculty of Medicine were retrospectively reviewed. Epstein-Barr virus, cytomegalovirus, hepatitis A virus, hepatitis B virus, varicella, measles, rubella and mumps serologies evaluated before transplantation, were recorded. The clinical characteristics of seronegative and seropositive patients were compared, and factors that affected seropositivity were investigated. RESULTS: The study included 253 children with a mean age of 16.7±6.23 years. The mean age at transplantation was 11.4±5.01 years. The seropositivity rates for vaccine-preventable viral infections varied: hepatitis B 89.7%, hepatitis A 60.5%, measles 78.7%, rubella 88.1%, mumps 61.2%, and varicella 71.9%. Cytomegalovirus seropositivity was 92.1% and Epstein-Barr virus seropositivity was 82.2%. Hepatitis B antibody positivity was 91.8% in patients undergoing hemodialysis, 94.5% in patients undergoing peritoneal dialysis, and 84.9% in pre-emptive transplantation patients (p=0.037). The mean age at transplantation was higher in patients with seropositivity for both cytomegalovirus and Epstein-Barr virus compared with seronegative patients (p<0.001 for both). The mean age at transplantation and diagnosis of glomerular disease was found to be effective for varicella seropositivity in multivariate regression analysis (OR 0.860, 95% CI: 0.808-0.915, p<0.001 and OR 2.502, 95% CI: 1.321-4.739, p=0.005, respectively). CONCLUSION: It is important to screen patients with chronic kidney disease in terms of vaccine-preventable diseases to identify risky groups of patients and to immunize these patients before end-stage kidney disease develops.

[Evaluation of Enzyme Immunoassay (EIA), Immunoblot and HIV RNA Polymerase Chain Reaction Test Results in the Diagnosis of Human Immunodeficiency Virus (HIV) Infection]. / Insan Immün Yetmezlik Virüsü (HIV) Enfeksiyonu Tanisinda Enzim 'Immunoassay' (EIA), Immünoblot ve HIV RNA Polimeraz Zincir Reaksiyonu Test Sonuçlarinin Degerlendirilmesi.

Acquired Immunodeficiency syndrome (AIDS) is an important global public health issue. Increasing HIV/AIDS cases reported each year has become a serious health problem for our country. The fourth generation enzyme immunoassay (EIA) test is the first step in the laboratory diagnosis of human immunodeficiency virus (HIV) infection. When the EIA test is repeatedly reactive, antibody-based tests such as immuno blot (IB), line immunoassay (LIA), HIV 1-2 antibody differentiation immunoassay, and HIV RNA tests for the early period of infection are used as confirmatory tests. The aim of this study was to evaluate the results of three different methods for the diagnosis of HIV infection. HIV 1-2 IB and quantitative HIV-1 RNA PCR tests were performed in 199 patient samples. These samples were detected as the reactive or gray zone with HIV 1-2 Ab+Ag EIA test between 2010 and 2015 at Akdeniz University Hospital, Microbiology Laboratory. HIV 1-2 Ab+Ag determination in serum samples was performed with the EIA method (Elecsys HIV combi PT test, Roche Diagnostics, Germany). A commercial kit (INNO-LIA HIV I-II Score, Innogenetics, Belgium) was used for HIV 1-2 IB method. The presence of HIV-1 RNA was investigated by automated nucleic acid extraction and real-time PCR method (Ampliprep/COBAS Tagman HIV-1 Test, Roche Diagnostics, Germany) in plasma samples. For statistical analysis, SPSS, Mann Whitney U test was used, ROC analysis was performed and p<0.05 value was considered statistically significant. HIV 1-2 Ab+Ag EIA COI (cut-off index) median value was higher with positive HIV 1-2 IB and HIV-1 RNA results than negative HIV 1-2 IB and HIV-1 RNA results. These values were 394 (range: 11.5-2272) and 1.79 (range: 1.01-83.3) respectively and this difference was statistically significant (p< 0.001). HIV-1 RNA test results were positive in one patient with gray zone and two patients with negative HIV 1-2 IB result (viral loads were > 10.000.000, > 10.000.000 and 5.040.000 copies/ml, respectively). For the kit that we used for HIV 1-2 Ab+Ag EIA COI ratio of >16.45 had a sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 97.6%, 98.1%, 97.6% and 98.1%, respectively for the detection of HIV infection (r= 0.994, p< 0.001). HIV 1-2 Ab+Ag EIA S/CO ratio of < 9.26 had a sensitivity, specificity, PPV and NPV of 100%, 92.5%, 91.1% and 100% (p< 0.001). HIV infection is diagnosed if HIV 1-2 Ab+Ag EIA test result is repeatedly reactive and HIV 1-2 IB test and HIV-1 RNA tests are positive. In our study, HIV 1-2 Ab+Ag EIA COI median value was 394 (range: 11.5-2272) in this group of patients (p< 0.001). HIV-1 RNA PCR test was positive in three patients with > 10.000.000, 5.040.000 and > 10.000.000 copies/ml whose EIA tests were repeatedly reactive. HIV IB test was detected as the gray zone in one of them and as negative in the remaining two (HIV EIA S/CO values were 265, 9.5 and 131.8, respectively). These patients were diagnosed as acute HIV infection with clinical and laboratory findings. In conclusion, HIV RNA should also be performed and included in the diagnostic algorithm for acute HIV infection.

[Evaluation of the Two Different Real Time Polymerase Chain Reaction Methods Used for BK Virus (BKV) Quantification and BKV Genotype Assignment]. / BK Virüs (BKV) Kantitasyonunda Kullanilan Iki Farkli Gerçek Zamanli Polimeraz Zincir Reaksiyonu Yönteminin Karsilastirmasi ve BKV Genotip Tayini.

BK virus (BKV) viral load quantification has a distinct role in the clinical control of BKV nephropathy and organ rejection among renal transplant recipients. In this study, it was aimed to compare BKV DNA measurement values performed with two different real-time polymerase chain reaction (PCR) methods and to determine BKV genotypes in renal transplant recipients. Totally, 150 clinical samples tested previously in two different laboratories (Lab-1 and Lab-2) from adult and pediatric renal transplantation patients were included in the study. Fifty plasma samples of 50 different patients from Lab-1, 50 plasma and 50 urine samples of 58 different patients from Lab-2 were included in the study. Viral nucleic acid extraction was performed with automatized systems in Lab-1 and Lab-2 (EZ1, Qiagen, Germany and MagNA Pure 96, Roche Diagnostics, Germany; respectively;). Real-time PCR procedure was carried out in Lab-1 with an amplification mixture of primer, probe sequences targeting VP-1 gene region using RotorGene (Qiagen, Germany) and in Lab-2 with an amplification mixture of primer, probe sequences targeting VP-2 gene region using ABI Prism 7500 (Applied Biosystems, USA). BKV genotyping was performed with multiplex PCR using primer, probe sequences for BKV genotypes I-IV. In both of the laboratories, 82 (54.6%) of the samples were found as positive, 37(24.6%) samples were found as negative and a moderate agreement was found between qualitative results of two real-time PCR methods (ƙ= 0.56, p<0.001). Median viral load values were 4.1 x 104 copies/ml (321-6 x 109) in Lab-1 and 3.3 x 105 copies/ml (224-8.3 x 1010) in Lab-2 for positive samples. According to the lineer regression analysis of quantitative results, moderate (R2= 0.52, p<0.001) and high (R2= 0.88, p<0.001) correlation was found for plasma (n= 52) and urine (n= 30) samples, respectively. Bland-Altman analysis yielded a mean difference of -0.58 log10 for all samples. For plasma samples mean difference was -0.29 log10, while it was -1.1 log10 for urine samples. In all samples, Lab-1 measurements were lower than Lab-2 measurements. A mean difference of -1.1 log10 indicated that the measurement values of Lab-2 were more higher than Lab-1 measurments with an average of 1.1 log10. Supporting this result, 71.9% of the samples had a measurement difference more than 0.5 log 10 and 29.2% of the samples had a measurement difference more than 1 log10. Only 28.1% of the samples were measured within clinically acceptable log difference range (less than 0.5 log10). BKV genotyping was performed only for 74 different patient samples with sufficient copy numbers and genotype I (81.7%), IV (15.5%), II (1.4%), I+IV (1.4%) were detected. When the results were compared; 66.6% (n= 12) of the genotype IV samples had more than 1 log10 and 83.3% of them had more than 0.5 log10 viral load measurement difference. Correlation and linear regression analyzes were insufficient for the comparison ofthe results of the two different tests. It will be appropriate for each center to monitor patients with the same test until the international BKV standard developed by the World Health Organization is optimized. The clinical correlation of the tests is limited to the currently used test. The result of incorrect BKV quantification affects the clinical decision. Measurements less than the actual value will lead to the development of BKV nephropathy, and higher measurements will lead to unnecessary allograft biopsy and unnecessary reduction of immunosuppression.

[Distribution of hepatitis C virus genotypes among patients with chronic hepatitis C infection in Akdeniz University Hospital, Antalya, Turkey: a five-year evaluation]. / Akdeniz Üniversitesi Hastanesinde kronik hepatit C enfeksiyonu olan hastalarda hepatit C virus genotipleri: Bes yillik sonuçlarin degerlendirilmesi.

Hepatitis C virus (HCV) is one of the major causes of chronic hepatitis. It is important to know the genotypes of HCV in the decision of the HCV related chronic hepatitis therapy. The aim of this study was to evaluate the HCV genotypes determined at the Microbiology Laboratory of Akdeniz University Hospital, and to evaluate the changes in the distribution of the genotypes within the last five years. A total of 422 blood samples from HCV-RNA positive chronic hepatitis C patients (219 male, 203 female; age range: 8-79 yrs, mean age 46.3 ± 15.5 yrs) which were sent to our laboratory for genotyping between 2009-2013 period, were analyzed retrospectively. HCV-RNA extractions were performed in an automated system (EZ1 Virus Mini Kit v2.0, Qiagen, Germany), and a commercial reverse hybridization line probe-based assay (LIPA; GEN-C RT-PCR, Italy) was carried out for genotyping, For viral load determinations, a real-time PCR method (Cobas TaqMan HCV, Roche Diagnostics, Germany) was used. Demographic data of the patients were obtained from the hospital information systems and electronic patients' files. Out of the 422 patients, genotype 1b was detected in 63.3% (n= 267), genotype 1a in 14.7% (n= 62), genotype 3a in 11.1% (n= 47), genotype 2b in 0.9% (n= 4), genotype 4e in 0.2% (n= 1). The subtypes couldn't be determined for 5.4% (n= 23), 2.6% (n= 11) and 1.4% (n= 6) of the patients infected with genotype 1, 2 and 4, respectively. One (0.2%) patient, was coinfected with genotype 1 and 4. Of the patients, 40 were foreign-born (16 cases from Russia; 4 of each from Ukraine and Georgia; 3 of each from Turkmenistan, Kyrgyzstan, and Germany; one of each from Tajikistan, Azerbaijan, Uzbekistan, Chechnya, Moldova, Switzerland and Romania) and among these patients genotype 3a (19/40; 47.5%) was the most common genotype followed by genotype 1b (17/40; 42.5%). Median values of HCV viral load were 668.500 IU/ml (range: 2.000-9.630.000) in the whole group; while it was 732.000 IU/ml (range: 2.000-9.630.000) in patients infected with genotype 1 and 444.000 IU/ml (range: 2.650- 8.330.000) in patients infected with the other genotypes (p> 0.05). Patients infected with genotype 1 were found to be older than those infected with other genotypes (47 ± 15.7 and 39.5 ± 12.2, respectively; p< 0.001). Among patients infected with different genotypes, there was no statistically significant difference in terms of genders (p> 0.05). In conclusion, the determination of HCV genotypes is of crucial importance for treatment decision-making of chronic HCV infection. Besides, it also allows monitoring the changes in the epidemiology of HCV. In this study, although genotype 1b was determined as the most common HCV genotype, the detection of other genotypes was remarkable. This finding was attributed to the presence of many foreign national people in Antalya region which was a high capacity tourism area in Turkey.

Epstein-Barr virus infection in children with renal transplantation: 17 years experience at a single center.

OBJECTIVES: The aim of this study was to detect the frequency, time of occurrence, management and outcome of Epstein-Barr virus (EBV) infection and related complications in pediatric renal transplant recipients. METHODS: Pediatric renal allograft recipients transplanted between August 1994 and December 2011 at our hospital was evaluated retrospectively. The patients were divided into two groups; Groups 1 and 2 were composed of patients transplanted before and after November 2007, respectively, when plasma EBV DNA levels were periodically measured. RESULTS: The study included 166 children, 89 (53.6%) boys, with a mean age of 12.2 ± 3.8 years. Prior to transplantation, 144 patients (86.7%) were EBV seropositive. Within a median follow-up period of 36 months, 11 of 22 seronegative children (50%) developed primary EBV infection. EBV reactivation was observed in 23 of 144 children (15.9%). Two patients with primary infection developed post-transplant lymphoproliferative disorder, one of whom died. Elevated serum creatinine levels or graft loss were not observed in any patient with EBV reactivation. CONCLUSIONS: EBV DNA monitoring by PCR in high-risk pediatric renal transplant recipients will provide early diagnosis and treatment of EBV infections.