[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.

COVID-19 disease characteristics in different pediatric age groups.

INTRODUCTION: Little is known about the COVID-19 disease characteristics and differences between different pediatric age groups. This study aimed to investigate the disease characteristics according to age groups. METHODOLOGY: We conducted a retrospective, single-center study of pediatric COVID-19 in a tertiary care hospital in Turkey. The patients were divided into three groups: 15 days-24 months old (Group 1), 25-144 months old (Group 2), and 145-210 months old (Group 3) according to age. RESULTS: A total of 139 pediatric patients with COVID-19 were examined. Twenty-nine patients (20.9%) were in Group 1, 52 (37.4%) were in Group 2, 58 (41.7%) were in Group 3. Thirty-nine patients (28.1%) were hospitalized. The most common symptoms were cough (55.4%) and fever (51.8%). The median chest X-ray (CXR) score of hospitalized patients was 1 (min 0-max 7), and the median CXR score of outpatients was 1 (min 0-max 6). Fever was significantly more frequent in Group 1, and chest pain was more frequent in Group 3. Group 1 had significantly higher WBC, lymphocyte, thrombocyte counts, AST, LDH, D-dimer, and Troponin T levels but lower hemoglobin, total protein, and albumin levels. The treatment included antibiotics, oseltamivir, hydroxychloroquine, and supportive therapy. Only one patient (0.7%) received non-invasive mechanical ventilatory support. CONCLUSIONS: As we know the clinical course of COVID-19 in children is less severe than in adults. We also found significant differences in both clinical and laboratory findings between different pediatric age groups which supports the theory that disease pathogenesis is highly variable according to age.

Incidence of multisystem inflammatory syndrome in children and the comorbidity scores in pediatric coronavirus disease 2019 cases.

BACKGROUND: We aimed to determine the incidence of multisystem inflammatory syndrome in children (MIS-C) in pediatric coronavirus disease 2019 (COVID-19) cases and to define the relationships between the need for hospitalization, the development of MIS-C, and the Charlson Comorbidity Index (CCI) and Pediatric Comorbidity Index (PCI) scores. METHODS: All pediatric COVID-19 cases between March 25, 2020, and December 28, 2020, in the Marmara University Pendik Training and Research Hospital were enrolled. Patients who needed hospitalization were determined. Hospital records were re-examined to identify those diagnosed as having MIS-C. The CCI and PCI were used to validate the comorbidity status. RESULTS: Among 2,055 pediatric COVID-19 cases, 1,340 were included in the study, and 213 patients (15.9%) had at least one comorbidity. All the patients or their parents were interviewed about the need for hospitalization, except for the acute period. Six patients had MIS-C, which corresponds to a MIS-C incidence of 0.4%. The need for hospitalization increased in the patients with comorbidities (P < 0.05). No correlation was found between the comorbidity scores and the development of MIS-C. The need for hospitalization increased in the patients with CCI scores of ≥2 and PCI scores of ≥4 (P < 0.05). CONCLUSIONS: Our study is the first to examine the incidence of MIS-C, which was 0.4%, by long-term follow up of pediatric COVID-19 cases and to demonstrate that the CCI and PCI can be used to predict the need for hospitalization and prognosis of pediatric patients with COVID-19.

Diversity of HIV-1 Subtypes and Transmitted Drug-resistance Mutations Among Minority HIV-1 Variants in a Turkish Cohort.

BACKGROUND: The World Health Organization (WHO) recommends the surveillance of transmitted drug resistance mutations (TDRMs) to ensure the effectiveness and sustainability of HIV treatment programs. OBJECTIVE: Our aim was to determine the TDRMs and evaluate the distribution of HIV-1 subtypes using and compared next-generation sequencing (NGS) and Sanger-based sequencing (SBS) in a cohort of 44 antiretroviral treatment-naïve patients. METHODS: All samples that were referred to the microbiology laboratory for HIV drug resistance analysis between December 2016 and February 2018 were included in the study. After exclusions, 44 treatment-naive adult patients with a viral load of >1000 copies/mL were analyzed. DNA sequencing for reverse transcriptase and protease regions was performed using both DeepChek ABL single round kit and Sanger-based ViroSeq HIV-1 Genotyping System. The mutations and HIV-1 subtypes were analyzed using the Stanford HIVdb version 8.6.1 Genotypic Resistance software, and TDRMs were assessed using the WHO surveillance drug-resistance mutation database. HIV-1 subtypes were confirmed by constructing a maximum-likelihood phylogenetic tree using Los Alamos IQ-Tree software. RESULTS: NGS identified nucleos(t)ide reverse transcriptase inhibitor (NRTI)-TDRMs in 9.1 % of the patients, non-nucleos(t)ide reverse transcriptase inhibitor (NNRTI)-TDRMs in 6.8 % of the patients, and protease inhibitor (PI)-TDRMs in 18.2 % of the patients at a detection threshold of ≥ 1 %. Using SBS, 2.3 % and 6.8 % of the patients were found to have NRTI- and NNRTI-TDRMs, respectively, but no major PI mutations were detected. M41L, L74I, K65R, M184V, and M184I related to NRTI, K103N to NNRTI, and N83D, M46I, I84V, V82A, L24I, L90M, I54V to the PI sites were identified using NGS. Most mutations were found in low-abundance (frequency range: 1.0 % - 4.7 %) HIV-1 variants, except M41L and K103N. The subtypes of the isolates were found as follows; 61.4 % subtype B, 18.2 % subtype B/CRF02_AG recombinant, 13.6 % subtype A, 4.5 % CRF43_ 02G, and 2.3 % CRF02_AG. All TDRMs, except K65R, were detected in HIV-1 subtype B isolates. CONCLUSION: The high diversity of protease site TDRMs in the minority HIV-1 variants and prevalence of CRFs were remarkable in this study. All minority HIV-1 variants were missed by conventional sequencing. TDRM prevalence among minority variants appears to be decreasing over time at our center.

Comparison of SARS-COV-2 antibody assays in PCR negative and PCR positive Turkish patients.

BACKGROUND: To the Editor, Serology may offer valuable information during COVID-19 pandemic; however, published papers mainly reported the results of symptomatic patients having positive RT-PCR on upper respiratory tract specimens [1]. More studies are needed to address whether asymptomatic patients, or patients with chest imaging compatible with COVID-19 but negative RT-PCR, have different antibody response that could influence assays performances. We wanted to share our data from Turkey where 4,323,596 COVID-19 cases were detected out of 44,087,628 PCR tests by April 20, 2021 but there are only a couple of published studies about serodiagnosis of the infection. DISCUSSION: The authors have no funding source for the study. The authors have no conflicts of interest to declare.

Relationship of the cycle threshold values of SARS-CoV-2 polymerase chain reaction and total severity score of computerized tomography in patients with COVID 19.

AIM: Studies analyzing viral load in COVID-19 patients and any data that compare viral load with chest computerized tomography (CT) severity are limited. This study aimed to evaluate the severity of chest CT in reverse transcriptase polymerase chain reaction (RT-PCR)-positive patients and factors associated with it. METHODOLOGY: SARS-CoV-2 RNA was extracted from nasopharyngeal swab samples by using Bio-speedy viral nucleic acid buffer. The RT-PCR tests were performed with primers and probes targeting the RdRp gene (Bioexen LTD, Turkey) and results were quantified as cycle threshold (Ct) values. Chest CT of SARS-CoV-2 RNA-positive patients (n = 730) in a period from 22 March to 20 May 2020 were evaluated. The total severity score (TSS) of chest CT ranged 0-20 and was calculated by summing up the degree of acute lung inflammation lesion involvement of each of the five lung lobes. RESULTS: Of the 284 patients who were hospitalized, 27 (9.5%) of them died. Of 236 (32.3%) patients, there were no findings on CT and 216 (91.5%) of them were outpatients (median age 35 years). TSS was significantly higher in hospitalized patients; 5.3% had severe changes. Ct values were lower among outpatients, indicating higher viral load. An inverse relation between viral load and TSS was detected in both groups. CT severity was related to age, and older patients had higher TSS (p < 0.01). CONCLUSION: Viral load was not a critical factor for hospitalization and mortality. Outpatients had considerable amounts of virus in their nasopharynx, which made them contagious to their contacts. Viral load is important in detecting early stages of COVID-19, to minimize potential spread, whereas chest CT can help identify cases requiring extensive medical care.

[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.