Comparison of the NeuMoDx™ HBV quant assay and artus QS-RGQ® kit for HBV DNA quantitation in plasma samples.

We aimed to compare the NeuMoDx HBV Assay with the artus HBV Assay using residual plasma samples and to evaluate the discordant results. The study included 200 patient samples analyzed with the NMD assay and stored at -80 °C. Samples were analyzed by artus in 2023. Discordant results were evaluated by cobas 6800 HBV DNA Test. Excellent agreement was found between both tests. Of the 100 samples that were HBV DNA negative by NMD, 93 were negative and 7 were positive by artus. With the Cobas test, 5 samples were positive. Of the100 HBV DNA positive samples detected by NMD, 99 were positive with the artus assay. This sample was also HBV DNA negative by the Cobas test. The sensitivity and specificity of NeuMoDx were found 93 % and 99 %, respectively. There was excellent qualitative agreement and strong quantitative correlation between the NeuMoDx and artus assays for HBV DNA detection and quantitation.

Pre-infection antibody levels of vaccinated healthcare workers with SARS-CoV-2 breakthrough infection: A nested case-control study.

AIM: To evaluate anti-RBD IgG antibody levels and neutralizing antibody titers between the health care workers (HCWs) with breakthrough SARS-CoV-2 infection and controls. METHODS: In this nested case-case control study, we followed 548 vaccinated HCWs with homologous (only with inactivated vaccine) or heterologous (both with inactivated and BNT162b2 vaccine) vaccination for 11 months, prospectively. We obtained blood samples from the participants for quantitative anti-RBD IgG and surrogate neutralization test. The participants with SARS-CoV-2 PCR positivity (at least 14 days after the last vaccination) were considered breakthrough infection. We chose 1:2 matched controls from the cohort, according to age, sex and vaccination status. We used R version 4.0.2 for the statistical analysis. RESULTS: Sixty-five cases and 130 controls were included in the study. The number of the breakthrough infections in HCWs were correlated with the pandemic waves in Türkiye and peaked during Omicron outbreak. The median age of the cases was 39 and 78.5% were female. The cases had more comorbidities than controls, significantly (p = 0.021). All cases experienced no or mild symptoms and recovered completely. Both pre-infection anti-RBD antibody and neutralizing antibody titers did not differ between cases and matched controls (p = 0.767, p = 0.628). CONCLUSION: In this study, we showed that there was no comparable difference in humoral response after homologous or heterologous vaccination between the cases of breakthrough infection and matched controls. Compliance with infection control measures should be ensured, in combination with vaccination.

Can Some Viral Respiratory Infections Observed Before the Pandemic Announcement Be Related to SARS-CoV-2?

OBJECTIVE: There have been doubts that SARS-CoV-2 has been circulating before the first case was announced. The aim of this study was to evaluate the possibility of COVID-19 in some cases diagnosed to be viral respiratory tract infection in the pre-pandemic period in our center. MATERIAL AND METHODS: Patients who were admitted to our hospital's pulmonary diseases, infectious diseases, and intensive care clinics with the diagnosis of viral respiratory system infection within a 6-month period between October 2019 and March 12, 2020, were screened. Around 248 archived respiratory samples from these patients were analyzed for SARS-CoV-2 ribonucleic acid by real-timequantitative polymerase chain reaction. The clinical, laboratory, and radiological data of the patients were evaluated. RESULTS: The mean age of the study group was 47.5 (18-89 years); 103 (41.5%) were female and 145 (58.4%) were male. The most common presenting symptoms were cough in 51.6% (n = 128), fever in 42.7% (n = 106), and sputum in 27.0% (n = 67). Sixty-nine percent (n = 172) of the patients were pre-diagnosed to have upper respiratory tract infection and 22.0% (n = 55) had pneumonia, one-third of the patients (n = 84, 33.8%) were followed in the service. Respiratory viruses other than SARS-CoV-2 were detected in 123 (49.6%) patients. Influenza virus (31.9%), rhinovirus (10.5%), and human metapneumovirus (6.5%) were the most common pathogens, while none of the samples were positive for SARS-CoV-2 RNA. Findings that could be significant for COVID-19 pneumonia were detected in the thorax computed tomography of 7 cases. CONCLUSION: The negative SARS-CoV-2 real-time-quantitative polymerase chain reaction results in the respiratory samples of the cases followed up in our hospital for viral pneumonia during the pre-pandemic period support that there was no COVID-19 among our cases during the period in question. However, if clinical suspicion arises, both SARS and non-SARS respiratory viral pathogens should be considered for differential diagnosis.

Evaluation of SARS-CoV-2 antibody persistence and viral spread in stool: a long-term care experience before COVID-19 vaccination.

BACKGROUND: Due to elderly residents, nursing homes/assisted living facilities were the most affected places in COVID-19 pandemic. Besides symptomatic patients, asymptomatic patients were detected during routine screening. AIM: This study aims to determine the factors that affect antibody response and viral shedding in stool samples after natural exposure to the virus in residents and staff who recovered from COVID-19 before the vaccine was available. METHODS: This prospective cross-sectional study was conducted at the nation's highest-capacity Residential and Nursing Home. Blood samples were collected between December 15, 2020 and January 15, 2021 from participating residents and staff for anti-SARS-CoV-2 antibody testing. Stool samples were obtained for SARS-CoV-2 PCR testing 2 months after COVID-19. The Social Sciences (SPSS) program version 15.0 was used for statistical analysis. The Mann-Whitney U test compared SARS-CoV-2 antibody concentration between two groups. RESULTS: Four hundred sixty-four (52.3%) residents and 424 (47.7%) staff participated. Entirely 259 (29.2%) participants were anti-SARS-CoV-2 IgG (+) and 255 (28.7%) were SARS-CoV-2 PCR (+). Both antibody and PCR positivity was detected in 196 (76.9%). In PCR (-) group, 63 (10.0%) participants were SARS-CoV-2 IgG (+). Antibody titers were found highest in SARS-CoV-2 PCR (+) male residents. SARS-CoV-2 IgG titers were significantly high in SARS-CoV-2 PCR (+) and hospitalized participants regardless of age. Stool samples were obtained from 61(23.9%) participants and were found negative. CONCLUSION: A durable SARS-CoV-2 IgG antibody response was monitored at least 9 months after the participants were diagnosed with COVID-19. SARS-CoV-2 antibody positivity was detected 76.9% in PCR (+) and 10.0% in PCR (-) participants. Knowing the duration of detectable antibodies is an important finding for developing disease prevention and public health strategies.

Electromechanical RT-LAMP device for portable SARS-CoV-2 detection.

Rapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal amplification (RT-LAMP) principle. The developed device can detect SARS-CoV-2 viral RNA down to 103 copies/mL and from a low amount of sample volumes (2 µL) in less than an hour of standalone operation without the need for professional labor and equipment. Integrated Peltier elements in the device keep the sample at a constant temperature, and an integrated camera allows automated monitoring of LAMP reaction in a stirring sample by using colorimetric analysis of unfocused sample images in the hue/saturation/value color space. This palm-fitting, portable and low-cost device does not require a fully focused sample image for analysis, and the operation could be stopped automatically through image analysis when the positive test results are obtained. Hence, viral infections can be detected with the portable device produced without the need for long, expensive, and labor-intensive tests and equipment, which can make the viral tests disseminated at the point-of-care.

Distribution of Viral Respiratory Pathogens During the COVID-19 Pandemic: A Single-Center Pediatric Study from Turkey.

OBJECTIVE: To evaluate the distribution and characteristics of respiratory viral pathogens and to assess the epidemiological data, clinical features, and prognoses of infected children in a pediatric emergency department during the COVID-19 pandemic. MATERIALS AND METHODS: Between September 1, 2020, and April 30, 2021, patients aged between 0 and 18 years arrived at the pediatric emergency department and were tested by nasopharyngeal/tracheal specimen polymerase chain reaction for both SARS-CoV-2 and other viral respiratory pathogens. Demographics, symptoms, laboratory and radiologic investigations, respiratory viruses detected by PCR, presence of co-infection and co-infecting viruses, need for respiratory support, hospitalization, length of hospital stay, and prognosis were recorded. RESULTS: There were 327 patients for whom PCR tests were performed and 118 (36.0%) of them had positive results for SARS-CoV-2 and/or other respiratory viruses. Rhinovirus was the most commonly detected pathogen with 74 (62.7%) cases, followed by enterovirus with 38 (32.2%) and adenovirus with 20 (16.9%) cases. There was no detection of influenza virus or respiratory syncytial. SARS-CoV-2 PCR results were positive in 14 (11.9%) cases and there was only 1 coinfection of SARS-CoV-2 occurring together with rhinovirus. For 43 (36.4%) patients, there was co-infection, and among co-infections, the most common was that of rhinovirus and enterovirus, seen in 37 (86.0%) cases. CONCLUSION: A decrease was observed in the positivity rate of respiratory viral pathogens, while no cases of influenza virus or respiratory syncytial virus were observed in our study. Circulating viruses may change due to multifactorial approaches during the COVID-19 pandemic.

Hepatitis E Infection in Solid Organ Transplant Recipients in Turkey.

BACKGROUND: Hepatitis E virus is a re-emerging pathogen with an increase in human cases that can lead to chronic infection in immunosuppressed patients. Turkey is located between Asia and Europe, 2 regions with distinct epidemiological and clinical features of hepatitis E virus infection. This multicenter cross-sectional study aimed to investigate the prevalence of hepatitis E virus infection in liver and kidney transplant recipients in Turkey and to determine the role of possible transmission factors. METHODS: A total of 485 plasma samples of solid organ recipients were collected from 7 transplantation centers in Turkey. Samples were tested for anti-hepatitis E virus immunoglobin M, immunoglobin G, and hepatitis E virus ribonucleic acid. Water- and food-related risk factors were evaluated by a questionnaire. RESULTS: Samples of 300 kidney and 185 liver recipients were collected. Hepatitis E virus ribonucleic acid was tested in 472 samples and none were positive. Anti-hepatitis E virus immunoglobin G and immunoglobin M were detected in 84 (17.3%) and 3 (0.6%) patients, respectively. Seropositivity was associated with older age, male gender, being a liver recipient, and being infected with hepatitis B virus and/or hepatitis C virus. None of the patients under the age of 30 were seropositive. Hepatitis E virus immunoglobin G prevalence was higher in the Central East and Southeast Anatolia. Eating raw meat was the only independent variable associated with hepatitis E virus seropositivity. CONCLUSION: This is the first prevalence study of hepatitis E virus infection in solid organ recipients in Turkey. Anti-hepatitis E virus immunoglobin G prevalence was 17.3% which was higher than the previously reported rate in blood donors. Seropositivity was significantly higher in liver recipients. Despite the high antibody prevalence, none of the patients were viremic.

Evaluation of COVID-19 antibody response with using three different tests.

BACKGROUND AND OBJECTIVES: In this study, the performance of three different commercial antibody assays for COVID-19 was examined and parameters affecting the antibody response were investigated. The correlation of patients' chest CT results, procalcitonin, CRP, and D-dimer levels with the antibody response were retrospectively evaluated. MATERIALS AND METHODS: COVID-19 antibodies were detected by three commercially available assays in each patient. Two of the assays were rapid immunochromatographic tests and - one was an ELISA-based IgG assay. SARS-CoV-2 RNA was tested by "COVID-19 RT-qPCR Detection Kit" using nasopharyngeal swab samples. The results of antibody tests were compared with each other, RT-qPCR, Biochemical parameters and chest CT findings. RESULTS: RT-qPCR was positive in 46.6% (41/88) of the evaluated patients among which 77.3% (68/88) were healthcare workers. Seventeen (41.4%) of viral RNA positive patients had a positive antibody result with at least two assays. Both of the rapid immunochromatographic tests had identical sensitivity of 36.6% and specificity of 100%, compared to RT-qPCR assay; while the sensitivity of the ELISA based Euroimmune test was 43.9%, and the specificity was 95.7%. The sensitivity and specificity of the immunochromatographic tests were 75% and 100% respectively, compared to ELISA test result. There was a correlation between antibody positivity and old age and male gender. The presence of typical chest CT findings increased the antibody positivity 13.62 times. Antibody positivity was also increased with the decrease in Ct value of the PCR assay. There was no significant relationship between the biochemical parameters (CRP, D-dimer and procalcitonin values) and the antibody or RT-qPCR results. CONCLUSION: There was a correlation between antibody response and male gender, older age, presence of symptoms, typical chest CT findings and low PCR-Ct value.

[Analysis of Nucleotide Changes in RT-PCR Primer/Probe Binding Regions in SARS-CoV-2 Isolates Reported from Turkey]. / Türkiye'den Bildirilen Sars-CoV-2 Izolatlarinda RT-PCR Primer/Prob Baglanma Bölgelerindeki Nükleotit Degisimlerinin Analizi.

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.

The Efficacy of Hydroxychloroquine and Azithromycin Combination Therapy on Hospital Mortality in COVID 19 Pneumonia Patients.

BACKGROUND/AIM: Effective therapeutic approaches for SARS-CoV-2 pandemic are urgently needed. Hydroxychloroquine (HCQ) alone or in combination with azithromycin has been used in several countries, without any clear evidence. This study aimed to determine the effectiveness and safety of hydroxychloroquine as compared to hydroxychloroquine and azithromycin combination in patients with COVID-19 pneumonia. MATERIALS AND METHODS: This retrospective study evaluated all patients admitted to two university hospitals between 18 March and 20 May 2020 with the diagnosis of COVID-19 pneumonia. Out of 496 patients, 370 met the eligibility criteria and were included in the final analysis. The primary outcome was in-hospital mortality. Secondary outcomes were time to recovery, presence of severe acute respiratory infection (SARI), the requirement for oxygen therapy, and/or mechanical ventilation, length of hospital stay, and adverse events. RESULTS: A total of 222 patients received hydroxychloroquine and 148 were treated with HCQ and azithromycin combination. The in-hospital mortality rates were similar in the two groups (10.8% vs. 6.8%, respectively, p=0.186). Additionally, the needs for oxygen therapy, invasive mechanic ventilation (IMV) and intensive care unit (ICU) admission were not different. The rate of the requirement of non-invasive mechanic ventilation (NIV) was higher in patients receiving HCQ plus azithromycin (10.1% vs. 4.5%, p=0.035). Time to recovery was 3.5 days in HCQ and 5.0 days in HCQ plus azithromycin group (p<0.001). The median length of hospital stay was longer in patients with the combination therapy (7.0 vs. 5.5 days, p<0.001). Amongst all patients, only 3 patients developed electrocardiographic changes needing discontinuation of therapy. LIMITATIONS: Observational design of the study is the main limitation. CONCLUSIONS: The present findings suggest that adding azithromycin to HCQ is not associated with any improvement in clinical outcome and mortality in patients with COVID-19 pneumonia and supports the current knowledge not to include azithromycin in the initial treatment of COVID-19.

Evaluation of COVID-19 Disease and the Effect of Trends in Intervention Measures: The Pediatric Perspective from a Tertiary Care Hospital in Turkey.

BACKGROUND: COVID-19 is an emerging disease of global public health concern. AIMS: To evaluate the epidemiological, clinical, laboratory, and radiologic findings and the clinical outcomes of children who were diagnosed with SARS-CoV-2 by polymerase chain reaction (PCR), and to evaluate the effect of the trends in intervention measures. STUDY DESIGN: Between April 2, 2020 and January 16, 2021, children aged 0-18 years who had presented at the pediatric emergency department and were diagnosed with confirmed SARS-CoV-2 by PCR were enrolled. METHODS: Details on demographics, epidemiologic characteristics, clinical findings, laboratory data, and radiologic investigations, hospital admissions, and prognosis were recorded. According to clinical severity, patients were divided into 5 groups as asymptomatic, mild, moderate, severe, or critical. We classified the outbreak into 3 periods. The first was between April 2, 2020, the date when the first pediatric case of our hospital was detected, and June 1, 2020, when restrictive measures were relaxed. The second period was between June 1, 2020 and November 15, 2020, when restrictive measures were reimplemented. The third period was between November 15, 2020 and January 16, 2021. RESULTS: A total of 600 patients [median age: 10.3 years (IQR: 4.4-15.1); 304 females] were enrolled. Among them, 25.0% were asymptomatic, while the 3 most common symptoms among symptomatic cases were fever, cough, and fatigue. There was contact with a COVID-19 PCRpositive individual in 73.5% of the cases, with 76.6% of those being a household contact. There were 23 (3.9%) moderate, severe, or critical cases in terms of clinical severity. The presence of chronic disease, a pathological physical chest examination, and procalcitonin levels of >0.05 ng/mL were identified as predictors of being moderate, severe, or critical. Twenty-four (4.0%) patients were admitted to the hospital; 14 (2.3%) to the ward and 10 (1.6%) to the pediatric intensive care unit. In the second intervention period, we observed a rapidly increasing number of new cases daily, especially in August. From September, an increase was observed, being particularly marked from October to November 18. Since then, there was a decrease in the daily number of cases. CONCLUSION: The majority of the cases were asymptomatic or had a mild clinical presentation. The presence of chronic disease, a pathological physical chest examination, and procalcitonin levels of >0.05 ng/mL were identified as predictors of being moderate, severe, or critical in terms of clinical severity. Strict intervention measures seem to be effective in containing the spread of COVID-19.

Genetic diversity of Pneumocystis jirovecii isolates among Turkish population based on mitochondrial large subunit ribosomal RNA and dihydropteroate synthase gene typing.

Pneumocystis jirovecii (P. jirovecii) is an atypical fungus that can cause severe interstitial pneumonia in immunocompromised patients. In this study, mitochondrial large subunit ribosomal RNA (mtLSU-rRNA) and dihydropteroate synthase (DHPS) gene polymorphism in P. jirovecii isolates were investigated in Western Turkey's Izmir province and its surroundings. For this purpose, a total of 157 P. jirovecii isolates obtained from bronchoalveolar lavage samples of hospitalized cases and lung tissue samples of autopsy cases who died outside hospital were examined. Genotypes were identified by direct sequencing of mtLSU-rRNA restriction fragment length polymorphism analysis of the DHPS gene amplicons. The mtLSU-rRNA analysis revealed that genotype 2 was the most common genotype with 58%. The following genotypes were genotype 3 (13%), genotype 1 (11.6%) and genotype 4 (5.1%), while genotype 5 (0.7%) was detected in only one autopsy case. In addition, 16 (11.6%) cases had dual or triple different genotypes (mixed infection). It was observed that the genotype distribution was not affected by characteristics such as age, gender and immune status. However, the predominance of genotype 2 in solid organ tumors and the predominance of mixed infection in patients with chronic pulmonary disease were statistically significant. On the other hand, DHPS gene amplification was positive in 137 (87.3%) of 157 samples. While no mutation was observed in 135 samples, the association of wild-type and 57th codon mutation was detected in two hospitalized cases (1.5%). In this study, important epidemiological data on the distribution of mtLSU-rRNA genotypes were obtained. Also the existence of DHPS gene mutations associated with potential drug resistance in our community was shown for the first time. Further studies are needed to evaluate the possible effects of genotypes on the prognosis of the disease to help with the clinician's treatment decisions. LAY ABSTRACT: Pneumocystis jirovecii (P. jirovecii) is an atypical fungus that can cause life-threatening pneumonia in immunocompromised patients. In this study, we investigated the mtLSU-rRNA and DHPS gene polymorphisms in P. jirovecii isolates from both hospital and autopsy cases.

[Evaluation of SARS-CoV-2 PCR Positive Cases in the Pediatric Emergency Department]. / Çocuk Acil Serviste SARS-CoV-2 PCR Pozitif Saptanan Olgularin Degerlendirilmesi.

In December 2019, a previously unknown type of coronavirus was detected in China and named as "severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)". The World Health Organization has named the SARS-CoV-2 related as coronavirus disease-2019 (COVID-19) and declared it as a pandemic. There is a limited data about the COVID-19 disease for the pediatric patients. In this study, it was aimed to evaluate the epidemiological, clinical, laboratory and radiologic findings, treatment and clinical outcomes of patients admitted to the pediatric emergency department with the suspicion of COVID-19. Between March 11 and June 16, 2020, patients aged between 1 month-18 years admitted to the pediatric emergency department and who have an indication for sampling for the polymerase chain reaction (PCR) method with the suspicion of COVID-19 according to the current guidelines published by the Ministry of Health were included in the study. The demographic characteristics, symptoms, durations and the history of contact with the suspected/definite COVID-19 cases were questioned in the patients with positive results. Physical examination, laboratory and imaging data of the patients were recorded. According to clinical severity, patients were divided into five groups. Treatment methods, ward/intensive care unit admission, length of stay at hospital, and prognosis were recorded. Of the 237 patients included in the study, 45 (18.9%) of the samples were positive and 192 (81.1%) were negative. There was a history of contact with COVID-19 positive case in 38 (85.6%) of COVID-19 PCR positive patients. The mean time for onset of symptoms after contact was 3.5 ± 1.7 days. Twenty-one of the patients (46.6%) were asymptomatic and the most common symptom was fever (34.1%) and cough (27.3%). Of the patients whose laboratory tests were requested, lymphopenia wasdetected in 50% and 52.3% of procalcitonin, 23.5% of C-reactive protein and 64.7% of D-dimer values were found to be high. Chest radiography was obtained from 45.4% of the patients; 90.0% were evaluated as normal, bronchovascular change, pleural effusion and consolidation were detected in one of each (5.0%) patient. Thorax computed tomography (CT) was obtained from 4 (9.0%) patients. One patient had normal CT findings, two patients had consolidation, one patient had peripheral ground-glass appearance and one patient had pleural effusion. Antibiotics were started in 38.6% of the patients and the most commonly used antibiotic was azithromycin (34.1%). Oseltamivir was started in one (2.3%) patient, and 10 (24.7%) patients were treated with hydroxychloroquine. There were no serious and critical cases according to the clinical severity. Pediatric patients constitute a small part of COVID-19 individuals in the community, and a significant part of them are asymptomatic, and patients who are symptomatic present with a mild clinic. In our study, most of the patients had a history of contact with COVID-19 positive cases, therefore, it should be questioned when evaluating a pediatric patient. There were no specific findings for COVID-19 positive patients in terms of laboratory and radiology.

[Evaluation of Real-Time Polymerase Chain Reaction in Pneumocystis jirovecii Laboratory Diagnosis]. / Pneumocystis jirovecii Laboratuvar Tanisinda Gerçek Zamanli Polimeraz Zincir Reaksiyonu Yönteminin Degerlendirilmesi.

Pneumocystis jirovecii is a human-specific species and causes fatal infections like P.jirovecii pneumonia (PCP) in immunocompromised persons. Although direct microscopy is the gold standard in the diagnosis of the microorganism, molecular methods such as polymerase chain reaction (PCR) are needed in non-human immune deficiency virus (HIV) immunosuppresive patients with low P.jirovecii burden. In this study, we aimed to evaluate the value of real-time PCR (Rt-PCR) in the laboratory diagnosis of P.jirovecii. Bronchoalveolar lavage (BAL) specimens of 658 patients sent to Dokuz Eylul University Hospital Central Medical Parasitology Laboratory on suspicion of PCP were included in the study. BAL fluids were evaluated for identification of P.jirovecii mitochondrial gene coding ribosomal large subunit (mtLSUrRNA) using Rt-PCR. In addition, Giemsa and Gomori's methenamine silver (GMG) staining assays were applied to all samples and nested PCR (n-PCR) assay was applied to positive samples detected by real time PCR. Ninety-two (14.3%) of these samples were positive by Rt-PCR. Of these 92 patients, 85 (92.4%) were positive with n-PCR. Only seven of the specimens had P.jirovecii cysts and trophozoites with microscopic examination. The mean cycle threshold (CT ) value of Rt-PCR positive patients was 29.7 (18.17 ≤ CT ≤ 37.96). P.jirovecii load in these patients was calculated as 2.6 x 101-6.15 x 107 copies/ml. The difference between the mean CT values of n-PCR positive and negative results was statistically significant (p< 0.01). The CT values of Rt-PCR of the samples with positive microscopy were; 18.2, 20.9, 22.2, 24.3, 24.7, 26.5, 29.7. The difference between the CT means of the samples with positive and negative microscopy was statistically significant (p< 0.05). When positive patients were grouped according to their diagnosis; the lowest mean CT value (CTmean= 24.8) was found in HIV-positive patients. On the other hand, CT values were found to be significantly lower in the organ transplantation patients (CTmean= 26.15) and in the collagen-vascular-inflammatory patient group (CTmean= 27.8). This study demonstrated that Rt-PCR was the effective method in the diagnosis of P.jirovecii in the laboratory. Conventional n-PCR method was found to be more unsuccessful than Rt-PCR in the presence of very low density organism; direct microscopy is generally found to be positive in samples with a higher burden of P.jirovecii.

Hepatitis A, B and C seropositivity among first-year healthcare students in western Turkey: a seroprevalence study.

BACKGROUND: The risk of viral hepatitis among healthcare students (HCSs) is greater than that among the general population. Therefore, this study was conducted to investigate the seroprevalence of the hepatitis A virus (HAV), hepatitis B virus (HBV) and hepatitis C virus (HCV) among first-year HCSs at a university in Turkey and as a secondary objective, to determine the factors associated with HAV and HBV seropositivity. METHODS: This cross-sectional study was performed in first-year HCSs in Izmir, western Turkey. Data were collected using a self-administered questionnaire including items on sociodemographic characteristics, medical history, and hygiene. A total of 650 HCSs were tested for the HAV, HBV and HCV markers. Categorical variables were compared using the chi-square test. The association between independent variables and anti-HAV seropositivity and anti-HBs seropositivity was assessed by multinomial logistic regression analysis. RESULTS: The overall frequency of total anti-HAV seropositivity was 34.9%. HBsAg, total anti-HBc and anti-HBs seropositivity were found in 0.3, 1.2 and 93.7% of samples, respectively. All of the HCSs were negative for anti-HCV. Total anti-HAV seropositivity was found to be 1.73 times higher in those ≥21 years old, and it was 1.61 times higher in those who perceived their economic status to be average and 2.75 times higher in those who perceived their economic status to be low. Total anti-HAV seropositivity was found to be 4.37 times higher in those who lived in provinces with intermediate human development index levels. Total anti-HBs seropositivity was found to be 2.48 times higher in those ≤20 years old, and it was 2.13 times higher in those who perceived their economic status to be average. CONCLUSIONS: Approximately two out of three HCSs were susceptible to HAV infection. Since HCSs are at high risk for HAV infection, they should be vaccinated before medical clerkships begin. Our results indicate that there is a high prevalence of anti-HBs seropositivity among HCSs. This result may be largely attributed to the implementation of a successful vaccination program in Turkey since 1998.

COVID-19 S: A new proposal for diagnosis and structured reporting of COVID-19 on computed tomography imaging.

PURPOSE: Because of the widespread use of CT in the diagnosis of COVID 19, indeterminate presentations such as single, few or unilateral lesions amount to a considerable number. We aimed to develop a new classification and structured reporting system on CT imaging (COVID-19 S) that would facilitate the diagnosis of COVID-19 in the most accurate way. METHODS: Our retrospective cohort included 803 patients with a chest CT scan upon suspicion of COVID 19. The patients' history, physical examination, CT findings, RT PCR, and other laboratory test results were reviewed, and a final diagnosis was made as COVID 19 or non-COVID 19. Chest CT scans were classified according to the COVID 19 S CT diagnosis criteria. Cohen's kappa analysis was used. RESULTS: Final clinical diagnosis was COVID-19 in 98 patients (12%). According to the COVID-19 S CT diagnosis criteria, the number of patients in the normal, compatible with COVID 19, indeterminate and alternative diagnosis groups were 581 (72.3%), 97 (12.1%), 16 (2.0%) and 109 (13.6%). When the indeterminate group was combined with the group compatible with COVID 19, the sensitivity and specificity of COVID-19 S were 99.0% and 87.1%, with 85.8% positive predictive value (PPV) and 99.1% negative predictive value (NPV). When the indeterminate group was combined with the alternative diagnosis group, the sensitivity and specificity of COVID-19 S were 93.9% and 96.0%, with 94.8% PPV and 95.2% NPV. CONCLUSION: COVID-19 S CT classification system may meet the needs of radiologists in distinguishing COVID-19 from pneumonia of other etiologies and help optimize patient management and disease control in this pandemic by the use of structured reporting.

Changes on Hepatitis C virus genotype distribution in Western Turkey: Evaluation of twelve-year data.

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.

[A Seven-Year Evaluation of Viral Central Nervous System Infections]. / Viral Etkenlere Bagli Santral Sinir Sistemi Enfeksiyonlarinin Yedi Yillik Degerlendirmesi.

Identification of viral agents causing central nervous system (CNS) infections increased by the application of nucleic acid tests. In this study, the results of polymerase chain reaction (PCR) for viral agents were evaluated in cerebrospinal fluid (CSF) samples taken from patients with CNS infection. CSF samples taken from 1185 patients between 2010 and 2017 were tested for the presence of Herpes simplex virus (HSV) type 1 and 2, Varicella Zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), adenovirus ve enterovirus by PCR in Dokuz Eylul University Hospital. Tests were performed according to the clinicians' orders and results were evaluated retrospectively. The number of tests performed were 1038 for HSV, 882 for adenovirus, 865 for enterovirus, 496 for VZV, 100 for EBV and 92 for CMV. Commercial tests were used for EBV, CMV (Artus QS-RGQ Kits, Qiagen, Germany) and enterovirus (GeneXpert, Cepheid, USA) while the other viruses (HSV, VZV, adenovirus) were tested by in-house real-time PCR assays. Ninety-one CSF (7.7%) samples were positive. The mean age was 13 (<1 to 76 years) while median was seven. The most frequently detected pathogens were enterovirus (63/91, 69%) and HSV-1 (14/91,15%). The number of patients positive for adenovirus, VZV, EBV and CMV were five, four, three and two, respectively. In one patient, both enterovirus (Ct: 29.5) and EBV (Ct: 38.53) were positive. The number of positive samples were increased in summer months. Enterovirus RNA positive patients (n= 60/63, 95.2%) were ≤ 18 years old while 29% were younger than one year of age. Enterovirus positive samples peaked in 2012 and 2014 and detected mainly in summer (60.3%) and autumn (20.6%) months. VZV was mostly detected in patients greater than 65 years of age. Mean Ct of the positive reactions was 31.87 ± 3.5 (22.88-40.32). The lowest and the highest Ct values were detected in HSV-1 assay. The mean Ct value of enterovirus assay (30.4; 25.7-35.9) was lower than the other pathogens' values. In the seven-year period, 7.7% of the1185 patients' CSF samples were positive for viral nucleic acids. As expected, enteroviruses were the most common pathogens in children and detected mainly in summer-autumn period. Syndromic approach in CNS infections could increase the viral pathogen detection.

[A Case of Congenital Syphilis and Prozone Phenomenon]. / Konjenital Sifilis Olgusu ve Prozon Fenomeni.

The screening for syphilis during pregnancy is important to prevent intrauterine transmission and complications. Prozone phenomenon may cause a false negative result in non-treponemal syphilis tests, which complicates an accurate diagnosis. In this case report a newborn syphilis case was presented to emphasize the importance of reverse algorithm in diagnosis and the prozone phenomenon which can cause problems in rapid plasma reagin (RPR) test. The 2920 g infant patient was born from a 24-year-old mother with no known diseases, at the 35th week of gestation by cesarean section due to premature rupture of membranes. The initial physical examination of the newborn revealed erythema and exfoliation of the bilateral hands and feet. Laboratory results revealed CRP: 90 mg/L, WBC: 19.2 x 103/µl, hemoglobin: 9.5 g/dl, platelet count: 214 x 103/µl, HIV-Ag/Ab: non-reactive, anti-Toxoplasma gondii IgM and IgG: negative, anti-cytomegalovirus IgM: negative, anti-cytomegalovirus IgG: positive (128.7 AU/ml), anti-Rubella IgM: negative, anti-Rubella IgG: positive (26 IU/ml), anti-Treponema pallidum (anti-T.pallidum) antibody [IgM and IgG by the chemiluminescence microparticle enzyme immunoassay (Architect Syphilis TP; Abbott Japan Co, Japan)]: positive (Signal Cut Off value (S/CO): 28.35), and RPR (Omega Diagnostics, UK): negative. All of the above ELISA tests were performed by using Architect (Abbott Diagnostics, Wiesbaden, Germany) kits. When the RPR test was repeated with serial dilutions of the serum in order to detect prozone phenomenon, positive reaction was detected starting from 1:2 and ending at 1:64 dilution. It was determined that the mother was not tested for syphilis during her pregnancy. When both the mother and the father were tested for syphilis, the mother's anti-T.pallidum total antibody test result was reactive (S/CO: 30.52) and the RPR was positive at 1:32 dilution, while the father's anti-T.pallidum total antibody test result was reactive (S/CO: 16.05) and the RPR was negative. A four-fold difference between the maternal and infant RPR dilutions is required by the guidelines for a laboratory diagnosis of congenital syphilis. Although this criterion was not met in the newborn, the case was accepted as congenital syphilis due to clinical findings. Congenital syphilis must be considered in the differential diagnosis in the presence of skin manifestations at the birth and early neonatal period. Accurate and early diagnosis of the disease is important to start appropriate treatment and prevent complications. As described in the presented case, the use of reverse syphilis test algorithm will enable to reach the correct diagnosis of the infection. If the result of the treponemal test is positive and the RPR test is negative, prozone phenomenon should be considered and the RPR test should be repeated with serial serum dilutions.

Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients.

Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent-specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real-time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8-year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016-2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season.