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.
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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.
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Abdullah SAYINER,
M. Sezai TAŞBAKAN ,
BEGÜM ERGAN ,
Oğuz KILINÇ ,
AYÇA ARZU SAYINER ,
Rüçhan SERTÖZ , Selin OZUYGUR,
Selin ERCAN ,
Yusuf SAVRAN ,
PERVİN KORKMAZ EKREN ,
Özen Kaçmaz BAŞOĞLU ,
Mustafa OZHAN
To evaluate the clinical features and outcomes of patients who were admitted with a diagnosis of coronavirus disease 2019(COVID-19) but who were not confirmed with polymerase chain reaction (PCR) positivity.MATERIAL AND METHODS: This is a retrospective analysis of all patients admitted to two tertiary care centers between March 15 andMay 15, 2020, with a diagnosis of COVID-19. From a common database prepared for COVID-19, we retrieved the relevant data andcompared the clinical findings and outcomes of PCR-positive patients with those of PCR-negative cases who had been diagnosed on thebasis of typical clinical and radiographic findings.RESULTS: A total of 349 patients were included in the analysis, of which 126 (36.1%) were PCR-negative. PCR-negative patients wereyounger (54.6 ± 20.8 vs. 60.8 ± 18.9 years, P = .009) but were similar to PCR-positive patients in terms of demographics, comorbidities,and presenting symptoms. They had higher lymphocyte counts (1519 ± 868 vs. 1331 ± 737/mm3, P = .02) and less frequently presentedwith bilateral radiographic findings (68.3% vs. 79.4%, P = .046) than PCR-positive patients. Besides, they had less severe disease andbetter clinical outcomes regarding admission to the intensive care unit (9.6% vs. 20.6%, P = .023), oxygen therapy (21.4% vs. 43.5%, P< .001), ventilatory support (3.2% vs. 11.2%, P = .03) and length of hospital stay (5.0 ± 5.0 vs. 9.7 ± 5.9 days, P < .001).CONCLUSION: This study confirms that about one-third of the COVID-19 patients are PCR-negative and diagnosed based on clinicaland radiographic findings. These patients have a more favorable clinical course, shorter hospital stays, and are less frequently admittedto the intensive care unit.
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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.
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Background: In Turkey, cytomegalovirus (CMV) seropositivity has been reported to be high, between 85 and 100%. CMV has been
responsible for disease exacerbation in inflammatory bowel disease (IBD). We aimed to evaluate the presence of CMV in intestinal tissue
by immunohistochemical staining in IBD and non-IBD patient groups, in a country with high CMV seroprevalence.
Methods: In this prospective cross-sectional study, the presence of intestinal CMV was investigated with tissue immunohistochemistry
(IHC) staining, which is accepted as the gold standard method, and with polymerase chain reaction (PCR) in tissue and blood. Patients
(≥18 years old, n = 189) who had a colonoscopic biopsy between January and May 2017 were included in the study at our hospital.
Clinical, laboratory, endoscopic, and histopathological data of patients were assessed by dividing them into IBD (n = 34) and non-IBD
(n = 155) groups.
Results: In this study, 567 colonic biopsy samples from 189 patients were evaluated. Tissue IHC staining was positive for 3 (1.58%) non-
IBD patients. One of them was diagnosed as CMV ileitis. CMV DNA was also detected in 14 plasma (7.40%, <80-469 copies/mL) and
20 tissue samples (10.69%, 7-15 289 copies/mL). Tissue IHC staining is accepted as the gold standard for CMV ileitis, and the sensitivity
and specificity of tissue PCR was 33% and 89.67%, while the sensitivity and specificity of plasma PCR was 66.66% and 93.54%,
respectively.
Conclusion: Although CMV seroprevalence is high in Turkey, CMV ileitis was diagnosed in only one non-IBD patient (0.53%). Compared
to tissue IHC staining, the sensitivity of tissue and blood CMV PCR was low while their specificity was higher.
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Objective: With the rapid spread of SARS-CoV-2, a new coronavirus,
around the world, a pandemic was declared by World Health Organization on March 2020. The first cases were reported in March 2020 from
Turkey. In our hospital, the first pediatric case was detected on April 2,
2020. However, there is no data on whether this virus had been present in our region or not before this date. The aim of our study was to
determine the first entry of SARS-CoV-2 virus to our region for pediatric
patients.
Material and Methods: SARS-CoV-2 positivity was investigated retrospectively with the RT-qPCR method in the pediatric respiratory tract
specimens taken between the October 1, 2019 and March 31, 2020. In
the specimens, SARS-CoV-2 RNA was studied using real-time PCR based
“COVID-19 RT-qPCR Detection Kit”.
Results: 886 samples were included in the study. Of the respiratory tract
specimens, 97.1% were nasopharyngeal swabs, 2.8% were bronchoalveolar lavage. Most frequently, rhinovirus (28.6%), influenza A subtype
H1N1 (pandemic H1N1) (18.5%) and influenza B (16%) were detected.
Rhinovirus and enterovirus were the most frequent double agents seen
together. No SARS-CoV-2 positivity was detected in the respiratory tract
specimens studied.
Conclusion: SARS-CoV-2 PCR test was conducted in a limited number
of centers at the beginning of the pandemics may have affected the detection of the first case in Turkey. Multicenter studies of archived samples
would enable more realistic results in tracking SARS-CoV-2 in our country.
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PURPOSEBecause of the widespread use of computed tomography (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.METHODSOur 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.RESULTSFinal 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.CONCLUSIONCOVID-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.
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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.
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Nihan ŞIK ,
Canan ÖZLÜ ,
Hatice KARAOĞLU ASRAK ,
İrem Ceren ERBAŞ ,
Ayşe ÇAKIL GÜZİN ,
Gizem ATAKUL ,
Özge ATAY ,
Özgür APPAK ,
AYÇA ARZU SAYINER ,
Nevin UZUNER ,
Suna ASİLSOY ,
Nurşen BELET ,
Durgül YILMAZ ,
Murat DUMAN
Aralık 2019 tarihinde Çin’de daha önce bilinmeyen bir koronavirüs türü saptanmış olup, “severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)” olarak adlandırılmıştır. Dünya Sağlık Örgütü, SARS-CoV-2 ilişkili hastalığı “coronavirus disease-2019 (COVID-19)” olarak adlandırmış ve pandemi olarak ilan etmiştir. Çocuk hastalar ile ilgili veriler kısıtlıdır. Bu çalışmada, COVID-19 şüphesi ile çocuk acil servise başvuran ve tanı alan hastaların epidemiyolojik, klinik, laboratuvar ve görüntüleme bulguları ile tedavi ve klinik sonlanımlarının değerlendirilmesi amaçlanmıştır. 11 Mart 2020-16 Haziran 2020 tarihleri arasında, çocuk acil serviste, yaşları 1 ay-18 yaş arasında değişen ve Sağlık Bakanlığı tarafından yayımlanan güncel kılavuzlara göre, COVID-19 şüphesiyle polimeraz zincir reaksiyonu (PCR) yönte-mi için örnek alma endikasyonu olan hastalar çalışmaya dahil edilmiştir. Pozitif sonuçlanan hastaların demografik özellikleri, semptomları ve süreleri, COVID-19 şüpheli/kesin olgu ile temas öyküsü sorgu-lanmıştır. Hastaların fizik muayene bulguları, laboratuvar verileri, görüntüleme sonuçları kaydedilmiştir. Klinik ağırlığa göre hastalar beş gruba ayrılmıştır. Hastalara uygulanan tedavi yöntemleri, servis/yoğun bakım yatışı ve süreleri ile prognozları kaydedilmiştir. Çalışmaya toplam 237 hasta dahil edilmiş olup, alınan örneklerin 45 (%18.9)’i pozitif, 192 (%81.1)’si negatif saptanmıştır. COVID-19 PCR pozitif has-taların 38 (%85.6)’inde temas öyküsü saptanmıştır. Temas sonrası semptomların başlamasına kadar geçen süre ortalama 3.5 ± 1.7 gün olarak bulunmuştur. Hastaların 21 (%46.6)’i asemptomatik olup, semptomatik olanlarda en sık başvuru yakınmalarının ateş yüksekliği (%34.1) ve öksürük (%27.3) ol-duğu belirlenmiştir. Laboratuvar tetkiki istenen hastaların %50’sinde lenfopeni saptanmış, %52.3’ünde prokalsitonin, %23.5’inde C-reaktif protein, %64.7’sinde D-dimer değerleri yüksek bulunmuştur. Has-taların %45.4’ünden akciğer grafisi istenmiş, %90.0’ı normal sonuçla değerlendirilmiş, birer (%5.0) hastada olmak üzere bronkovasküler değişiklik, plevral efüzyon ve konsolidasyon gözlenmiştir. Toraks bilgisayarlı tomografisi (BT) istenen hasta sayısı 4 (%9.0) olup, bir hastanın BT’si normal saptanmış, iki hastada konsolidasyon, bir hastada periferik buzlu cam görünümü ve bir hastada plevral efüzyon izlen-miştir. Hastaların %38.6’sına antibiyotik başlanmış ve en sık kullanılan antibiyotik azitromisin (%34.1) olmuştur. Bir (%2,3) hastaya ise oseltamivir başlanmış, 10 (%22.7) hasta hidroksiklorokin ile tedavi edilmiştir. Klinik ağırlığa göre ciddi ve kritik olgu saptanmamıştır. Çocuk hastaların önemli bir bölümü asemptomatik seyretmekte, semptomatik olan hastalar da hafif klinik göstermektedir. Çoğu hastada temas öyküsü mevcuttur, bu nedenle hastayı değerlendirirken bu durum mutlaka sorgulanmalıdır. La-boratuvar ve radyolojik olarak COVID-19 pozitif hastalara özgül bir bulguya rastlanmamıştır.
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İnsana özgül bir tür olan Pneumocystis jirovecii, immün sistemi baskılanmış kişilerde P.jirovecii pnömonisi (PCP)’ne neden olarak ölümcül enfeksiyonlara yol açmaktadır. Mikroorganizmanın tanısında direktmikroskopi altın standart olsa da düşük P.jirovecii yükünün gözlendiği insan immün yetmezlik virüsü (HIV)dışı immünsupresif hastalarda polimeraz zincir reaksiyonu (PCR) gibi moleküler yöntemlere gereksinimduyulmaktadır. Bu çalışmada gerçek zamanlı PCR (Rt-PCR) yönteminin P.jirovecii laboratuvar tanısındakideğerinin ortaya konulması amaçlanmıştır. Dokuz Eylül Üniversitesi Hastanesi Merkez Tıbbi Parazitoloji Laboratuvarına PCP şüphesiyle gönderilen 658 hastanın bronkoalveoler lavaj (BAL) örneği çalışmayadahil edilmiştir. BAL sıvısı örnekleri P.jirovecii ribozomal RNA büyük alt ünitesini kodlayan mitokondriyalgeni (mtLSUrRNA) çoğaltan Rt-PCR yöntemi ile değerlendirilmiştir. Tüm örneklere Giemsa ve Gomori’ninmetenamin gümüş (GMG) boyaları uygulanırken Rt-PCR ile pozitif saptanan örnekler ayrıca nested-PCR(n-PCR) yöntemi ile de değerlendirilmiştir. Bu örneklerin 92 (%14.3)’si Rt-PCR ile pozitif olarak bulunmuştur. n-PCR ile 92 hastanın 85 (%92.4)’inde pozitiflik saptanmıştır. Mikroskobik inceleme sonucundaise örneklerin yalnızca yedisinde P.jirovecii kist ve trofozoitlerine rastlanmıştır. Rt-PCR pozitif hastalarınortalama “cycle threshold (CT)” değeri 29.7 (18.17 ≤ CT ≤ 37.96) olarak saptanmıştır. Bu hastalardakiP.jirovecii yükü 2.6 x 101-6.15 x 107 kopya/ml olarak hesaplanmıştır. n-PCR ile pozitif saptanan örneklerinRt-PCR’deki CT değerlerinin ortalaması (CTort= 29.2) ile negatif bulunanların ortalaması (CTort= 36.7)arasındaki fark istatistiksel olarak anlamlı bulunmuştur (p< 0.01). Mikroskopisi pozitif olan örneklerin RtPCR’deki CT değerlerinın sırasıyla; 18.2, 20.9, 22.2, 24.3, 24.7, 26.5, 29.7 olduğu görülmüştür. Mikroskopisi pozitif ve negatif olan örneklerin CT ortalamaları arasındaki fark yine istatistiksel olarak anlamlıydı (p<0.05). Pozitif bulunan hastalar tanılarına göre gruplandığında; en düşük CT değer ortalamasının (CTort=24.8) HIV pozitif hastalarda olduğu görülmüştür. Organ transplantasyonu hastaları (CTort= 26.15) vekolajen-vasküler-enflamatuvar hasta grubunda (CTort= 27.8) saptanan CT değer ortalamaları diğer gruplardan istatistiksel olarak anlamlı düzeyde düşük bulunmuştur. Bu çalışma, Rt-PCR’nin P.jirovecii laboratuvar tanısında etkili bir yöntem olduğunu ortaya koymuştur. Konvansiyonel n-PCR yönteminin çok düşükyoğunluktaki etken varlığında Rt-PCR’ye göre daha başarısız olduğu; direkt mikroskopinin ise genellikleetkenin yoğun olduğu örneklerde pozitif sonuç verdiği anlaşılmaktadır.
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