Highlights There are limited number of studies analyzing viral load in COVID19 patients and any data that compare viral load to chest computerized tomography (CT) severity. There are limited number of studies that give the amount of SARS-CoV-2 RNA in clinical specimens by reporting cycle threshold (Ct) value for RT-PCR. The total stress score (TSS) was suggested to quantify pulmonary inflammation and correlate to the clinical classifications. TSS is a quantification method to score the severity of inflammation on CT images based on summing up degree of acute lung inflammation lesions involvement of each lobe (including ground-glass opacity or consolidation or other fuzzy interstitial opacities). To our knowledge, this is the first study that analyse TSS of chest CT and Ct values of SARS-CoV-2 RNA in both hospitalised and outpatients.

Introduction: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19). First COVID-19 case was detected in March, 10, 2020 in Turkey and as of May, 18, 2020 148,067 cases have been identified and 4096 citizens have died. Tuberculosis (TB) is a worldwide public health concern, incidence of tuberculosis (per 100,000 people) in Turkey was reported at 14, 1 in 2018. During pandemic COVID-19 was the main concern in every clinic and as we discuss here overlapping respiratory diseases may result in delaying of the diagnosis and treatment. Methodology: There were 4605 respiratory samples examined between March 23 and May 18 for COVID-19 and 185 samples for Mycobacterium tuberculosis in our laboratory. The Xpert Ultra assay was performed for the diagnosis of pulmonary tuberculosis; SARS-CoV-2 RNA was determined by real-time PCR (RT-PCR) analysis in combined nasopharyngeal and deep oropharyngeal swabs of suspected cases of COVID-19. Results: Both of SARS-CoV-2 and M. tuberculosis tests were requested on the clinical and radiological grounds in 30 patients. Here we discussed 2 patients who were both COVID-19 and TB positive. One patient already diagnosed with tuberculosis become COVID-19 positive during hospitalization and another patient suspected and treated for COVID-19 received the final diagnosis of pulmonary TB and Human Immunodeficiency Virus infection. Conclusions: We want to emphasize that while considering COVID-19 primarily during these pandemic days, we should not forget one of the “great imitators”, tuberculosis within differential diagnoses.

ÖZETHepatit C virusu (HCV) kronik hepatitlerin en önemli nedenlerinden biridir. HCV'ye bağlı kronik hepatitlerin seyrinde ve tedavinin planlanmasında HCV genotipleri önem taşımaktadır. Bu çalışmada, Akdeniz Üniversitesi Hastanesi Mikrobiyoloji Laboratuvarında yapılan HCV genotiplendirilmesine ait sonuçların retrospektif olarak değerlendirilmesi ve son beş yıl içinde genotip dağılımındaki değişimin incelenmesi amaçlanmıştır. Çalışmaya, 2009-2013 yılları arasında laboratuvarımıza HCV genotip tayini için gönderilen, HCV-RNA pozitif kronik hepatit C'li 422 hastaya (219 erkek, 203 kadın; yaş aralığı: 8-79 yıl, yaş ortalaması 46.3 ± 15.5 yıl) ait kan örnekleri dahil edilmiştir. Genotiplendirme için, plazma örneklerinden HCV-RNA ekstraksiyonu otomatize sistem (EZ1 Virus Mini Kit v2.0, Qiagen, Almanya) ile yapılmış ve ters hibridizasyon esaslı ticari bir "line prob assay" (LIPA; GEN-C RT-PCR, İtalya) yöntemi uygulanmıştır. Viral yük tayini için ise, HCV-RNA düzeyleri gerçek zamanlı PCR yöntemi (Cobas TaqMan HCV, Roche Diagnostics, Almanya) ile araştırılmıştır. Hastaların demografik verileri, hastane elektronik bilgi sisteminden ve hasta dosyalarından elde edilmiştir. Hastaların %63.3 (n= 267)'ünde genotip 1b, %14.7 (n= 62)'sinde genotip 1a, %11.1 (n= 47)'inde genotip 3a, %0.9 (n= 4)'unda genotip 2b ve %0.2 (n= 1)'sinde genotip 4e saptanmış; 1 hastada (%0.2) ise genotip 1 ve 4 birlikteliği izlenmiştir. Genotip 1, 2 ve 4 ile enfekte hastaların sırasıyla; %5.4 (n= 23), %2.6 (n= 11) ve %1.4 (n= 6)'ünde alt tip tayini yapılamamıştır. Kırk hastanın yabancı uyruklu olduğu (Rusya'dan 16; Ukrayna ve Gürcistan'dan

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Objective: We aimed to analyse the positivity rate and cycle threshold values indicating viral loads for SARS CoV-2 among different respiratory specimens and also to evaluate the diagnostic efficacy of saliva samples. Materials and Methods: We included combined oropharyngeal and nasopharyngeal swab (cONS), sputum, and tracheal aspirate (TA) specimens of patients. Unpreserved saliva samples were collected prospectively from hospitalized patients within 72 hours of admission. SARS CoV-2 RNA was extracted by using Bio-Speedy viral nucleic acid buffer than RT-PCR was performed with Bio-Speedy COVID-19 qPCR detection kit. Results: Retrospective evaluation revealed SARS CoV-2 RNA in 19.66% of cONS (n: 5819), 30.77% of sputum (n: 39), 29.41% of TA samples (n: 34) from 4812 patients. In the majority (86.72%) of the samples, the first cONS sample was positive. Consecutive cONS and sputum/TA samples were investigated in 52 patients of whom 11 were positive with either of these samples. Saliva positivity was detected in 60% of cONS positive (n: 20) and 30% of cONS negative (n: 12) patients. Conclusion: Although, cONS samples show the greatest diagnostic guidance, repeated sampling from multiple sites of the respiratory tract increases the possibility of COVID-19 diagnosis. Saliva samples might be considered as an alternative specimen.