Muhammed Alper Özarslan

Introduction: The aim of this study was to compare the performance of different clinical specimens—nasopharyngeal (NP) swabs collected by healthcare professionals (HCP-NP), self-collected nasal swabs (Sc-N), and saliva samples (S)—in diagnostic tests for investigating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and influenza A/B RNA. Methodology: These clinical samples were collected from 404 symptomatic cases and tested with the SARS-CoV-2 and influenza A/B RNA tests on the cobas 6800 System of Roche Molecular Systems (Roche Molecular Systems, Pleasanton, USA). The SARS-CoV-2 or influenza virus infection status was determined for all patients based on the predefined criteria and corresponding algorithms. Positive and negative predictive values (PPV, NPV), sensitivity, specificity, coefficient of variation (CV), interrater reliability, correlation, ,and days of sample collection of these three sample types were analyzed. Results: There was almost perfect agreement between the these sample types for the diagnosis of SARS-CoV-2 and influenza A. The overall performance (PPV, NPV, sensitivity) and reproducibility (CV ≤ 6%) were favorable. Additionally, they showed similar trends for days of sample collection. Conclusions: Diagnostic detection of SARS-CoV-2 and influenza RNA from Sc-N and S samples was comparable to HCP-NP samples. Using these samples would provide an advantage in diagnosing SARS-CoV-2 and influenza A infection, as they can be easily collected without the need for viral transport media.

Yersinia pseudotuberculosis is a rare pathogenic organism in humans and is encountered mostly in patients with acquired or hereditary iron overload. This case report presents such a case with no known risk factors for iron overload, except heterozygous mutations in MPEG1 and HFE genes, while presenting the first patient with Y. pseudotuberculosis liver abscess in Turkiye. Here we present a 63-years-old male with known long-standing hypertension, type 2 diabetes, peripheral artery disease and chronic kidney disease presenting with right upper quadrant pain, nausea, vomiting and fever, whose imaging studies revealed multiple liver abscesses. While investigating the etiology, Yersinia pseudotuberculosis growth was observed in his abscess aspiration material and blood culture. Genetic analysis conducted after the detection of a ferritin level of 13725 µg/L, showed a heterozygous H63D mutation in HFE. Consequent whole-exon-sequencing reported an additional heterozygous p. Thr73Ala m-tation in MPEG1. Even though, Y. pseudotuberculosis is detected mostly in patients with primary hemochromatosis, even heterozygous carriers of hemochromatosis may present clinically if concomitant comorbidities exist and may pose a challenge not only to clinicians but also to laboratory diagnosticians

Various clinical outcomes, reinfections, vaccination programs, and antibody responses resulted from the COVID-19 pandemic. This study investigated the time-dependent changes in SARS-CoV-2 antibody responses in infected and/or vaccinated and unvaccinated individuals and to provide insights into spike and nucleocapsid antibodies, which fluctuate during infectious and non-infectious states. This cohort study was carried out at the Ege University Faculty of Medicine hospital in İzmir (western Turkey) and the Erciyes University Faculty of Medicine hospital in Kayseri (central Turkey) between December 2021 and January 2023, which coincided with the second half of COVID-19 pandemic. The study included 100 COVID-19 PCR-positive patients and 190 healthcare workers (HCWs). Antibody levels were followed up via quantitative anti-SARS-CoV-2 spike and qualitative anti-nucleocapsid immunoassays (Elecsys™). Antibody levels declined after infection but persisted for at least 6–8 months. Individuals who had received only CoronaVac had higher anti-nucleocapsid antibody levels in the early months than those who received mixed vaccination. However, anti-spike antibodies persisted longer and at higher levels in individuals who had received mixed vaccinations. This suggests that combining two different vaccine platforms may provide a synergistic effect, resulting in more durable and broad-spectrum immunity against SARS-CoV-2. The study provides information about the vaccination and antibody status of healthcare workers in the second half of the pandemic and provides valuable insights into the dynamics of antibody responses to COVID-19 infection and vaccination.

Influenza virus-induced autophagy is often accompanied by apoptosis and results in cell death in virus-infected cells. It is well known that autophagy is modulated by the mTOR/PI3K/Akt pathway, which plays an important role in the response to the presence of energy sources and external stimuli. This pathway is modulated by mucin 1 (MUC1), which has extracellular and intracellular components and plays an important role in metastasis and chemotherapeutic resistance. In this study, it was aimed to investigate the expression of MUC1 after the inoculation of influenza viruses into the cancer-derived cell cultures and, accordingly, the changes in autophagy markers such as mTOR and LC3B. In this study, MCF-7, He-La and A-549 cell lines were used which have adenocarcinoma origin. To control the growth of influenza virus in these cells, the MDCK cell line was also inoculated. Centrifuge-enhanced shell-vial cell culture method was used in all experiments. Influenza A (H1N1) pdm09 strain was inoculated into these cell lines then the expressions of viral nucleic acid and cycle threshold (Ct) of MUC1, mTOR, LC3B associated genes were investigated by quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) method in the samples taken from the supernatants of all cells at the end of the 48-hour incubation period. To investigate whether these markers were present in cells, after all cells were permeabilized with paraformaldehyde, cell-coated infected coverslips were stained with fluorescent labeled monoclonal antibodies developed against MUC1, mTOR, LC3B and influenza virus antigens. In the examination of fluorescence microscopy, all of the cell cultures (MCF-7, He-La and A-549) infected with influenza virus yielded positive results in terms of LC3B, mTOR and MUC1 monoclonal antibody staining, whereas all of the non-infected cells were found negative. Cycle threshold values of MUC1, LC3B and mTOR associated genes were found to be lower in A-549 cell line inoculated with influenza virus. Although protein expression was demonstrated in MCF-7 and He-La cell lines, similar changes were not detected in the 1/Ct values of genes in the autophagy pathway. The Ct value of the MUC1 gene was found to be higher only in the MCF-7 cell line after inoculation. In conclusion, it was observed that the specific expression pattern for influenza virus-induced autophagy was formed only in the A-549 cell line among the adenocarcinoma cells. It was thought that this relationship could constitute a dataset in further research on lung adenocarcinoma. However, in future studies, the determination of the expression of these genes at the protein level by using further tests will provide better comparison of the results.

Ayşe Sultan Karakoyun1, Nevzat Ünal1,2, Banu Metin3, Esra Yıldırım Servi3, Bram Spruijtenburg4,5, Muhammed Alper Özarslan6, Ramazan Gümral7, Aylin Döğen8,