Tenofovir disoproxil fumarate in the treatment of COVID-19: Evaluation of 78 patients.

One of the drugs that has been suggested for the treatment of SARS-CoV-2 infection is tenofovir disoproxil (TDF). Herein, it was aimed to evaluate the outcomes of TDF receiving COVID-19 cases in terms of day 7-10 PCR negativity and day 30 survival. Patients who received TDF due to PCR-confirmed COVID-19 between 27.04.2021 and 31.12.2021 were included in our study. The primary outcome was considered to be 7-10 days of PCR negativity, while the secondary outcome was considered 30-day survival after diagnosis of COVID-19. Patients who died before completing the treatment period (7-10 days) were also considered as PCR failures. Data were analyzed both in terms of intention to treat basis and in the subgroup that survived to the end of treatment. A total of 78 patients (30 women, mean age: 61.15±18.5 years) met the inclusion criteria. In the intention to treat analysis group, one-month-mortality was 44.87% (35/78) in the overall cohort. In the end of treatment analysis group, one-month-mortality was 29.5% (18/61) in the overall cohort. Day 7-10 PCR negativity was detected in 55.7% of the overall EOT cohort. Our data suggest that TDF may be an alternative salvage treatment option in antiviral unresponsive patients. We suggest evaluating TDF in well-designed controlled trials involving treatment-naïve cases.

Importance of screening severe COVID-19 patients for IFN-λ1, IL-6 and anti-S1 IgG levels.

Cytokine storm is an important cause of death in COVID-19 patients. A recent clinical study showed that administration of recombinant interferon lambda 1 (IFN-λ1 or IL-29) may prevent severe COVID-19. On the other hand, IL-6 has been associated as a prognostic marker of worsening for COVID-19 patients. The objective of this study is to screen IFN-λ1, IL-6 and antibody levels in consecutive serum sample sets of COVID-19 patients. A total of 365 serum samples collected from 208 hospitalized COVID-19 patients were analyzed for IFN-λ1 and IL-6 levels as well as SARS-CoV-2 neutralizing antibodies and anti-S1 IgG antibodies. Analyses of serum samples for cytokine levels showed that IFN-λ1 (>8 pg/mL) and IL-6 (>2 pg/mL) were detected in approximately 64% and 21% patients, respectively. A decrement in IFN-λ1 levels and IL-6 levels above 35 pg/mL can be sign of clinical severity and upcoming dead. An increment in IL-6 levels wasn't detected in every COVID-19 patient but a decrement in IL-6 levels was related to clinical improvement. Importantly, the detection of IFN-λ1 level together with an increase in anti-S1 IgG antibody response were observed in clinically improved patients. Screening severe COVID-19 patients for IFN-λ1, IL-6, and anti-S1 IgG antibody levels during their hospital stay especially in intensive care units may be beneficial to monitor the clinical status and management of treatment strategies. Importantly, detection of IFN-λ1 together with protective IgG antibody response can be an indication of clinical improvement in severe COVID-19 patients and these patients may be discharged from the hospital soon.

Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection.

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

Cardiac Assessment in Children with MIS-C: Late Magnetic Resonance Imaging Features.

Multisystem Inflammatory Syndrome (MIS-C) is a new entity that emerges 2-4 weeks after the SARS-CoV-2 infection in children. MIS-C can affect all systems, the most severe of which is cardiac involvement. The duration of the cardiac symptoms is still uncertain and may be persistent or prolonged. The American College of Rheumatology Clinical Guidelines recommends cardiac magnetic resonance imaging (MRI) 2-6 months after the diagnosis of MIS-C in patients presenting with significant transient left ventricular (LV) dysfunction in the acute phase of illness (LV ejection fraction 50%) or persistent LV dysfunction. There are a few studies investigating cardiac MRI findings in MIS-C patients. In this study, we aimed to evaluate cardiac MRI findings, at the earliest 3 months after diagnosis, and compare these findings with the echocardiograms in children with MIS-C. A retrospective study including 34 MIS-C patients was conducted at a tertiary-level University Hospital between June 2020 and July 2021. Centers for Disease Control and Prevention criteria were used in the diagnosis of MIS-C. Cardiac MRI was performed at least 3 months after MIS-C diagnosis. The study included 17 (50%) boys and 17 (50%) girls with a mean age of 9.31 ± 4.72 years. Initial echocardiographic evaluation revealed cardiac abnormality in 13 (38.2) patients; 4 (11.8%) pericardial effusion, 4 (11.8%) left ventricular ejection fraction (LVEF) < 55%, and 5 (14.7%) coronary artery dilatation. Echocardiography showed normal LV systolic function in all patients during follow-up; coronary dilatation persisted in 2 of 5 (40%) patients at the 6th-month visit. Cardiac MRI was performed in 31 (91.2%) patients, and myocardial hyperemia was not detected in any patients (T1 relaxation time was < 1044 ms in all children). However, 9 (29%) patients' MRI showed isolated elevated T2 levels, and 19 (61.3%) revealed at least one of the following findings: pericardial effusion, right ventricular dysfunction, or LVEF abnormality. In patients with MIS-C, a high rate of cardiac involvement, particularly pericardial effusion was determined by cardiac MRI performed at the earliest 2-6 months after diagnosis. Even if echocardiography does not reveal any abnormality in the initial phase, cardiac MRI should be suggested in MIS-C patients in the late period. This is the first study reporting cardiac MRI findings in the late period of MIS-C patients.

SARS-CoV-2 reinfections in the pediatric cohort-a single-center experience.

BACKGROUND: This study focused on timelines of infection episodes and dominant variants and aims to determine disease severity and outcome of pediatric patients with reinfection. MATERIALS AND METHODS: This study retrospectively evaluated the medical records of the hospitalized patients and/or outpatients aged 0-18 with a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction between March 2020 and September 2022 at Ege University Children's Hospital. RESULTS: Ninety-one pediatric patients reinfected with SARS-CoV-2 were included in the study. There was an underlying disease in 26.4% of the patients. The median time between the two infection episodes was 184 (90-662) days. There were 24 patients (26.3%) with the first infection in pre-Delta period; 17 (18.6%) of them were reinfected in Omicron BA.1 period, while 7 (7.6%) in Omicron BA.4/BA.5 period. Forty-five patients (49.4%) were infected initially in the Delta period; 35 patients (38.4%) were reinfected in the Omicron BA.1 period, while 10 patients (10.9%) were reinfected in the Omicron BA.4/BA.5 period. Twenty-two patients (24.1%) had the first infection in the Omicron BA.1 period and then reinfected in the Omicron BA.4/BA.5 period. Patients with reinfection more frequently displayed a symptom (84.6% vs. 94.5%, p = 0.03). The hospitalization rate significantly declined in reinfection (15.3% vs. 7.6%, p = 0.03). Severe disease, treatment needs and steroid use were decreased in reinfections without a significant difference (p > 0.05). Intensive care unit admission was not altered. CONCLUSION: This study revealed that reinfections frequently develop in previously healthy children but do not cause more severe outcomes. The risk of symptomatic reinfections is still high due to the effect of the Omicron variant.

[Autophagy Markers Induced by Influenza Virus and MUC1 Expressions in Cancer-Derived Cell Lines]. / Kanser Kökenli Hücre Dizilerinde Influenza Virüsünün Indükledigi Otofaji Belirteçleri ile MUC1 Ekspresyonu Arasindaki Iliskinin Arastirilmasi.

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, HeLa 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 (qRTPCR) 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.

Severe influenza virus infection in children admitted to the PICU: Comparison of influenza A and influenza B virus infection.

Although the influenza virus usually causes a self-limiting disease, deaths are reported even in children without risk factors. We aimed to identify the clinical features, mortality associated with severe influenza A and B virus infections of children admitted to the pediatric intensive care unit (PICU). We conducted a retrospective study of children with confirmed influenza infection between 2012 and 2019 who were admitted to the PICU. Demographic features, risk factors, clinical data, microbiological data, complications, and outcomes were collected. Over seven influenza seasons (2012-2011 to 2015-2016), 713 children diagnosed with laboratory-confirmed influenza-related LRTI, and PICU admission was needed in 6% (46/713) of the patients. Thirty-one patients (67.4%) were diagnosed with influenza A and 15 patients were diagnosed with influenza B. Epidemiologic and clinical characteristics were similar in both influenza types, lactate dehydrogenase levels were significantly higher for influenza A than for influenza B infections. Although the influenza A to B ratio among the patients admitted to the PICU was 2.06, the percentage of cases requiring PICU admission was nearly two times higher in influenza B cases. There was no statistically significant difference in disease severity and complications in patients with influenza A and influenza B.

Benign acute childhood myositis associated with influenza A/B in the paediatric emergency department and the efficacy of early-onset oseltamivir.

AIM: To investigate the association of benign acute childhood myositis (BACM) with respiratory viruses. Also, we aimed to assess the effect of antiviral treatment on the improvement and complications. METHODS: This study was conducted at an urban-academic emergency department during four influenza-seasons (2016-2019), retrospectively. Demographics, clinical findings, laboratories, metabolic disease analyses and serological features were extracted from the medical records. Treatments, complications and outcomes were also recorded. RESULTS: A total of 114 children were included. The median age was 7.0 (min 1.25-max 17) years and 78.9% were male. The most common symptoms were leg pain (91.2%), anorexia (54.4%), fever (45.6%), sore throat (42.1%) and walking difficulty (32.5%). On admission, the median creatine phosphokinase level was 3332 IU/L (range, 1634-50 185), median aspartate aminotransferase 107 U/L (range, 38-1798). In the multiplex polymerase chain reaction analysis, 40.4% influenza B, 36.8% influenza A, 7.8% adenovirus, 7.8% parainfluenza virus, 5.3% rhinovirus, 5.3% respiratory syncytial virus and 1.8% Mycoplasma pneumoniae were detected. Rhabdomyolysis was developed in 6.7% and acute renal failure was seen in two patients. Oseltamivir was given in 44 (38.6%) patients who had influenza A/B. Metabolic disease screening tests were performed in 33.3% of patients and metabolic diseases were detected in 4 (3.5%) patients. The median recovery time was lower in patients with oseltamivir treatment (4 (min 2-max 5) - 5 (min 3-max 10) days) (P < 0.001). CONCLUSION: Rhabdomyolysis is more common in BACM due to the influenza A virus. The early use of oseltamivir treatment was significantly associated with a shorter recovery time.

Fluorescent bioassay for SARS-CoV-2 detection using polypyrene-g-poly(ε-caprolactone) prepared by simultaneous photoinduced step-growth and ring-opening polymerizations.

The construction of a rapid and easy immunofluorescence bioassay for SARS-CoV-2 detection is described. We report for the first time a novel one-pot synthetic approach for simultaneous photoinduced step-growth polymerization of pyrene (Py) and ring-opening polymerization of ε-caprolactone (PCL) to produce a graft fluorescent copolymer PPy-g-PCL that was conjugated to SARS-CoV-2-specific antibodies using EDC/NHS chemistry. The synthesis steps and conjugation products were fully characterized using standard spectral analysis. Next, the PPy-g-PCL was used for the construction of a dot-blot assay which was calibrated for applications to human nasopharyngeal samples. The analytical features of the proposed sensor showed a detection range of 6.03-8.7 LOG viral copy mL-1 (Ct Scores: 8-25), the limit of detection (LOD), and quantification (LOQ) of 1.84 and 6.16 LOG viral copy mL-1, respectively. The repeatability and reproducibility of the platform had a coefficient of variation (CV) ranging between 1.2 and 5.9%. The fluorescence-based dot-blot assay was tested with human samples. Significant differences were observed between the fluorescence intensity of the negative and positive samples, with an overall correct response of 93.33%. The assay demonstrated a high correlation with RT-PCR data. This strategy opens new insights into simplified synthesis procedures of the reporter molecules and their high potential sensing and diagnosis applications.

Clinical and Laboratory Findings of SARS-CoV-2 Infection in Children Younger than 6 Months Old: Neutropenia is More Common Not Lymphopenia.

BACKGROUND: Studies on age-related differences in clinical and laboratory features of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited. We aimed to evaluate the demographic, clinical, laboratory findings of SARS-CoV-2 infection in children younger than 6 months old and compare them with older children. METHODS: A single-center retrospective study, including 209 confirmed SARS-CoV-2 infection cases, was conducted between 11 March 2020 and 1 September 2021. The case group consisted of 47 patients younger than 6 months old, whereas the control group consisted of 162 patients older than 6 months old. RESULTS: The mean age of the case group was 2.77 ± 1.52 months, and the control group was 101.89 ± 65.77 months. Cough was statistically higher in the control group, and poor feeding was higher in the case group (p = 0.043, 0.010). The underlying disease rate was statistically higher in the control group; however, the hospitalization rate was higher in the case group (p = 0.036, 0.001). The case group had significantly lower median values of the absolute neutrophil count, hemoglobin and higher median values of white blood cell, absolute lymphocyte count and platelet than the control group (p < 0.05). C-reactive protein, fibrinogen values were significantly lower, and procalcitonin, D-dimer, troponin T, N-terminal pro-B-type natriuretic peptide significantly higher in the case group (p < 0.05). Lymphopenia was more common in the control group, whereas neutropenia was more common in the case group (p = 0.001, 0.011). CONCLUSIONS: We showed that most children younger than 6 months old had mild and asymptomatic SARS-CoV-2 infection; however, the hospitalization rate was higher, and neutropenia was more common in older children. Lay summaryStudies on age-related differences in clinical and laboratory features on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pediatric patients are limited. We aimed to evaluate the demographic, clinical and laboratory findings of SARS-CoV-2 infection in children younger than 6 months old and compare them with older children. A single-center retrospective study was conducted, including 209 SARS-CoV-2 infection cases. The case group consisted of 47 patients younger than 6 months old, and the control group consisted of 162 patients older than 6 months old. Most children younger than 6 months old had mild and asymptomatic SARS-CoV-2 infection; however, the hospitalization rate was higher than older children. Neutropenia was more common in patients younger than 6 months than older children with SARS-CoV-2 infection, even if underlying diseases were excluded.

The longitudinal evaluation of COVID-19 in pediatric patients and the impact of delta variant.

BACKGROUND: Pediatric patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) displayed milder symptoms than adults. However, they play an important role in case numbers and virus transmission. Therefore, we aimed to determine the epidemiological features of all pediatric patients infected with SARS-CoV-2 and put forth case numbers longitudinally throughout the delta variant dominant period. METHODS: A retrospective study was conducted at a university hospital and included patients between 0 and18 years old with a SARS-CoV-2 polymerase chain reaction (PCR) positive result, including inpatients and outpatients. Epidemiological and clinical features were recorded from electronic files, and telephone visits were performed between March 2020 and December 2021. RESULTS: During the study period, 3175 coronavirus disease 2019 (COVID-19) pediatric patients were admitted to our hospital with a mean age of 10.61 ± 4.6 years. Of the 1815 patients who could be interviewed, 85.7% reported at least one symptom. Before the delta variant period, 0-4 years aged children were more commonly infected, while school-aged children and adolescents were more common, and the rate of pediatric cases to all COVID-19 cases increased to 35.8% after the delta variant became dominant. Symptomatic cases were significantly higher before the delta variant (87.8% vs. 84.06%, p = 0.016). The hospitalization rate was higher before the delta variant (p < 0.001), whereas PICU admission showed no statistical difference. CONCLUSIONS: The frequency of school-aged children and adolescents raised with the impact of both school openings and the delta variant, and the rate of pediatric cases increased in total COVID-19 patient numbers.

Rapid Point-of-Care COVID-19 Diagnosis with a Gold-Nanoarchitecture-Assisted Laser-Scribed Graphene Biosensor.

The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has revealed the urgent need for accurate, rapid, and affordable diagnostic tests for epidemic understanding and management by monitoring the population worldwide. Though current diagnostic methods including real-time polymerase chain reaction (RT-PCR) provide sensitive detection of SARS-CoV-2, they require relatively long processing time, equipped laboratory facilities, and highly skilled personnel. Laser-scribed graphene (LSG)-based biosensing platforms have gained enormous attention as miniaturized electrochemical systems, holding an enormous potential as point-of-care (POC) diagnostic tools. We describe here a miniaturized LSG-based electrochemical sensing scheme for coronavirus disease 2019 (COVID-19) diagnosis combined with three-dimensional (3D) gold nanostructures. This electrode was modified with the SARS-CoV-2 spike protein antibody following the proper surface modifications proved by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) characterizations as well as electrochemical techniques. The system was integrated into a handheld POC detection system operated using a custom smartphone application, providing a user-friendly diagnostic platform due to its ease of operation, accessibility, and systematic data management. The analytical features of the electrochemical immunoassay were evaluated using the standard solution of S-protein in the range of 5.0-500 ng/mL with a detection limit of 2.9 ng/mL. A clinical study was carried out on 23 patient blood serum samples with successful COVID-19 diagnosis, compared to the commercial RT-PCR, antibody blood test, and enzyme-linked immunosorbent assay (ELISA) IgG and IgA test results. Our test provides faster results compared to commercial diagnostic tools and offers a promising alternative solution for next-generation POC applications.

Simple workflow to repurpose SARS-CoV-2 swab/serum samples for the isolation of cost-effective antibody/antigens for proteotyping applications and diagnosis.

Supply shortage for the development and production of preventive, therapeutic, and diagnosis tools during the COVID-19 pandemic is an important issue affecting the wealthy and poor nations alike. Antibodies and antigens are especially needed for the production of immunological-based testing tools such as point-of-care tests. Here, we propose a simple and quick magnetic nanoparticle (MNP)-based separation/isolation approach for the repurposing of infected human samples to produce specific antibodies and antigen cocktails. Initially, an antibody cocktail was purified from serums via precipitation and immunoaffinity chromatography. Purified antibodies were conjugated onto MNPs and used as an affinity matrix to separate antigens. The characterization process was performed by ELISA, SDS-PAGE, electrochemistry, isothermal titration calorimetry, and LC-Q-TOF-MS/MS analyses. The MNP-separated peptides can be used for mass spectrometry-based as well as paper-based lateral flow assay diagnostic. The exploitation of the current workflow for the development of efficient diagnostic tools, specific treatments, and fundamental research can significantly impact the present or eventual pandemic. This workflow can be considered as a two birds, one stone-like strategy.

[Evaluation of viral etiology in central nervous system infections from a university hospital point of view in Izmir based on seven years data]. / Santral sinir sistemi enfeksiyonlarinda viral etiyolojinin Izmir'de bir üniversite hastanesinin yedi yillik verileri üzerinden degerlendirilmesi.

The serious diseases of the central nervous system (CNS); encephalitis and meningitis, have high mortality and morbidity rate especially not diagnosed and treated in time. Nucleic acid testing (NAT) is the tool of choice for viral diagnosis in CNS infections. In this study, viral etiological agents found in cerebrospinal fluid (CSF) samples sent to our university hospital virology laboratory for laboratory diagnosis of CNS infections were retrospectively evaluated and results were compared with other reports from our country. Viral etiological agents found in cerebrospinal fluid (CSF) samples sent to Ege University Faculty of Medicine Department of Medical Microbiology Virology Laboratories for laboratory diagnosis of CNS infection between 01.01.2009-31.12.2015 were evaluated retrospectively. A total of 3778 CSF tests were performed for cell culture of enterovirus (EV) in 487 samples and 3291 tests for nucleic acid testing (NAT) by real time polymerase chain reaction (PCR) in herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2), varicella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), human herpes virus 6 (HHV6) and EV. VZV and EV NAT's were performed during the last one and five years period, respectively. NAT positive results for HSV1, HSV2, CMV, EBV, VZV, HHV6 and EV were 1.80% (24/1333), 0.08% (1/1333), 3.28% (19/580), 4.35% (22/506), 0.46% (1/216), 1.05% (5/478) and 3.37% (6/178), respectively. EV was isolated in 30 (6.20%) of 487 CSF samples by viral culture. Positive samples were mainly from pediatric, neurology and infectious diseases clinics as expected. The number of higher positive results were found in samples sentin december (35.3%), july (12.9%) and november (10.6%). Overall 80% of positive samples belonged to patients over 18 years old. When the results of other studies reported from Turkey are examined, although the positivity rates are generally similar, it is seen that the rates specific to certain factors are higher in selected smaller patient groups like HSV1 and EV. Rapid nucleic acid tests like multiplex PCR and microarray will provide more practical and effective laboratory diagnosis approach in CNS infections, since many more microorganisms may be causative agents.

[Prevalence and seasonal distribution of respiratory viruses in patients with acute respiratory tract infections, 2002-2014]. / Akut solunum yolu enfeksiyonu olan hastalarda solunum viruslarinin prevalansi ve mevsimsel dagilimi, 2002-2014.

The aim of this study was to investigate the prevalence and seasonal distribution of respiratory viruses in pediatric and adult outpatients and inpatients who were admitted to hospital with the symptoms of upper and lower respiratory tract infections, during a 12-year period. A total of 5102 clinical samples (4372 nasopharyngeal swabs, 316 bronchoalveolar lavages, 219 transtracheal aspirates, 163 nasopharyngeal aspirates, 20 sputum, 10 nasal swabs) examined in our laboratory between January 1st 2002 and July 17th 2014, were evaluated retrospectively. Of the specimens, 1107 (21.7%) were obtained from outpatients and 3995 (78.3%) from hospitalized patients. Of the patients, 2851 (55.9%) were male and 2251 (44.1%) were female, while 1233 (24.2%) were adults and 3869 (75.8%) were children (age range: 1 day - 93 years; median: 3 years). Respiratory samples were investigated for the presence of respiratory syncytial virus (RSV), influenza virus type A and B (INF-A, INF-B), adenovirus (AdV), parainfluenza viruses (PIV types 1-4), human rhinoviruses (HRV), human coronaviruses (HCoV), human metapneumovirus (HMPV) and human bocavirus (HBoV). All specimens were tested by both direct immunofluorescence antibody (DFA) and shell vial cell culture (SVCC) methods. In DFA assay the samples were initially screened by fluorescent-labeled polyclonal antibodies, and the positive ones were typed by using monoclonal antibodies (Light Diagnostics, Merck Millipore, USA). In SVCC, HEp-2, MDCK, A-549 and Vero cell lines were used for the isolation of viruses. In addition to these methods, real-time multiplex PCR methods (RealAccurate®, Respiratory RT PCR, PathoFinder, Netherlands and Seeplex® RV15 ACE Detection, Seegene, South Korea) were used for the detection of respiratory viruses in samples (n= 2104) obtained from 2007 to 2014. Respiratory viruses were detected in a total of 1705 (33.4%) patients, of them 967 (19%) were male and 738 (14.4%) were female. Three hundred and eighteen (18.6%) of the 1705 patients were infected with multiple respiratory viruses. The most frequently observed co-infections were RSV+INF-A (40/318; 12.6%), and RSV+PIV (33/318; 10.4%). The rate of positivity for the respiratory viruses in pediatric and adult groups were 35.4% (1369/3869) and 27.3% (336/1233), respectively (p< 0.000). The most frequently detected virus in pediatric group was RSV (336/1369; 24.5%), followed by influenza viruses (314/1369; 22.9%), PIV (197/1369; 14.4%), HRV (118/1369; 8.6%), AdV (75/1369; 5.5%) and the others (49/1369; 3.6%). On the other hand the most frequently detected virus in adult group was influenza viruses (181/336; 53.8%) followed by AdV (37/336; 11%), RSV (24/336; 7.1%), PIV (24/336; 7.1%), HRV (23/336; 6.8%) and the others (9/336; 2.7%). The rate of multiple virus infections in pediatric and adult groups were 7.2% (280/3869) and 3% (38/1233), respectively. Most of the coinfections (280/318; 88%) were detected in children. Respiratory viruses were detected positive in 40.2% (445/1107) of outpatients, and in 31.5% (1260/3995) of inpatients (p< 0.000). The most frequent viruses detected in pediatric outpatients and inpatients were HRV and RSV, respectively, while influenza viruses were the first in line among both adult outpatients and inpatients. During the study period, a PIV-3 outbreak (n= 96) have emerged between December 2004-April 2005, and an influenza A (H1N1)pdm09 outbreak (n= 207) between November 2009-January 2010. When the seasonal distribution was considered, the isolation rates of 1705 respiratory viruses in winter, spring, summer and autumn were 44.4%, 27%, 8.3% and 20.3%, respectively. RSV was most frequently detected from December to March, influenza viruses from November to March, HRV from December to June, and mixed infections from January to February. In conclusion, the data of our study obtained in about 12-year period indicated that the prevalence of respiratory viruses in acute respiratory infections is 33.4%, and they typically active during the months of winter and early spring in our region.

[Simultaneous detection of respiratory viruses and influenza A virus subtypes using multiplex PCR]. / Solunum viruslari ve influenza A virus alt tiplerinin multipleks PCR yöntemi ile ayni anda saptanmasi

This study was conducted to investigate the respiratory viruses and subtyping of influenza A virus when positive by multiplex PCR in patients with flu-like symptoms, after the pandemic caused by influenza A (H1N1)pdm09. Nasopharyngeal swab samples collected from 700 patients (313 female, 387 male; age range: 24 days-94 yrs, median age: 1 yr) between December 2010 - January 2013 with flu-like symptoms including fever, headache, sore throat, rhinitis, cough, myalgia as defined by the World Health Organization were included in the study. Nucleic acid extractions (Viral DNA/RNA Extraction Kit, iNtRON, South Korea) and cDNA synthesis (RevertAid First Strand cDNA Synthesis Kits, Fermentas, USA) were performed according to the manufacturer's protocol. Multiplex amplification of nucleic acids was performed using DPO (dual priming oligonucleotide) primers and RV5 ACE Screening Kit (Seegene, South Korea) in terms of the presence of influenza A (INF-A) virus, influenza B (INF-B) virus, respiratory syncytial virus (RSV), and the other respiratory viruses. PCR products were detected by automated polyacrylamide gel electrophoresis using Screen Tape multiple detection system. Specimens which were positive for viral nucleic acids have been further studied by using specific DPO primers, FluA ACE Subtyping and RV15 Screening (Seegene, South Korea) kits. Four INF-A virus subtypes [human H1 (hH1), human H3 (hH3), swine H1 (sH1), avian H5 (aH5)] and 11 other respiratory viruses [Adenovirus, parainfluenza virus (PIV) types 1-4, human bocavirus (HBoV), human metapneumovirus (HMPV), rhinovirus types A and B, human coronaviruses (HCoV) OC43, 229E/NL63] were investigated with those tests. In the study, 53.6% (375/700) of the patients were found to be infected with at least one virus and multiple respiratory virus infections were detected in 15.7% (59/375) of the positive cases, which were mostly (49/59, 83%) in pediatric patients. RSV and rhinovirus coinfections were the most prevalent (18/29, 62.7%) dual infections. The distribution of 436 respiratory viruses identified from 375 patients were as follows; 189 (43.3%) RSV, 93 (21.4%) rhinovirus, 86 (19.8%) INF-A, seven (1.6%) INF-B, 22 (5%) PIV types 1-3, 14 (3.2%) HMPV, 11 (2.5%) HCoV, nine (2%) HBoV, and five (1.2%) adenovirus. Fifty-five (64%) out of 86 INF-A viruses were subtyped as hH3, 24 (27.9%) were sH1 and seven (8.1%) were hH1. Avian H5 was not detected in any samples. The overall prevalence rates of INF-A, INF-B, RSV and other respiratory viruses were 12%, 1%, 27%, and 14.6%, respectively. RSV was the most prevalent respiratory agent in pediatric (161/313, 51%) cases, while INF-A virus in adult (24/62, 38.7%) patients. Influenza viruses were detected as responsible pathogens in 13.3% (93/700) of the patients with flu-like symptoms. Among the cases, a 1-month-old baby was infected with three virus strains (INF-A hH1+INF-A sH1+HCoV OC43) and a 82-year-old patient was infected with two INF-A virus subtypes (hH3 + sH1). INF-A viruses were mostly detected (79/86) in winter period, from December to March. INF-A virus sH1, was the most prevalent subtype in flu cases till February 2011 (22/86), after replaced by INF-A virus hH3. Beginning from February 2012, a significant increase observed in the cases infected with INF-A virus subtype hH3 (39/86). In conclusion, the identification and surveillance of influenza virus types and subtypes circulating in populations have importance both for epidemiological data and selection of vaccine strains.

Organotypic lung tissue culture as a preclinical model to study host- influenza A viral infection: A case for repurposing of nafamostat mesylate.

Reliable and effective models for recapitulation of host-pathogen interactions are imperative for the discovery of potential therapeutics. Ex vivo models can fulfill these requirements as the multicellular native environment in the tissue is preserved and be utilized for toxicology, vaccine, infection and drug efficacy studies due to the presence of immune cells. Drug repurposing involves the identification of new applications for already approved drugs that are not related to the prime medical indication and emerged as a strategy to cope with slow pace of drug discovery due to high costs and necessary phases to reach the patients. Within the scope of the study, broad-spectrum serine protease inhibitor nafamostat mesylate was repurposed to inhibit influenza A infection and evaluated by a translational ex vivo organotypic model, in which human organ-level responses can be achieved in preclinical safety studies of potential antiviral agents, along with in in vitro lung airway culture. The safe doses were determined as 10 µM for in vitro, whereas 22 µM for ex vivo to be applied for evaluation of host-pathogen interactions, which reduced virus infectivity, increased cell/tissue viability, and protected total protein content by reducing cell death with the inflammatory response. When the gene expression levels of specific pro-inflammatory, anti-inflammatory and cell surface markers involved in antiviral responses were examined, the significant inflammatory response represented by highly elevated mRNA gene expression levels of cytokines and chemokines combined with CDH5 downregulated by 5.1-fold supported the antiviral efficacy of NM and usability of ex vivo model as a preclinical infection model.

COVID-19 Antibody Levels among Various Vaccination Groups, One-Year Antibody Follow-Up in Two University Hospitals from Western and Central Turkey.

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 Izmir (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.

The clinical features, treatment and prognosis of neutropenic fever and Coronavirus disease 2019 results of the multicentre teos study.

This multicentre (22 centres in Turkey) retrospective cohort study aimed to assess the clinical outcomes of patients with neutropenic fever and SARS-CoV-2 positivity. Study period was 15 March 2020-15 August 2021. A total of 170 cases (58 female, aged 59 ± 15.5 years) that fulfilled the inclusion criteria were included in the study. One-month mortality rate (OMM) was 44.8%. The logistic regression analysis showed the following significant variables for the mentioned dependent variables: (i) achieving PCR negativity: receiving a maximum of 5 days of favipiravir (p = 0.005, OR 5.166, 95% CI 1.639-16.280); (ii) need for ICU: receiving glycopeptide therapy at any time during the COVID-19/FEN episode (p = 0.001, OR 6.566, 95% CI 2.137-20.172), the need for mechanical ventilation (p < 0.001, OR 62.042, 95% CI 9.528-404.011); (iii) need for mechanical ventilation: failure to recover from neutropenia (p < 0.001, OR 17.869, 95% CI 3.592-88.907), receiving tocilizumab therapy (p = 0.028, OR 32.227, 95% CI 1.469-707.053), septic shock (p = 0.001, OR 15.4 96% CI 3.164-75.897), and the need for ICU (p < 0.001, OR 91.818, 95% CI 15.360-548.873), (iv) OMM: [mechanical ventilation (p = 0.001, OR 19.041, 95% CI 3.229-112.286) and septic shock (p = 0.010, OR 5.589,95% CI 1.509-20.700)]. Although it includes a relatively limited number of patients, our findings suggest that COVID-19 and FEN are associated with significant mortality and morbidity.

Efficacy of coronavirus disease 2019 vaccines in patients with rheumatic diseases.

Objectives: In this study, we report the immune response to the BNT162b2 vaccine and CoronaVac vaccine after a two-dose vaccination and the effects of conventional drugs, immunosuppressive drugs, and new-generation therapies on vaccine responses in patients with rheumatic and musculoskeletal diseases (RMDs). Patients and methods: This is a prospective observational study conducted with 94 patients (65 males, 29 females; mean age: 42.7±12.1 years; range, 19 to 69 years) between May 2021 and January 2022. The immunogenicity of the two-dose regimens of the BNT162b2 and CoronaVac vaccines in adult patients with RMD was analyzed according to disease and treatments. Serum immunoglobulin G antibody levels against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) spike proteins were measured four weeks after the second dose of vaccines. Results: Patients on regimens including mycophenolate, rituximab, and steroids were less likely to develop an antibody response (p=0.001, p=0.06, and p=0.001, respectively). Impairment of vaccine response by other conventional disease-modifying antirheumatic drugs and by anti-tumor necrosis factor treatments was not shown. Younger participants appeared more likely to develop an antibody response. The CoronaVac vaccine was less likely to develop an antibody response compared to the BNT162b2 vaccine (p=0.002). Systemic lupus erythematosus and vasculitis had the lowest antibody titers compared to other RMDs. Conclusion: Patients receiving mycophenolate mofetil, rituximab, and steroids should be warned about the risk of a suboptimal vaccine response. If possible, vaccination strategies should be changed, and the dose modification of drugs should be made during the vaccination. Further studies are required to determine the responses to SARS-CoV-2 vaccination and optimization of vaccine response in patients with RMDs.