The Performance of the Current Algorithm of HIV Diagnosis.

Background: We aimed to evaluate the performance of the current algorithm the HIV diagnosis that has been performed for four years. Results of HIV Ag/Ab tests, anti-HIV 1/2 confirmatory tests, HIV-1 RNA tests and the time for official results to be approved were evaluated.

Methods: The relationship of HIV Ag/Ab tests, anti-HIV 1/2 confirmation tests and HIV-1 RNA PCR tests, their result times and suitability to the algorithm were examined at Izmir Dokuz Eylül University between May 2017 and June 2021.

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.

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.

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.

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 10 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.

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.

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.

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.

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.

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.

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.

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.

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

Unlabelled: 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.

[Evaluation of SARS-CoV-2 PCR Positive Cases in the Pediatric Emergency Department].

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.

[Evaluation of Real-Time Polymerase Chain Reaction in Pneumocystis jirovecii Laboratory Diagnosis].

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.

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.

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.

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.

[A Seven-Year Evaluation of Viral Central Nervous System Infections].

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.

[A Case of Congenital Syphilis and Prozone Phenomenon].

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.

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.

[Atypical profile problem in serological diagnosis of EBV].

Epstein-Barr virus (EBV) is the causative agent of infectious mononucleosis. Burkitt's lymphoma, nasopharyngeal carcinoma and post-transplant lymphoproliferative diseases are also associated with EBV. Diagnosis is frequently based on detection of specific antibodies.

[Role of atypical pathogens in infectious exacerbations of COPD].

Bacterial and viral infections are major causes of chronic obstructive pulmonary disease (COPD) exacerbations This study aimed to find out the frequency of typical and atypical pathogens in the etiology of COPD exacerbations, to evaluate the effect of these infections on the prognosis of the disease and their relationship with the history, clinical and laboratory findings of the patients. Typical agents were determined in 32.9% and atypical agents in in 37.

YMDD motif variants in inactive hepatitis B carriers detected by Inno-Lipa HBV DR assay.

Introduction: Mutations of hepatitis B virus (HBV) polymerase, especially occurring at the highly conserved YMDD region, are related to resistance to lamivudine. Although these mutations are frequently secondary to lamivudine use, they can also occur naturally. The aim of the present study was to determine the prevalence of YMDD variants that exist naturally in patients who are inactive HBV carriers.