Tracking the circulating SARS-CoV-2 variants in Turkey: Complete genome sequencing and molecular characterization of 1000 SARS-CoV-2 samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease, named coronavirus disease 2019 (COVID-19). COVID-19 has a deep impact on public health as one of the most serious pandemics in the last century. Tracking SARS-CoV-2 is important for monitoring and assessing its evolution. This is only possible by detecting all mutations in the viral genome through genomic sequencing. Moreover, accurate detection of SARS-CoV-2 and tracking its mutations is also required for its correct diagnosis. Potential effects of mutations on the prognosis of the disease can be observed. Assignment of epidemiological lineages in an emerging pandemic requires efforts. To address this, we collected 1000 SARS-CoV-2 samples from different geographical regions in Turkey and analyze their genome comprehensively. To track the virus across Turkey we focus on 10 distinct cities in different geographic regions. Each SARS-CoV-2 genome was analyzed and named according to the nomenclature system of Nextclade and Pangolin Lineage. Furthermore, the frequency of the variations observed in 10 months was also determined by region. In this way, we have observed how the virus mutations and what kind of transmission mechanism it has. The effects of age and disease severity on lineage distribution were other considered parameters. The temporal rates of SARS-CoV-2 variants by time in Turkey were close to the global trend. This study is one of the most comprehensive whole genome analyses of SARS-CoV-2 that represents a general picture of the distribution of SARS-CoV-2 variations in Turkey in 2021. Author SummarySince the outbreak of the COVID-19 pandemic in 2019, the viral genome of SARS-CoV-2 was analysed intensively all over the world both to detect its zoonotic origin and the emerging variants worldwide together with the variants effect on the prognosis and treatment, respectively, of the infection. Remarkable COVID-19 studies were also made in Turkey as it was in the rest of the world. To date, indeed, almost all studies on COVID-19 in Turkey either sequenced only a small number of the viral genome or analysed the viral genome which was obtained from online databases. In respect thereof, our study constitutes a milestone regarding both the huge sample size consisting of 1000 viral genomes and the widespread geographic origin of the viral genome samples. Our study provides new insights both into the SARS-CoV-2 landscape of Turkey and the transmission of the emerging viral pathogen and its interaction with its vertebrate host.

The investigation of levels of endothelial cell-specific molecule, progranuline, clusterin, and human epididymis protein 4 in the differential diagnosis of malignant pleural effusions.

BACKGROUND: Progranulin (PGRN), endothelial cell-specific molecule-1, clusterin (CLU), and human epididymis protein 4 (HE-4) are novel proteins reported to have diagnostic and prognostic potential in lung cancer. Here, we aimed to identify the markers with high sensitivity and specificity in distinguishing malignant pleural fluids from other pleural fluids. METHODS: This prospective, descriptive study was conducted at a medical faculty hospital between 2016 and 2019. The study population consisted of 90 patients <18 years of age with pleural effusion (PE). Levels of pleural fluids of PGRN, endothelial cell-specific molecule-1, CLU, and HE-4 were measured with enzyme-linked immunosorbent assay kits under the manufacturer's manual. RESULTS: Of 90 patients, 54 were men, and 36 were women (mean age 65 ±â€…16 years). Of pleural fluids investigated, 23 (25%) and 67 (74%) were transudates and exudates, respectively. Of exudates, while 27 (40%) and 19 (28%) were parapneumonic PE and tuberculous PE, respectively, 20 (29%) were malignant pleural effusion (MPE). Levels of all biomarkers in exudate fluids were found significantly higher than those of transudate fluids. CLU, HE-4, and PGRN levels in MPE were also found significantly higher than benign fluids (P < .05). Cutoff values were achieved by receiver operating characteristics analysis for CLU, HE-4, and PGRN to distinguish between malignant and benign groups. For diagnosis of MPE, the sensitivity and specificity values were found as 0.66 and 0.67 for a cutoff value of CLU of 18.29 mg/L (P = .00), as 0.76 and 0.76 for a cutoff value of HE-4 of 9.33 mg/L (P = .00), and as 0.66 and 0.67 for a cutoff value of PGRN of 105.91 mg/L (P = .001). CONCLUSION: HE-4 having high sensitivity and specificity can be a potential diagnostic marker in distinguishing between malignant and benign effusions, and these findings can constitute a basis for future research.