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.

Synthesis and in Vitro Toxicity Assessment of Different Nano-Calcium Phosphate Nanoparticles

Abstract Nanoscale biomaterials are commonly used in a wide range of biomedical applications such as bone graft substitutes, gene delivery systems, and biologically active agents. On the other hand, the cytotoxic potential of these particles hasn't yet been studied comprehensively to understand whether or not they exert any negative impact on the cellular structures. Here, we undertook the synthesis of beta-tricalcium phosphate (ß-TCP) and biphasic tricalcium phosphate (BCP) nanoparticles (NPs) and determine their concentration-dependent toxic effects in human fetal osteoblastic (hFOB 1.19) cell line. Firstly, BCP and β-TCP were synthesized using a water-based precipitation technique and characterized by X-Ray Diffraction (XRD), Raman Spectroscopy, and Transmission Electron Microscopy (TEM). The cytological effects of β-TCP and BCP at different concentrations (0-640 ppm) were evaluated by using 3- (4,5-dimethylthiazol-2-yl) -2,5-diphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) assays. The total oxidative status (TOS) parameter was used for investigating oxidative stress potentials of the NPs. In addition, the study assessed the DNA damage product 8-hydroxy-2′-deoxyguanosine (8-Oxo-dG) level in hFOB 1.19 cell cultures. The results indicated that the β-TCP (above 320 ppm) and BCP (above 80 ppm) NPs exhibited cytotoxicity effects on high concentrations. It was also observed that the oxidative stress increased relatively as the concentrations of NPs increased, aligning with the cytotoxicity results. However, the NPs concentrations of 160 ppm and above increased the level of 8-OH-dG. Consequently, there is a need for more systematic in vivo and in vitro approaches to the toxic effects of both nanoparticles.

Combined metabolic cofactor supplementation accelerates recovery in mild-to-moderate COVID-19

There is a need to treat COVID-19 patients suffering from respiratory problems, resulting in decreased oxygen levels and thus leading to mitochondrial dysfunction and metabolic abnormalities. Here, we investigated if a high oral dose of a mixture of Combined Metabolic Activators (CMA) can restore metabolic function and thus aid the recovery of COVID-19 patients. We conducted a placebo-controlled, open-label phase 2 study and a double-blinded phase 3 clinical trials to investigate the time of symptom-free recovery on ambulatory patients using a mixture of CMA consisting of NAD+ and glutathione precursors. The results of both studies showed that the time to complete recovery was significantly shorter in the CMA group (6.6 vs 9.3 days) in phase 2 and (5.7 vs 9.2 days) in phase 3 trials. A comprehensive analysis of the blood metabolome and proteome showed that the plasma levels of proteins and metabolites associated with inflammation and antioxidant metabolism are significantly improved in patients treated with the metabolic activators as compared to placebo. The results show that treating patients infected with COVID-19 with a high dose of CMAs leads to a more rapid symptom-free recovery, suggesting a role for such a therapeutic regime in the treatment of infections leading to respiratory problems.

Seroprevalence of Coronavirus Disease 2019 (COVID-19) Among Health Care Workers from Three Pandemic Hospitals of Turkey

COVID-19 is a global threat with an increasing number of infections. Research on IgG seroprevalence among health care workers (HCWs) is needed to re-evaluate health policies. This study was performed in three pandemic hospitals in Istanbul and Kocaeli. Different clusters of HCWs were screened for SARS-CoV-2 infection. Seropositivity rate among participants was evaluated by chemiluminescent microparticle immunoassay. We recruited 813 non-infected and 119 PCR-confirmed infected HCWs. Of the previously undiagnosed HCWs, 22 (2.7%) were seropositive. Seropositivity rates were highest for cleaning staff (6%), physicians (4%), nurses (2.2%) and radiology technicians (1%). Non-pandemic clinic (6.4%) and ICU (4.3%) had the highest prevalence. HCWs in "high risk group" had similar seropositivity rate with "no risk" group (2.9 vs 3.6 p=0.7), indicating the efficient implementation of protection measures in the hospitals in Turkey. These findings might lead to the re-evaluation of infection control and transmission dynamics in hospitals.