SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26^th 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26^th until March 23^rd. We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient questionnaires was used to facilitate the interpretation of phylogenetic observations. The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected first on March 2^nd, although the first sample identified belonged to B.1.1. Within B.1, 68·2% of our samples fall within a clade defined by the SNP C15324T (‘Basel cluster’), including 157 identical sequences at the root of the ‘Basel cluster’, some of which we can specifically trace to regional spreading events. We infer the origin of B.1-C15324T to mid-February in our tri-national region. The other genomes map broadly over the global phylogenetic tree, showing several introduction events from and/or dissemination to other regions of the world via travellers. Family transmissions can also be traced in our data. A single lineage variant dominated the outbreak in the Basel area while other lineages, such as the first (B.1.1), did not propagate. A mass gathering event was the predominant initial source of cases, with travel returners and family transmissions to a lesser extent. We highlight the importance of adding specific questions to epidemiological questionnaires, to obtain data on attendance of large gatherings and their locations, as well as travel history, to effectively identify routes of transmissions in up-coming outbreaks. This phylogenetic analysis in concert with epidemiological and contact tracing data, allows connection and interpretation of events, and can inform public health interventions.Trial Registration: ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT04351503","term_id":"NCT04351503"}}NCT04351503.     

Characterization of the minimum domain required for targeting budding yeast myosin II to the site of cell division

Background  

All eukaryotes with the exception of plants use an actomyosin ring to generate a constriction force at the site of cell division (cleavage furrow) during mitosis and meiosis. The structure and filament forming abilities located in the C-terminal or tail region of one of the main components, myosin II, are important for localising the molecule to the contractile ring (CR) during cytokinesis. However, it remains poorly understood how myosin II is recruited to the site of cell division and how this recruitment relates to myosin filament assembly. Significant conservation between species of the components involved in cytokinesis, including those of the CR, allows the use of easily genetically manipulated organisms, such as budding yeast (Saccharomyces cerevisiae), in the study of cytokinesis. Budding yeast has a single myosin II protein, named Myo1. Unlike most other class II myosins, the tail of Myo1 has an irregular coiled coil. In this report we use molecular genetics, biochemistry and live cell imaging to characterize the minimum localisation domain (MLD) of budding yeast Myo1.     

Copper,Chromium, Manganese,Iron, Nickel,and Zinc Levels in Biological Samples of Diabetes Mellitus Patients

There is accumulating evidence that the metabolism of several trace elements is altered in diabetes mellitus and that these nutrients might have specific roles in the pathogenesis and progress of this disease. The aim of present study was to compare the level of essential trace elements, chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), and zinc (Zn) in biological samples (whole blood, urine, and scalp hair) of patients who have diabetes mellitus type 2 (n = 257), with those of nondiabetic control subjects (n = 166), age ranged (45–75) of both genders. The element concentrations were measured by means of an atomic absorption spectrophotometer after microwave-induced acid digestion. The validity and accuracy was checked by conventional wet-acid-digestion method and using certified reference materials. The overall recoveries of all elements were found in the range of (97.60–99.49%) of certified values. The results of this study showed that the mean values of Zn, Mn, and Cr were significantly reduced in blood and scalp-hair samples of diabetic patients as compared to control subjects of both genders (p < 0.001). The urinary levels of these elements were found to be higher in the diabetic patients than in the age-matched healthy controls. In contrast, high mean values of Cu and Fe were detected in scalp hair and blood from patients versus the nondiabetic subjects, but the differences found in blood samples was not significant (p < 0.05). These results are consistent with those obtained in other studies, confirming that deficiency and efficiency of some essential trace metals may play a role in the development of diabetes mellitus.     

Evaluation of Calcium and Magnesium in Scalp Hair Samples of Population Consuming Different Drinking Water: Risk of Kidney Stone

The objective of this study was to examine the relationship between calcium (Ca) and magnesium (Mg) in underground water (UGW), bottled mineral water (BMW), and domestic treated water (DTW) with related to risk of kidney stones. The water samples were collected from different areas of Sindh, Pakistan. The scalp hair samples of both genders, age ranged 30–60 years, consuming different types of water, have or have not kidney disorders, were selected. The Ca and Mg concentrations were determined in scalp hair of study subjects and water by flame atomic absorption spectroscopy. The Ca and Mg contents in different types of drinking water, UGW, DTW, and BMW, were found in the range of 79.1–466, 23.7–140, and 45–270 mg/L and 4.43–125, 5.23–39.6, and 7.16–51.3 mg/L, respectively. It was observed that Ca concentration in the scalp hair samples of kidney stone patients consuming different types of drinking water was found to be higher (2,895–4721 μg/g) while Mg level (84.3–101 μg/g) was lower as compare to referents subjects (2,490–2,730 μg/g for Ca, 107–128 μg/g for Mg) in both genders. The positive correlation was found between Ca and Mg levels in water with related to kidney stone formations in population, especially who consumed underground water. A relative risk and odd ratio were calculated; the relative risk had a strong positive association with incidence of kidney stone which depends on types of drinking water.     

Obesity‐related hypertension: Pathogenesis,cardiovascular risk,and treatment—A position paper of the The Obesity Society and the American Society of Hypertension

In light of the worldwide epidemic of obesity, and in recognition of hypertension as a major factor in the cardiovascular morbidity and mortality associated with obesity, The Obesity Society and The American Society of Hypertension agreed to jointly sponsor a position paper on obesity‐related hypertension to be published jointly in the journals of each society. The purpose is to inform the members of both societies, as well as practicing clinicians, with a timely review of the association between obesity and high blood pressure, the risk that this association entails, and the options for rational, evidenced‐based treatment. The position paper is divided into six sections plus a summary as follows: pathophysiology, epidemiology and cardiovascular risk, the metabolic syndrome, lifestyle management in prevention and treatment, pharmacologic treatment of hypertension in the obese, and the medical and surgical treatment of obesity in obese hypertensive patients. Obesity (2012)     

Estimation of Copper and Iron Burden in Biological Samples of Various Stages of Hepatitis C and Liver Cirrhosis Patients

There is accumulative evidence that the metabolism of iron (Fe) and copper (Cu) is altered in human due to infections, indicating that both elements have roles in pathogenesis and progress of viral diseases. In the present study, the correlation of Cu and Fe was evaluate in biological samples (serum and scalp hair) of hepatitis C (hepatitis C virus (HCV)) patients of both genders at different stages. For comparative study, the scalp hair and serum samples of healthy individuals of same age group (30–50 years) and socioeconomic status were collected. The biological samples were analyzed for Fe and Cu by atomic absorption spectroscopy after microwave-assisted acid digestion. The validity and accuracy of methodology were checked by certified reference materials of same matrixes. The levels of Cu and Fe in biological samples were enhanced in hepatic disorder patients, including acute (after diagnosis test, anti-HCV sero-positive) hepatic fibrosis and liver cirrhosis as compared to healthy referents. The difference was significant (p?<?0.01) in the case of liver cirrhotic patients. It was observed that the data of Cu and Fe in referents and patients of both genders had normal distributions. The inter-elemental correlation (r) among Cu vs Fe in serum and scalp hair samples of referents and patients were not significant in both genders (p?>?0.1) except in the first stage of HCV (p?<?0.1). It was concluded that the increase of Cu and Fe content in human body seems to contribute to the development of cirrhosis in patients with viral hepatitis C.     

Determination of Arsenic in Scalp Hair of Children and its Correlation with Drinking Water in Exposed Areas of Sindh Pakistan

This study was focused on the analysis of arsenic (As) levels in scalp hair of children (age, <10 years) collected from two towns of Khairpur, Pakistan, to evaluate the effects of As-contaminated groundwater. For comparative purposes, scalp hair samples of children were also collected from that area having low levels of As (<10 μg/L) in drinking water. Groundwater and scalp hair samples of children were collected and analyzed by electrothermal atomic absorption spectrometry prior to microwave-assisted acid digestion. The average As concentrations in groundwater samples of two towns, Thari Mirwah and Gambat, were found to be 28.5 and 98.3 μg/L, respectively. The range of As concentrations in scalp hair samples of children who belong to Thari Mirwah and Gambat was 1.25-1.61 μg/g and 1.73-3.63 μg/g, respectively. Twenty percent of the total children who belong to Gambat have skin lesions on their hands and feet. A positive correlation coefficient (R = 0.91-0.99) was obtained between As contents in drinking water and scalp hairs of children of both towns.     

Comparison of renal effects of ibuprofen versus indomethacin during treatment of patent ductus arteriosus in contiguous historical cohorts

Background

The study aimed to investigate the pharmacokinetics of intravenous ciprofloxacin and the adequacy of 400 mg every 12 hours in critically ill Intensive Care Unit (ICU) patients on continuous veno-venous haemodiafiltration (CVVHDF) with particular reference to the effect of achieved flow rates on drug clearance.

Methods

This was an open prospective study conducted in the intensive care unit and research unit of a university teaching hospital. The study population was seven critically ill patients with sepsis requiring CVVHDF. Blood and ultrafiltrate samples were collected and assayed for ciprofloxacin by High Performance Liquid Chromatography (HPLC) to calculate the model independent pharmacokinetic parameters; total body clearance (TBC), half-life (t_1/2) and volume of distribution (Vd). CVVHDF was performed at prescribed dialysate rates of 1 or 2 L/hr and ultrafiltration rate of 2 L/hr. The blood flow rate was 200 ml/min, achieved using a Gambro blood pump and Hospal AN69HF haemofilter.

Results

Seventeen profiles were obtained. CVVHDF resulted in a median ciprofloxacin t_1/2 of 13.8 (range 5.15-39.4) hr, median TBC of 9.90 (range 3.10-13.2) L/hr, a median V_dss of 125 (range 79.5-554) L, a CVVHDF clearance of 2.47+/-0.29 L/hr and a clearance of creatinine (Cl_cr) of 2.66+/-0.25 L/hr. Thus CVVHDF, at an average flow rate of ~3.5 L/hr, was responsible for removing 26% of ciprofloxacin cleared. At the dose rate of 400 mg every 12 hr, the median estimated C_pmax/MIC and AUC_0-24/MIC ratios were 10.3 and 161 respectively (for a MIC of 0.5 mg/L) and exceed the proposed criteria of >10 for C_pmax/MIC and > 100 for AUC_0-24/MIC. There was a suggestion towards increased ciprofloxacin clearance by CVVHDF with increasing effluent flow rate.

Conclusions

Given the growing microbial resistance to ciprofloxacin our results suggest that a dose rate of 400 mg every 12 hr, may be necessary to achieve the desired pharmacokinetic - pharmacodynamic (PK-PD) goals in patients on CVVHDF, however an extended interval may be required if there is concomitant hepatic impairment. A correlation between ciprofloxacin clearance due to CVVHDF and creatinine clearance by the filter was observed (r² = 0.76), providing a useful clinical surrogate marker for ciprofloxacin clearance within the range studied.

Trial Registration

Current Controlled Trials ISRCTN52722850