Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses.

Background: Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling.

Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic.

In the Czech Republic, the current pandemic led to over 1.67 million SARS-CoV-2- positive cases since the recording of the first case on 1 March 2020. SARS-CoV-2 genome analysis is an important tool for effective real-time quantitative PCR (RT-qPCR) diagnostics, epidemiology monitoring, as well as vaccination strategy.

Excellent option for mass testing during the SARS-CoV-2 pandemic: painless self-collection and direct RT-qPCR.

The early identification of asymptomatic yet infectious cases is vital to curb the 2019 coronavirus (COVID-19) pandemic and to control the disease in the post-pandemic era. In this paper, we propose a fast, inexpensive and high-throughput approach using painless nasal-swab self-collection followed by direct RT-qPCR for the sensitive PCR detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This approach was validated in a large prospective cohort study of 1038 subjects, analysed simultaneously using (1) nasopharyngeal swabs obtained with the assistance of healthcare personnel and analysed by classic two-step RT-qPCR on RNA isolates and (2) nasal swabs obtained by self-collection and analysed with direct RT-qPCR.

Performance of Targeted Library Preparation Solutions for SARS-CoV-2 Whole Genome Analysis.

Single next-generation sequencing (NGS) proved to be an important tool for monitoring the SARS-CoV-2 outbreak at the global level Until today, thousands of SARS-CoV-2 genome sequences have been published at GISAID (Global Initiative on Sharing All Influenza Data) but only a portion are suitable for reliable variant analysis. Here we report on the comparison of three commercially available NGS library preparation kits. We discuss advantages and limitations from the perspective of required input sample quality and data quality for advanced SARS-CoV-2 genome analysis.

Direct-RT-qPCR Detection of SARS-CoV-2 without RNA Extraction as Part of a COVID-19 Testing Strategy: From Sample to Result in One Hour.

Due to the lack of protective immunity in the general population and the absence of effective antivirals and vaccines, the Coronavirus disease 2019 (COVID-19) pandemic continues in some countries, with local epicentres emerging in others. Due to the great demand for effective COVID-19 testing programmes to control the spread of the disease, we have suggested such a testing programme that includes a rapid RT-qPCR approach without RNA extraction. The Direct-One-Step-RT-qPCR (DIOS-RT-qPCR) assay detects severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in less than one hour while maintaining the high sensitivity and specificity required of diagnostic tools.

Field demonstration of enhanced removal of chlorinated solvents in groundwater using biochar-supported nanoscale zero-valent iron.

The application of biochar-supported nanoscale zero-valent iron (biochar-nZVI) was successfully implemented in a field demonstration for the first time. To overcome the significant shortcomings of nZVI agglomeration for in-situ groundwater remediation, biochar-nZVI was injected into groundwater using direct-push and water pressure driven packer techniques for a site impacted by chlorinated solvents in the North China Plain. The field demonstration comprising two-step injections was implemented to demonstrate the effectiveness of nZVI and biochar-nZVI respectively.

Molecular insights of oxidation process of iron nanoparticles: spectroscopic, magnetic, and microscopic evidence.

Oxidation behavior of nano-Fe(0) particles in an anoxic environment was determined using different state-of-the-art analytical approaches, including high resolution transmission electron microscopy (HR-TEM) combined with energy filtered transmission electron microscopy (EFTEM), X-ray absorption spectroscopy (XAS), and magnetic measurements. Oxidation in controlled experiments was compared in standard double distilled (DD) water, DD water spiked with trichloroethene (TCE), and TCE contaminated site water. Using HR-TEM and EFTEM, we observed a surface oxide layer (∼3 nm) formed immediately after the particles were exposed to water.

A field comparison of two reductive dechlorination (zero-valent iron and lactate) methods.

Two parallel pilot experiments were performed at Kurivody (Czech Republic) in order to compare two reductive remedial technologies for chlorinated ethenes - microbial dehalogenation assisted by lactate and chemical dehalogenation with zero-valent iron (nZVI) nanoparticles. The methods were applied at a site contaminated by tetrachlorethylene (PCE) and trichlorethylene (TCE), with total concentrations from 10 to 50 mg/l. Concentrations of chlorinated ethenes, inorganic components of interest, pH and oxidation reduction potential (ORP) were monitored at the site for a period up to 650 days.

Environmental applications of chemically pure natural ferrihydrite.

Fresh precipitates, deposited from seepage waters of complex-ore mine-tailing impoundment at Zlaté Hory, Czech Republic, were characterized by means of X-ray diffraction, transmission electron microscopy, low temperature and in-field Mössbauer spectroscopy, and Brunauer-Emmett-Teller surface area measurements. The prevailing phases (approximately 96 wt %) found in precipitates are poorly crystalline, 2-6 nm sized two-line ferrihydrite, forming globular aggregates of about 150 nm in diameter, rimmed by acicular irregular nanocrystals of goethite. These nanocrystalline ferrihydrite-goethite precipitates are of a relatively high chemical purity (approximately 3% SiO2, Zn approximately 1300 ppm, trace and rare earth elements < 100 ppm) and thus applicable in various nanotechnologies.