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. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols. METHODS: The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results. RESULTS: The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol. CONCLUSION: Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.

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. Of these subjects, 28.6% tested positive for SARS-CoV-2 using nasopharyngeal swab sampling. Our direct RT-qPCR approach for self-collected nasal swabs performed well with results similar to those of the two-step RT-qPCR on RNA isolates, achieving 0.99 positive and 0.98 negative predictive values (cycle threshold [Ct] < 37). Our research also reports on grey-zone viraemia, including samples with near-cut-off Ct values (Ct ≥ 37). In all investigated subjects (n = 20) with grey-zone viraemia, the ultra-small viral load disappeared within hours or days with no symptoms. Overall, this study underscores the importance of painless nasal-swab self-collection and direct RT-qPCR for mass testing during the SARS-CoV-2 pandemic and in the post-pandemic era.

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. XAS analysis followed the dynamic change in total metallic iron concentration and iron oxide concentration for the experimental duration of 35 days. The metallic iron concentration in nano-Fe(0) particles exposed to water, was ∼40% after 35 days; in contrast, the samples containing TCE were reduced to ∼15% and even to nil in the case of TCE contaminated site water, suggesting that the contaminants enhance the oxidation of nano-Fe(0). Frequency dependence measurements confirmed the formation of superparamagnetic particles in the system. Overall, our results suggest that nano-Fe(0) oxidized via the Fe(0) - Fe(OH)2 - Fe3O4 - (γ-Fe2O3) route and the formation of superparamagnetic maghemite nanoparticles due to disruption of the surface oxide layer.

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. The method of biological reductive dechlorination supported by lactate showed a considerable removal of PCE and TCE, but temporary accumulation of transient reaction product 1,2-cis-dihloroethene. Reductive dechlorination with nZVI showed a significant reduction in the concentration of chlorinated ethenes without a formation of intermediate products. The development of pH showed only small changes due to the high buffering capacity of the aquifer. Both methods differ in the initial development of ORP, but over the long term showed similar values around 100 mV. Significant differences were observed for chemical oxygen demand, where groundwater after the application of nZVI showed no change in comparison to the application of lactate. The reductive effects of both agents were verified by changes in inorganic compound concentrations.

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. To date, there is no comprehensive report on the distribution of SARS-CoV-2 genome variants in either the Czech Republic, including Central and Eastern Europe in general, during the first year of pandemic. In this study, we have analysed a representative cohort of SARS-CoV-2 genomes from 229 nasopharyngeal swabs of COVID-19 positive patients collected between March 2020 and February 2021 using validated reference-based sequencing workflow. We document the changing frequency of dominant variants of SARS-CoV-2 (from B.1 -> B.1.1.266 -> B.1.258 -> B.1.1.7) throughout the first year of the pandemic and list specific variants that could impact the diagnostic efficiency RT-qPCR assays. Moreover, our reference-based workflow provided evidence of superinfection in several samples, which may have contributed to one of the highest per capita numbers of COVID-19 cases and deaths during the first year of the pandemic in the Czech Republic.

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. This optimised protocol allows for the direct use of swab transfer media (14 µL) without the need for RNA extraction, achieving comparable sensitivity to the standard method that requires the time-consuming and costly step of RNA isolation. The limit of detection for DIOS-RT-qPCR was lower than seven copies/reaction, which translates to 550 virus copies/mL of swab. The speed, ease of use and low price of this assay make it suitable for high-throughput screening programmes. The use of fast enzymes allows RT-qPCR to be performed under standard laboratory conditions within one hour, making it a potential point-of-care solution on high-speed cycling instruments. This protocol also implements the heat inactivation of SARS-CoV-2 (75 °C for 10 min), which renders samples non-infectious, enabling testing in BSL-2 facilities. Moreover, we discuss the critical steps involved in developing tests for the rapid detection of COVID-19. Implementing rapid, easy, cost-effective methods can help control the worldwide spread of the COVID-19 infection.

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.

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. The outcome of the demonstration revealed a sharp reduction of contaminant concentrations of chlorinated solvents in 24 h following the first injection of nZVI, but the rebound of the concentrations of these contaminants in groundwater has occurred within the next two weeks. However, application of biochar-nZVI greatly enhanced the removal of chlorinated solvents in groundwater over the longer period of 42 days. The enhanced removal of chlorinated solvents in groundwater by biochar-nZVI is mainly attributed to the synergistic effects of adsorption and reduction. The adsorption by biochar significantly reduced the level of chlorinated solvents in groundwater. Overall increases in ferrous iron and chloride concentrations after the injections indicated that the reduction has occurred during the removal of chlorinated solvents in groundwater. In summary, biochar-supported nZVI could be potentially used for the effective remediation of chlorinated solvents in groundwater.

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. With a surface area of 270 m2 g(-1), precipitate possesses a high catalytic activity in the decomposition of hydrogen peroxide, which is comparable with that found for commercially accessible FeO(OH) catalyst. Another superior aspect of such natural nanoparticles presents a cheap and suitable precursor for a thermally induced solid-state synthesis of the stable core-shell alpha-Fe-FeO nanoparticles that are well applicable in reductive technologies of groundwater treatment. Just the possibility of using the undesirable waste contaminating the environment in further environmental technologies is the key practical benefit discussed in this paper.