ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox.

Summary: Accurate pathogen identification is crucial during outbreaks, especially with the emergence of new variants requiring frequent primer updates. However, resources for maintaining up-to-date verification of primer sequences are often limited, which poses challenges for reliable diagnosis and hinders potential monitoring efforts based on genome sequencing. To address this, we introduce ViralPrimer, a web server facilitating primer design, SARS-CoV-2 and Mpox variant monitoring, and adaptation to future threats.

Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.

Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time.

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads.

Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.

Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.

Identification of mutations in SARS-CoV-2 PCR primer regions.

Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.

The COMPARE Data Hubs.

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications.

Worldwide human mitochondrial haplogroup distribution from urban sewage.

Community level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups.

Uniaxial strain induced topological phase transition in bismuth-tellurohalide-graphene heterostructures.

We explore the electronic structure and topological phase diagram of heterostructures formed of graphene and ternary bismuth tellurohalide layers. We show that mechanical strain inherently present in fabricated samples could induce a topological phase transition in single-sided heterostructures, turning the sample into a novel experimental realisation of a time reversal invariant topological insulator. We construct an effective tight binding description for low energy excitations and fit the model's parameters to ab initio band structures.

Formation of Two-Dimensional Micelles on Graphene: Multi-Scale Theoretical and Experimental Study.

Graphene and related two-dimensional (2D) materials possess outstanding electronic and mechanical properties, chemical stability, and high surface area. However, to realize graphene's potential for a range of applications in materials science and nanotechnology there is a need to understand and control the interaction of graphene with tailored high-performance surfactants designed to facilitate the preparation, manipulation, and functionalization of new graphene systems. Here we report a combined experimental and theoretical study of the surface structure and dynamics on graphene of pyrene-oligoethylene glycol (OEG) -based surfactants, which have previously been shown to disperse carbon nanotubes in water.

Reversible thermal switching of aqueous dispersibility of multiwalled carbon nanotubes.

Easily reversible aqueous dispersion/precipitation of multiwalled carbon nanotubes (MWNTs) has been demonstrated using small-molecule non-ionic pyrene-based surfactants, which exhibit lower critical solution temperature (LCST) phase behaviour. The MWNTs are dispersed by means of non-covalent interactions. The dispersibility can be switched "off" (i.

Precursor configurations and post-rupture evolution of Ag-CO-Ag single-molecule junctions.

Experimental correlation analysis and first-principles theory are used to probe the structure and evolution of Ag-CO-Ag single-molecule junctions both before the formation and after the rupture of the junctions. Two dimensional correlation histograms and conditional histograms demonstrate that prior to the single-molecule bridge configuration the CO molecule is already bound parallel to the Ag single-atom contact. This molecular precursor configuration is accompanied by the opening of additional conductance channels compared to the single-channel transport in pure Ag monoatomic junctions.

A study of planar anchor groups for graphene-based single-molecule electronics.

To identify families of stable planar anchor groups for use in single molecule electronics, we report detailed results for the binding energies of two families of anthracene and pyrene derivatives adsorbed onto graphene. We find that all the selected derivatives functionalized with either electron donating or electron accepting substituents bind more strongly to graphene than the parent non-functionalized anthracene or pyrene. The binding energy is sensitive to the detailed atomic alignment of substituent groups over the graphene substrate leading to larger than expected binding energies for -OH and -CN derivatives.