SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.

The use of RNA sequencing from wastewater samples is a valuable way for estimating infection dynamics and circulating lineages of SARS-CoV-2. This approach is independent from testing individuals and can therefore become the key tool to monitor this and potentially other viruses. However, it is equally important to develop easily accessible and scalable tools which can highlight critical changes in infection rates and dynamics over time across different locations given sequencing data from wastewater. Here, we provide an analysis of lineage dynamics in Berlin and New York City using wastewater sequencing and present PiGx SARS-CoV-2, a highly reproducible computational analysis pipeline with comprehensive reports. This end-to-end pipeline includes all steps from raw data to shareable reports, additional taxonomic analysis, deconvolution and geospatial time series analyses. Using simulated datasets (in silico generated and spiked-in samples) we could demonstrate the accuracy of our pipeline calculating proportions of Variants of Concern (VOC) from environmental as well as pre-mixed samples (spiked-in). By applying our pipeline on a dataset of wastewater samples from Berlin between February 2021 and January 2022, we could reconstruct the emergence of B.1.1.7(alpha) in February/March 2021 and the replacement dynamics from B.1.617.2 (delta) to BA.1 and BA.2 (omicron) during the winter of 2021/2022. Using data from very-short-reads generated in an industrial scale setting, we could see even higher accuracy in our deconvolution. Lastly, using a targeted sequencing dataset from New York City (receptor-binding-domain (RBD) only), we could reproduce the results recovering the proportions of the so-called cryptic lineages shown in the original study. Overall our study provides an in-depth analysis reconstructing virus lineage dynamics from wastewater. While applying our tool on a wide range of different datasets (from different types of wastewater sample locations and sequenced with different methods), we show that PiGx SARS-CoV-2 can be used to identify new mutations and detect any emerging new lineages in a highly automated and scalable way. Our approach can support efforts to establish continuous monitoring and early-warning projects for detecting SARS-CoV-2 or any other pathogen.

De Novo-Whole Genome Assembly of the Roborovski Dwarf Hamster (Phodopus roborovskii) Genome: An Animal Model for Severe/Critical COVID-19.

The Roborovski dwarf hamster Phodopus roborovskii belongs to the Phodopus genus, one of the seven within Cricetinae subfamily. Like other rodents such as mice, rats, or ferrets, hamsters can be important animal models for a range of diseases. Whereas the Syrian hamster from the genus Mesocricetus is now widely used as a model for mild-to-moderate coronavirus disease 2019, Roborovski dwarf hamster shows a severe-to-lethal course of disease upon infection with the novel human coronavirus severe acute respiratory syndrome coronavirus 2.

Calcium carbonate vaterite particles for drug delivery: Advances and challenges.

The recent successful application of lipid-based nanoparticles as delivery vehicles in COVID-19 vaccines demonstrated the superior potential of nanoparticle-based technology for targeted drug delivery in biomedicine. Among novel, rapidly advancing delivery platforms, the inorganic nano/microparticles gradually reach new heights and attract well-deserved attention among scientists and clinicians. Calcium carbonate in its vaterite form is used as a biocompatible carrier for a progressively increasing number of biomedical applications. Its growing popularity is conferred by beneficial porosity of particles, high mechanical stability, biodegradability under certain physiological conditions, ability to provide a continuous steady release of bioactives, preferential safety profile, and low cost, which make calcium carbonate a suitable entity of highly efficacious formulations for controlled drug delivery and release. The focal point of the current review is the success of the recent vaterite applications in the delivery of various diagnostics and therapeutic drugs. The manuscript highlights the nuances of drug loading in vaterite particles, connecting it with particle morphology, size, and charge of the loaded molecules, payload concentration, mono- or multiple drug loading. The manuscript also depicts recent successful methods of increasing the loading capacity developed for vaterite carriers. In addition, the review describes the various administration routes for vaterite particles with bioactive payloads, which were reported in recent years. Special attention is given to the multi-drug-loaded vaterite particles ("molecular cocktails") and reports on their successful delivery in vitro and in vivo.