From a Novel

Virus-like nanoparticles as a novel delivery tool in gene therapy.

Virus contamination of water is a threat to human health in many countries. Current solutions for inactivation of viruses mainly rely on environmentally burdensome chemical oxidation or energy-intensive ultraviolet irradiation, which may create toxic secondary products. Here, we show that renewable plant biomass-sourced colloidal lignin particles (CLPs) can be used as agglomeration agents to facilitate removal of viruses from water. We used dynamic light scattering (DLS), electrophoretic mobility shift assay (EMSA), atomic force microscopy and transmission electron microscopy (AFM, TEM), and UV spectrophotometry to quantify and visualize adherence of cowpea chlorotic mottle viruses (CCMVs) on CLPs. Our results show that CCMVs form agglomerated complexes with CLPs that, unlike pristine virus particles, can be easily removed from water either by filtration or centrifugation. Additionally, cationic particles formed by adsorption of quaternary amine-modified softwood kraft lignin on the CLPs were also evaluated to improve the binding interactions with these anionic viruses. We foresee that due to their moderate production cost, and high availability of lignin as a side-stream from biorefineries, CLPs could be an alternative water pretreatment material in a large variety of systems such as filters, packed columns, or flocculants.

Agglomeration of Viruses by Cationic Lignin Particles for Facilitated Water Purification.

RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity.

Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants.

Background Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population. Methods Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico. Results In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico. Conclusion This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact.

Effect of HPV16 L1 virus-like particles on the aggregation of non-functionalized gold nanoparticles.

Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1-S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.

Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.

Mauricio Díaz-Sánchez

Papers

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact.

Effect of HPV16 L1 virus-like particles on the aggregation of non-functionalized gold nanoparticles.

Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.