Impact of mutations on the stability of SARS-CoV-2 nucleocapsid protein structure.

The nucleocapsid (N) protein of SARS-CoV-2 is known to participate in various host cellular processes, including interferon inhibition, RNA interference, apoptosis, and regulation of virus life cycles. Additionally, it has potential as a diagnostic antigen and/or immunogen. Our research focuses on examining structural changes caused by mutations in the N protein. We have modeled the complete tertiary structure of native and mutated forms of the N protein using Alphafold2. Notably, the N protein contains 3 disordered regions. The focus was on investigating the impact of mutations on the stability of the protein's dimeric structure based on binding free energy calculations (MM-PB/GB-SA) and RMSD fluctuations after MD simulations. The results demonstrated that 28 mutations out of 37 selected mutations analyzed, compared with wild-type N protein, resulted in a stable dimeric structure, while 9 mutations led to destabilization. Our results are important to understand the tertiary structure of the N protein dimer of SARS-CoV-2 and the effect of mutations on it, their behavior in the host cell, as well as for the research of other viruses belonging to the same genus additionally, to anticipate potential strategies for addressing this viral illness․.

The Use of Biosilica to Increase the Compressive Strength of Cement Mortar: The Effect of the Mixing Method.

In this work, the effect of biosilica concentration and two different mixing methods with Portland cement on the compressive strength of cement-based mortars were investigated. The following values of the biosilica concentration of cement weight were investigated։ 2.5, 5, 7.5, and 10 wt.%. The mortar was prepared using the following two biosilica mixing methods: First, biosilica was mixed with cement and appropriate samples were prepared. For the other mixing method, samples were prepared by dissolving biosilica in water using a magnetic stirrer. Compressive tests were carried out on an automatic compression machine with a loading rate of 2.4 kN/s at the age of 7 and 28 days. It is shown that, for all cases, the compressive strength has the maximum value of 10% biosilica concentration. In particular, in the case of the first mixing method, the compressive strength of the specimen over 7 days of curing increased by 30.5%, and by 36.5% for a curing period of 28 days. In the case of the second mixing method, the compressive strength of the specimen over 7 days of curing increased by 23.4%, and by 47.3% for a curing period of 28 days. Additionally, using the first and second mixing methods, the water absorption parameters were reduced by 22% and 34%, respectively. Finally, it is worth noting that the obtained results were intend to provide valuable insights into optimizing biosilica incorporation in cement mortar. With the aim of contributing to the advancement of construction materials, this research delves into the intriguing application of biosilica in cement mortar, emphasizing the significant impact of mixing techniques on the resultant compressive strength.

Molecular Analysis of SARS-CoV-2 Lineages in Armenia.

The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase were caused by the 20B clade, the third peak caused by the 20I (Alpha), while the last two peaks were caused by the 21J (Delta) and 21K (Omicron) variants. The functional analyses of mutations in sequences largely affected epitopes associated with protective HLA loci and did not cause the loss of the signal in PCR tests targeting ORF1ab and N genes as confirmed by RT-PCR. We also compared the performance of nanopore and Illumina short-read sequencing and showed the utility of nanopore sequencing as an efficient and affordable alternative for large-scale molecular epidemiology research. Thus, our paper describes new data on the genomic diversity of SARS-CoV-2 variants in Armenia in the global context of the virus molecular genomic surveillance.