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The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we in silico targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we in silico constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity. [ABSTRACT FROM AUTHOR]

Raw milk contains wide microbial diversity, composed mainly of lactic acid bacteria (LAB), which are used as probiotics in both human and animal husbandry. We isolated, characterized, and evaluated LAB from indigenous Bangladeshi raw milk to assess probiotic potential, including antagonistic activity (against Escherichia coli O157: H7, Enterococcus faecalis, Salmonella Typhimurium, Salmonella Enteritidis, and Listeria monocytogenes), survivability in simulated gastric juice, tolerance to phenol and bile salts, adhesion to ileum epithelial cells, auto- and co-aggregation, hydrophobicity, a-glucosidase inhibitory activity, and antibiotic susceptibility tests. The 4 most promising LAB strains showed probiotic potential and were identified as Lactobacillus casei, Lactobacillus plantarum (which produced plantaricin EF), Lactobacillus fermentum, and Lactobacillus paracasei. These strains inhibited all pathogens tested at various degrees, and competitively excluded pathogens with viable counts of 3.0 to 6.0 log cfu/mL. Bacteriocin, organic acids, and low-molecular-weight substances were mainly responsible for antimicrobial activity by the LAB strains. All 4 LAB strains were resistant to oxacillin and 3 were resistant to vancomycin and streptomycin, with multiple antibiotic resistance indices >0.2. After further in vivo evaluation, these LAB strains could be considered probiotic candidates with application in the food industry. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19., Competing Interests: Keith A. Crandall is an Academic Editor for PeerJ. The authors declare there are no competing interests., (©2020 Rahman et al.)