Furin and the adaptive mutation of SARS-COV2: a computational framework

SARS-CoV2 Nsp3 protein triggers cell death and exacerbates amyloid β42-mediated neurodegeneration

JOURNAL/nrgr/04.03/01300535-202406000-00044/inline-graphic1/v/2023-10-30T152229Z/r/image-tiff

Infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) virus, responsible for the coronavirus disease 2019 (COVID-19) pandemic, induces symptoms including increased inflammatory response, severe acute respiratory syndrome (SARS), cognitive dysfunction like brain fog, and cardiovascular defects. Long-term effects of SARS-CoV2 COVID-19 syndrome referred to as post-COVID-19 syndrome on age-related progressive neurodegenerative disorders such as Alzheimer’s disease remain understudied. Using the targeted misexpression of individual SARS-CoV2 proteins in the retinal neurons of the Drosophila melanogaster eye, we found that misexpression of nonstructural protein 3 (Nsp3), a papain-like protease, ablates the eye and generates dark necrotic spots. Targeted misexpression of Nsp3 in the eye triggers reactive oxygen species production and leads to apoptosis as shown by cell death reporters, terminal deoxynucleotidyl transferase (TdT) dUTP Nick-end labeling (TUNEL) assay, and dihydroethidium staining. Furthermore, Nsp3 misexpression activates both apoptosis and autophagy mechanism(s) to regulate tissue homeostasis. Transient expression of SARS-CoV2 Nsp3 in murine neuroblastoma, Neuro-2a cells, significantly reduced the metabolic activity of these cells and triggers cell death. Misexpression of SARS-CoV2 Nsp3 in an Alzheimer’s disease transgenic fly eye model (glass multiple repeats [GMR]>amyloid β42) further enhances the neurodegenerative rough eye phenotype due to increased cell death. These findings suggest that SARS-CoV2 utilizes Nsp3 protein to potentiate cell death response in a neurodegenerative disease background that has high pre-existing levels of neuroinflammation and cell death.

Mutations in SARS-CoV-2 structural proteins: a global analysis

BACKGROUND

Emergence of new variants mainly variants of concerns (VOC) is caused by mutations in main structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, we aimed to investigate the mutations among structural proteins of SARS-CoV-2 globally.

METHODS

We analyzed samples of amino-acid sequences (AASs) for envelope (E), membrane (M), nucleocapsid (N), and spike (S) proteins from the declaration of the coronavirus 2019 (COVID-19) as pandemic to January 2022. The presence and location of mutations were then investigated by aligning the sequences to the reference sequence and categorizing them based on frequency and continent. Finally, the related human genes with the viral structural genes were discovered, and their interactions were reported.

RESULTS

The results indicated that the most relative mutations among the E, M, N, and S AASs occurred in the regions of 7 to 14, 66 to 88, 164 to 205, and 508 to 635 AAs, respectively. The most frequent mutations in E, M, N, and S proteins were T9I, I82T, R203M/R203K, and D614G. D614G was the most frequent mutation in all six geographical areas. Following D614G, L18F, A222V, E484K, and N501Y, respectively, were ranked as the most frequent mutations in S protein globally. Besides, A-kinase Anchoring Protein 8 Like (AKAP8L) was shown as the linkage unit between M, E, and E cluster genes.

CONCLUSION

Screening the structural protein mutations can help scientists introduce better drug and vaccine development strategies.

Forecasting the action of CAR-T cells against SARS-corona virus-II infection with branching process

The CAR-T cells are the genetically engineered T cells, designed to work specifically for the virus antigens (or other antigens, such as tumour specific antigens). The CAR-T cells work as the living drug and thus provides an adoptive immunotherapy strategy. The novel corona virus treatment and control designs are still under clinical trials. One of such techniques is the injection of CAR-T cells to fight against the COVID-19 infection. In this manuscript, the hypothesis is based on the CAR-T cells, that are suitably engineered towards SARS-2 viral antigen, by the N protein. The N protein binds to the SARS-2 viral RNA and is found in abundance in this virus, thus for the engineered cell research, this protein sequence is chosen as a potential target. The use of the sub-population of T-reg cells is also outlined. Mathematical modeling of such complex line of action can help to understand the dynamics. The modeling approach is inspired from the probabilistic rules, including the branching process, the Moran process and kinetic models. The Moran processes are well recognized in the fields of artificial intelligence and data science. The model depicts the infectious axis “virus—CAR-T cells—memory cells”. The theoretical analysis provides a positive therapeutic action; the delay in viral production may have a significant impact on the early stages of infection. Although it is necessary to carefully evaluate the possible side effects of therapy. This work introduces the possibility of hypothesizing an antiviral use by CAR-T cells.