The emergence of numerous variants of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) of concern for increased infectivity has been increasingly reported worldwide, but these strains are often It seems to affect the vaccine, leading to a decrease in inpatients and a decrease in the severity of the disease. efficacy To a minimum.
Mutations in peplomer and receptor binding domains are responsible for these changes in immunogenicity profile, in a recently uploaded paper in an open access journal. Antibiotics Ambrose Et al. (May 6thTh, 2021) These mutations correlate with various disease parameters. In Sirico We have found that certain features are responsible for the increased infectivity and reduced severity of the disease observed in these strains.
How was the study done?
This group obtained SARS-CoV-2 genomic data from an international repository, used software to translate the genome into protein sequences, and performed and translated it against B-cell and T-cell epitope prediction tools. We have identified a peptide sequence that binds to. Spike protein It has a high affinity and promotes removal by these immune cells.
The four SARS-CoV-2 variants of concern were specifically selected for further analysis. Each variant is known to result in numerous mutations in peplomer, which promotes infectivity.
The D614G mutation was first identified in several SARS-CoV-2 strains in February 2020, and the N501Y mutation was identified in December 2020. It was later discovered that the N501Y mutation evolved independently in beta B.1.351 at about the same time. Variants of gamma P.1 and delta B.1.617.2 also have numerous mutations in peplomer, many of which are common to other strains, but did these mutations evolve independently? It is not yet clear if it has evolved since then.
A phylogenetic tree was computer-constructed for five strains of SARS-CoV-2, SARS-CoV-1, bat coronavirus, and MERS, with multiple variants of SARS-CoV-2 and their direct bat coronavirus ancestors. A close genetic relationship with was demonstrated. Although SARS-CoV-1 is more closely associated with both than MERS, it is clear that MERS also shares a common ancestor with each.
Identification of high affinity epitopes
T cell epitopes identified In Sirico For the peplomer sequence of each variant, each producing a different number of complementary peptides. In later varieties, the peptides with the highest affinity showed higher antigenicity than those produced for wild-type strains. However, all epitopes were found to be 100% conserved from wild type to later strains.
Interestingly, many studies have shown that antibodies generated against previous strains of SARS-COV-2 are less effective in neutralizing more recently emerged strains, but new. Immunity developed against strains often applies to previous variants. This may be due, at least in part, to the highly conserved high-affinity T cell epitope sites identified in this study, and the vaccine remains effective against newly emerging variants. It also explains why.
Potential linear B cell epitopes were also computer-identified on the peplomer. B.1.1.7 and B.1.351 variants were predicted to bind more antigenic peptides. Again, the peptides with the highest affinity differed between variants, but were found to be less conserved than in the case of T cell epitopes. Interestingly, the variants B.1.351 and B.1.617.1 were more similar in this case, and the variants B.1.617.2 were more similar, but P.1 and B.1.617. The two variants were the most similar in the highest-scoring peptide. Variants of 1.1.7 and B.1.429, B.1.427.
Representation of Potential Discontinuous B Cell Epitope Regions Mapped to SAR-SCoV-2 Variant Peplomers: (A) Wuhan Original L Strain, (B) England –B.1.1.7 Alpha, (C) USA- B. 1.429, B.1.427 Epsilon, (D) India-B.1.617.1 Kappa, and (E) South Africa-B.1.351 Beta, highlighted as a sphere.
Next, instead of linear chains, we examined structurally appropriate peplomers from each line and evaluated the peptides with the highest affinity for the peplomers in each line.
The original L strain has a characteristic GKQ motif at positions 181-183, while the variants B.1.1.7 and B.1.429, B.1.427 both have the sequence GTNG at positions 72-75. I’m waiting. Only the B.1.617.1 variant shows the NLK sequence at positions 460-462, and both this and the B.1.351 variant have the NHTS sequence at positions 1158-1161. The group found that all of the highest-ranked B-cell and T-cell epitopes for each late-stage peplomer showed higher antigenicity than that for the wild-type original L strain, presumably the diseases observed in these late stages. Note that it indicates why the severity of the disease is low. variant.
We also investigated the binding conformation of the spike proteins of each strain during antibody binding. In Sirico, Everything turned out to be stable over 6,000 picoseconds. The protein-peptide complexes of the B.1.1.7 and B.1.617.1 variants had the least structural variation, and the B.1.429 and B.1.427 variants had some variation and stabilized after 6 nanoseconds. Prior to stabilization, the variants showed moderate deviations between 8,000 and 1,000 nanoseconds. The original wild-type L strain had more conformational deviations than any of the later strains and took longer to stabilize.This suggests that mutations in the binding region resulted in structural changes that increased binding affinity while maintaining the stiffness of the complex, and subsequently improved capacity. Neutralizing antibody Target later strains and potentially reduce the severity of the disease. After infection, it takes days or weeks for the antibody to reach sufficient levels, so there is no effect on infectivity.
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