Project description:The spread of the latest SARS-CoV-2 variant Omicron is particularly concerning because of the large number of mutations present in its genome and lack of knowledge about how these mutations would affect the current SARS-CoV-2 vaccines and treatments. Here, by performing phylogenetic analysis using the Omicron spike (S) protein sequence, we found that the Omicron S protein presented the longest evolutionary distance in relation to the other SARS-CoV-2 variants. We predicted the structures of S, M, and N proteins of the Omicron variant using AlphaFold2 and investigated how the mutations have affected the S protein and its parts, S1 NTD and RBD, in detail. We found many amino acids on RBD were mutated, which may influence the interactions between the RBD and ACE2, while also showing the S309 antibody could still be capable of neutralizing Omicron RBD. The Omicron S1 NTD structures display significant differences from the original strain, which could lead to reduced recognition by antibodies resulting in potential immune escape and decreased effectiveness of the existing vaccines. However, this study of the Omicron variant was mainly limited to structural predictions, and these findings should be explored and verified by subsequent experiments. This study provided basic data of the Omicron protein structures that lay the groundwork for future studies related to the SARS-CoV-2 Omicron variant.

| S-EPMC8765807 | biostudies-literature

human ACE2 receptor bound to SARS-CoV-2 variant Omicron BA.4/5 Spike

Project description: Not available

| EMPIAR-11176 | biostudies-other

mouse ACE2 receptor bound to SARS-CoV-2 variant Omicron BA.4/5 Spike

Project description: Not available

| EMPIAR-11177 | biostudies-other

Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins

Project description:Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and recently-emerging BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of receptor binding domain (RBD) of the spike(S) protein. However, the underlying mechanism of interplay between two factors remains elusive. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. From the ACE2/RBD structures of these sub-variants, in comparison with the known complex structures as well, we found that R493 but not Q493 was regulated by R346T substitution through long-range conformation alterations. Furthermore, we found that R493Q and F486V exert a balanced impact and immune evasion was somewhat compromised to achieve an optimal receptor binding, and proposed a "two-steps-forward and one-step-backward" model to describe such a compromise between the two factors. These results enhance our comprehension of the balance between receptor binding and immune evasion of Omicron sub-variants.

| S-SCDT-10_1038-S44318-024-00062-Z | biostudies-other

SARS-CoV-2 S Omicron Spike B.1.1.529

Project description: Not available

| EMPIAR-10947 | biostudies-other

Predicted HLA Class I and Class II Epitopes From Licensed Vaccines Are Largely Conserved in New SARS-CoV-2 Omicron Variant of Concern.

Project description:The potential effect of emerging SARS-CoV-2 variants on vaccine efficacy is an issue of critical importance. In this study, the possible impact of mutations that facilitate virus escape from the cytotoxic and the helper cellular immune responses in the new SARS-CoV-2 Omicron variant of concern was analyzed for the 551 and 41 most abundant HLA class I and II alleles, respectively. Computational prediction showed that almost all of these 592 alleles, which cover >90% of the human population, contain enough epitopes without escape mutations in the emerging SARS-CoV-2 Omicron variant of concern. These data suggest that both cytotoxic and helper cellular immune protection elicited by currently licensed vaccines are virtually unaffected by the highly contagious SARS-CoV-2 Omicron variant of concern.

| S-EPMC8831693 | biostudies-literature

Single-particle cryo-EM unaligned micrographs of prefusion SARS-CoV-2 spike omicron B.1.1.529 variant

Project description: Not available

| EMPIAR-11871 | biostudies-other