http://www.cell.com/article/S0092867421014963/pdf

mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant

The newly reported Omicron variant is poised to replace Delta as the most prevalent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant across the world. Cryo–electron microscopy (cryo-EM) structural analysis of the Omicron variant spike protein in complex with human angiotensin-converting enzyme 2 (ACE2) reveals new salt bridges and hydrogen bonds formed by mutated residues arginine-493, serine-496, and arginine-498 in the receptor binding domain with ACE2. These interactions appear to compensate for other Omicron mutations such as the substitution of asparagine for lysine at position 417 (K417N) that are known to reduce ACE2 binding affinity, resulting in similar biochemical ACE2 binding affinities for the Delta and Omicron variants. Neutralization assays show that pseudoviruses that display the Omicron spike protein exhibit increased antibody evasion. The increase in antibody evasion and the retention of strong interactions at the ACE2 interface thus represent important molecular features that likely contribute to the rapid spread of the Omicron variant. Description Antibody-evading Omicron keeps function The Omicron variant of severe acute respiratory syndrome coronavirus 2 was reported in November 2021 and was quickly identified as a variant of concern because of its rapid spread. Relative to the original Wuhan-Hu-1 strain, this variant has 37 mutations in the spike protein that is responsible for binding and entry into host cells. Fifteen mutations are in the receptor-binding domain, which binds the host angiotensin-converting enzyme 2 (ACE2) receptor and is also the target of many neutralizing antibodies. Mannar et al. report a structure of the Omicron variant spike protein bound to human ACE2. The structure rationalizes the evasion of antibodies elicited by previous vaccination or infection and shows how mutations that weaken ACE2 binding are compensated for by mutations that make new interactions. —VV Cryo-EM analysis of the Omicron spike protein reveals how ACE2 binding occurs despite high mutational escape from antibodies.

https://www.science.org/doi/pdf/10.1126/science.abn7760?download=true

SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein–ACE2 complex

http://www.cell.com/article/S0092867422000770/pdf

Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron

The novel SARS-CoV-2 Omicron variant (B.1.1.529), first found in early November 2021, has sparked considerable global concern and it has >50 mutations, many of which are known to affect transmissibility or cause immune escape. In this study, we sought to investigate the virological characteristics of the Omicron variant and compared it with the Delta variant which has dominated the world since mid-2021. Omicron variant replicated more slowly than the Delta variant in transmembrane serine protease 2 (TMPRSS2)-overexpressing VeroE6 (VeroE6/TMPRSS2) cells. Notably, the Delta variant replicated well in Calu3 cell line which has robust TMPRSS2 expression, while the Omicron variant replicated poorly in this cell line. Competition assay showed that Delta variant outcompeted Omicron variant in VeroE6/TMPRSS2 and Calu3 cells. To confirm the difference in entry pathway between the Omicron and Delta variants, we assessed the antiviral effect of bafilomycin A1, chloroquine (inhibiting endocytic pathway), and camostat (inhibiting TMPRSS2 pathway). Camostat potently inhibited the Delta variant but not the Omicron variant, while bafilomycin A1 and chloroquine could inhibit both Omicron and Delta variants. Moreover, the Omicron variant also showed weaker cell-cell fusion activity when compared with Delta variant in VeroE6/TMPRSS2 cells. Collectively, our results suggest that Omicron variant infection is not enhanced by TMPRSS2 but is largely mediated via the endocytic pathway. The difference in entry pathway between Omicron and Delta variants may have an implication on the clinical manifestations or disease severity. 

SARS-CoV-2 Omicron variant shows less efficient replication and fusion activity when compared with Delta variant in TMPRSS2-expressed cells

Abstract Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant. 

/pdf/sars-cov-2-omicron-is-an-immune-escape-variant-with-an-3gfu5pci.pdf

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has outcompeted previously prevalent variants and become a dominant strain worldwide. We report the structure, func...

Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.

The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has outcompeted previously prevalent variants and become a dominant strain worldwide. We report here structure, function and antigenicity of its full-length spike (S) trimer in comparison with those of other variants, including Gamma, Kappa, and previously characterized Alpha and Beta. Delta S can fuse membranes more efficiently at low levels of cellular receptor ACE2 and its pseudotyped viruses infect target cells substantially faster than all other variants tested, possibly accounting for its heightened transmissibility. Mutations of each variant rearrange the antigenic surface of the N-terminal domain of the S protein in a unique way, but only cause local changes in the receptor-binding domain, consistent with greater resistance particular to neutralizing antibodies. These results advance our molecular understanding of distinct properties of these viruses and may guide intervention strategies.

https://www.biorxiv.org/content/biorxiv/early/2021/08/17/2021.08.17.456689.full.pdf

Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant

Gasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. Here we discover gasdermin homologs encoded in bacteria that execute prokaryotic cell death. Structures of bacterial gasdermins reveal a conserved pore-forming domain that is stabilized in the inactive state with a buried lipid modification. We demonstrate that bacterial gasdermins are activated by dedicated caspase-like proteases that catalyze site-specific cleavage and removal of an inhibitory C-terminal peptide. Release of autoinhibition induces the assembly of >200 A pores that form a mesh-like structure and disrupt membrane integrity. These results demonstrate that caspase-mediated activation of gasdermins is an ancient form of regulated cell death shared between bacteria and animals.

https://www.biorxiv.org/content/biorxiv/early/2021/06/07/2021.06.07.447441.full.pdf

Bacterial gasdermins reveal an ancient mechanism of cell death

Much remains to be explored regarding the diversity of host-associated microbes. Here, we report the discovery of microbial structures in the mouths of bottlenose dolphins that we refer to as rectangular cell-like units (RCUs). DNA staining revealed multiple paired bands that suggested cells in the act of dividing along the longitudinal axis. Deep sequencing of samples enriched in RCUs through micromanipulation indicated that the RCUs are bacterial and distinct from Simonsiella, a genus with somewhat similar morphology and division patterning found in oral cavities of animals. Cryogenic transmission electron microscopy and tomography showed that RCUs are composed of parallel membrane-bound segments, likely individual cells, encapsulated by an S-layer-like periodic surface covering. RCUs displayed pilus-like appendages protruding as bundles of multiple threads that extend parallel to each other, and splay out at the tips and/or intertwine, in stark contrast to all known types of bacterial pili that consist of single, hair-like structures. These observations highlight the diversity of novel microbial forms and lifestyles that await discovery and characterization using tools complementary to genomics such as microscopy.

/pdf/previously-uncharacterized-rectangular-bacteria-in-the-djg0cqpg60.pdf

Megan L. Mayer

Papers

Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.

Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant

Bacterial gasdermins reveal an ancient mechanism of cell death

Previously uncharacterized rectangular bacteria in the dolphin mouth