Spike and host glycan determinants of HKU1 airway tropism

Structural characterization of antibodies binding the conserved central helix and membrane-proximal lower stalk of coronavirus spike glycoprotein 2248624

Monoclonal antibodies from COVID-19 convalescent donors are identified that target two conserved epitopes in the S2 domain of the coronavirus Spike glycoprotein: the central helix and the lower stalk, advancing knowledge of two conserved and structurally vulnerable sites within the coronavirus S2 subunit.

coronavirus hemagglutinin-esterase receptor-binding site: a major shift in ligand specificity through modest changes in architecture

Retroviruses use different IP6 binding mechanisms to alter the properties of their capsids

HIV-1 uses the metabolite inositol hexakisphosphate (IP6) as a host factor to assemble its capsid, but whether this strategy is unique to lentiviruses or represents a common feature of retroviral capsids remains unclear. Here we show that IP6 binding is conserved across diverse retroviruses but occurs through distinct capsid sites and mechanisms, and influences viral behaviour. In contrast to HIV-1, the beta-retrovirus Mason-Pfizer Monkey Virus (MPMV) and the gamma-retrovirus Murine Leukaemia Virus (MLV) bind IP6 at the threefold lattice interface between capsomers rather than within capsomer pores. Cryo-EM structures of core-like particles reveal that two lysine residues from each capsomer coordinate IP6 between either two discrete three-lysine rings (MPMV) or a single heterogeneous six-lysine ring (MLV). MPMV and MLV are largely insensitive to IP6 availability in producer cells, but this binding mode renders them highly dependent on IP6 in target cells – the opposite of the dependency pattern of HIV-1. The way in which retroviruses use IP6 to build their capsids alters their dependence on the metabolite at different stages of the replicative cycle and in key capsid behaviours, such as assembly and stability. Diverse retroviruses conserve IP6 as a molecular glue for core assembly but use it differently: HIV-1 binds IP6 within capsomer pores and needs it during virus production, while MPMV and MLV bind IP6 between capsomers and require it during infection.

Impact of mutations on spike protein-ACE2 interactions through molecular dynamics simulations

Elucidating how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants modulate binding between the receptor-binding domain (RBD) and the human Angiotensin-converting enzyme 2 (ACE2) receptor remains central to understanding viral evolution and guiding therapeutic design. This study presents a molecular dynamics (MD) investigation of ACE2–RBD complexes for the wild-type virus and five major variants, Alpha, Beta, Gamma, Delta, and Omicron, using an integrated computational framework that combines structural dynamics, interfacial contact mapping, hydrogen bonding profiles, and advanced network-based analysis. Hierarchical clustering of residue-level contact frequencies and interaction networks enabled classification of variant-specific binding strategies and evolutionary divergence. A conserved hydrogen bonding “anchor” network, centered on ACE2 residues S19, Q24, and Y83 and RBD residues A475, S477, and N487, was identified across all variants, suggesting structural constraints essential for receptor engagement. Conversely, Delta and Omicron displayed substantial interfacial rewiring, characterized by the loss of canonical interactions and the emergence of novel cation–π, π–π, and hydrophobic contacts. Principal component analysis revealed that the ACE2–RBD interface is comparatively less flexible than other regions, while clustering results delineated early versus late variant groups. This work demonstrates the utility of MD-driven contact network analysis and clustering approaches in uncovering conserved interfacial motifs and adaptive strategies, providing a computational framework for monitoring and interpreting the molecular evolution of emerging SARS-CoV-2 variants.

Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity

Conserved epitopes within the coronavirus spike S2 domain elicit broadly reactive antibodies, yet many characterized responses show limited neutralizing and variable protective activity, leaving their contribution to antiviral immunity unclear. Building on our previous mapping of evolutionarily conserved spike “coldspots”, we isolated human monoclonal antibodies targeting four conserved epitopes in the spike S2 domain: the internal fusion peptide (iFP), the central helix (CH), the connector domain (CD), and a membrane-proximal epitope in the heptad repeat 2 that we term the lower stalk (LS). A crystal structure of an LS-directed antibody defined a previously unresolved mode of antibody recognition of this membrane-proximal epitope, while cryogenic electron microscopy (cryo-EM) structures revealed that genetically diverse CH-specific antibodies use distinct binding modes to converge on conserved features of the prefusion S2 apex. Despite minimal neutralizing activity, CH- and LS-directed antibodies exhibited distinct antiviral functions. LS-directed antibodies mediated Fcγ receptor-dependent effector activity in vitro, whereas the broadly reactive CH-directed antibody ch.007 lacked detectable antibody-dependent cellular cytotoxicity (ADCC) or cellular phagocytosis (ADCP) activity yet protected mice from lethal SARS-CoV-2 MA10 challenge, with protection abrogated by Fcγ receptor-silencing mutations. Together, these findings expand the genetic, structural and functional landscape of human antibody responses to conserved coronavirus S2 epitopes and demonstrate that CH-directed antibodies can contribute to protective immunity through Fc-dependent mechanisms not predicted by in vitro neutralization or conventional in vitro Fc effector assays.

Bovine coronavirus evolution preserves spike architecture while remodeling key functional regions

Bovine coronavirus (BCoV) is a major pathogen of cattle and the closest known ancestor of the human coronavirus OC43, yet how viral evolution reshapes spike protein structure and function remains poorly understood. Here, we combined comparative genomics, glycoproteomics, cryo-EM, and antigenic characterization to define the structural mechanisms underlying spike evolution across representative BCoV lineages. We identify a previously unrecognized lineage-specific N-glycosylation site in contemporary European viruses and validate its occupancy by glycoproteomics. High-resolution cryo- EM structures reveal that BCoV evolution preserves the overall prefusion architecture of the spike glycoprotein while selectively remodeling key functional regions involved in receptor recognition, conformational dynamics, and antigenicity. Comparative analysis with OC43 demonstrates increased conformational heterogeneity of the receptor-binding loop, whereas the Mebus vaccine strain exhibits enhanced membrane-proximal stalk flexibility despite maintaining thermal stability. Finally, structural modeling together with antibody-binding experiments reveals substantial antigenic remodeling despite >90% spike sequence identity between BCoV and OC43. Together, these findings establish a mechanistic framework for Embecovirus spike evolution and provide structural insights that may inform the development of vaccines based on contemporary circulating strains.