This work reframes the understanding of coronavirus spike evolution, revealing that tissue tropism operates through mechanisms fundamentally distinct from those dictating protease preference, and that protease preference and tissue tropism are mechanistically uncoupled.
Abstract
Throughout the COVID-19 pandemic, SARS-CoV-2 has undergone rapid adaptation, with the Omicron variant exhibiting an unexpected shift towards upper airway infection and preference for membrane fusion activated by endosomal cathepsins, a reversion to ancestral sarbecovirus entry mechanisms. This phenotype coincides with convergent acquisition of the spike mutation H655Y, which reduces TMPRSS2-mediated activation. Here, using a comprehensive panel of 13 spikes of SARS-CoV-2 variants, we interrogated whether H655Y-mediated protease switching explains Omicron’s upper airway phenotype, challenging several existing hypotheses, from spike stability, shedding and acquired intra-molecular interactions by H655Y. Our findings reveal that protease preference and tissue tropism are mechanistically uncoupled. While spike pre-processing by furin determines protease preference in pre-Omicron variants, this relationship breaks down in H655Y-bearing viruses. Notably, mutations in the NTD and RBD of BA.2.86 can override the H655Y phenotype entirely, indicating that RBD-mediated interactions, rather than protease usage, represent the critical determinants of Omicron’s upper airway adaptation. This work reframes our understanding of coronavirus spike evolution, revealing that tissue tropism operates through mechanisms fundamentally distinct from those dictating protease preference.
HRBD demonstrated potent and broad-spectrum inhibition against Pangolin-CoV, SARS-CoV, SARS-CoV, SARS-CoV-2, and its variants, lowering the half-maximal inhibitory concentration (IC50) by approximately 1000-fold compared to the monomeric RBD.
Jintao Zou, Lingyu Su, Jiansheng Lu et al.· Antiviral Research· 0 citations
SARS-CoV-2 evolution has reduced the efficacy of clinical monoclonal antibodies, underscoring the need for therapeutics targeting conserved viral regions. The Spike (S) heptad repeat 2 (HR2) stem helix is highly conserved across SARS-CoV-2 variants and related betacoronaviruses. Although antibodies to this region can neutralize infection, their natural occurrence and evolution remain poorly understood. We previously identified human neutralizing antibodies to a conserved peptide within this region (HR2 coldspot). Here, we show that plasma IgG reactivity to this region remains rare, even after repeated antigen exposure. Longitudinal analysis over 30 months revealed continued somatic hypermutation of HR2-specific antibodies, yet none surpassed the potency or breadth of hr2.016, which emerged shortly after primary infection. Crystal structures of four HR2 stem helix antibodies revealed convergent recognition across distinct antibody lineages. Comparison of hr2.016 with its non-neutralizing clonal relative hr2.086 showed that structural convergence masks distinct binding kinetics. Surface plasmon resonance and molecular dynamics simulations revealed a more stable interaction network for hr2.016, with slower dissociation and prolonged S residence time. Neutralization required the IgG format, supporting an avidity-driven mechanism. Together, these findings define kinetic and avidity constraints governing neutralization at the HR2 stem helix and position hr2.016 as a resilient therapeutic candidate.
Virginia Crivelli, Concetta Guerra, M. Abernathy et al.· bioRxiv· 0 citations
This study provides direct experimental evidence for a pronounced attenuation in pathogenicity along the evolutionary trajectory from Wild-type through Delta to Omicron EG.5.5, and offers crucial insights for risk assessment of emerging variants.
Xiaofang Peng, Qi Zhang, Pingping Zhou et al.· Frontiers in Immunology· 0 citations
The findings demonstrate that the pathogenicity of the Omicron subvariants has not been fully attenuated in the absence of pre-existing immunity, since they caused severe lung disease in immunologically naïve macaques and their enhanced propagation in the upper airway likely facilitates efficient transmission among humans.
H. Ishigaki, Kenichi Otaki, Naoko Kitagawa et al.· Virology· 0 citations
Human coronavirus HKU1 comprises two distinct serotypes, A and B, whose spike proteins are substantially divergent. Here, we show that spikes from both serotypes preferentially bind 9-O-acetylated α2,8-linked disialosides. Cryo-electron microscopy of the B-type N5 spike reveals a conserved extended binding site in domain S1A that accommodates both the terminal and penultimate sialic acid residues, with interactions involving the penultimate residue substantially enhancing binding. Spike N-glycan processing modulates affinity and linkage selectivity; glycans flanking the binding pocket offer a plausible structural basis for these effects. In contrast to the HKU1-A spike, which adopts open S1B-up conformations upon ligand binding, the N5 apo structure showed that the ligand-binding site was already formed and the e1 relay element register-shifted in most protomers. Nevertheless, we detected neither spontaneous opening nor a transition to an S1B-up state following ligand binding. These findings, obtained with a minimally modified ectodomain, differ from recent reports of ligand-independent opening. Molecular dynamics simulations indicated that membrane-embedded GT3, but not GD3, presents its glycan chain in a geometry compatible with S1A-mediated engagement. Concordantly, in human nasal epithelial cultures cell surface GT3-like O-acetylated trisialoside glycotopes were detected in ciliated cells, linking their cell-type-specific presentation to HKU1 tropism.
Robert Creutznacher, Louisa Elizabeth Wallace, Oliver J. Debski-Antoniak et al.· bioRxiv· 0 citations