Positively bound: Remapping of Increased Positive Charge Drives SARS-CoV-2 Spike Evolution to Optimize its Binding to Cell Surface Receptors

The SARS-CoV-2 Omicron sub-lineage contains a significant number of mutations in the spike protein relative to earlier SARS-CoV-2 variants. Most notably, these mutations significantly increased the positive charge of the spike protein that is postulated to confer increased infectivity, potentially through enhanced interactions with cell surface receptors, and an altered host-cell entry mechanism. While heparan sulfate (HS) was shown to be a key co-receptor in the host-cell entry of SARS-CoV-2, the effect of spike charge on its interactions with heparan sulfate has not been clearly elucidated. Here, we investigate the role of evolving spike positive charge in accelerating long-range interactions to heparan sulfate and ACE2 in the glycocalyx. We show that the positively charged Omicron evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discovered that while the Omicron spike-ACE2 affinity is comparable to Delta, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-HS-ACE2 with a larger proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. We leveraged this understanding for the successful and sensitive detection of the Omicron variant. The evolving enhanced binding of SARS-Cov-2 to heparan sulfate presents new therapeutic and diagnostic opportunities.