Abstract
Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans.
Highlights
Emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies
The virus has evolved in the human host during the pandemic[9–11] and we and others have demonstrated that the predominant D614G substitution, located in a monomer-monomer interface of the spike trimer, increases its propensity to adopt the open conformation that is competent to bind receptor[12–14]
This is the first cleaved SARS-CoV-2 spike protein in complex with ACE2 we have observed to remain fully trimeric upon receptor binding
Summary
Examination of the 2D class averages (Supplementary Fig. 2) of ACE2-bound Alpha spike with its furin site intact reveals that all spikes in this dataset are present as trimers (Fig. 1a, Supplementary Table 1). To test if the cleavage of the S1-S2 subunits is directly responsible for the greater stability of the trimeric ACE2-bound S1/S2 complex, we expressed the Alpha spike in the presence of a furin inhibitor, decanoyl-Arg-Val-Lys-Arg-chloromethylketone, which resulted in an almost completely uncleaved protein (Supplementary Fig. 3b). The most striking feature of the structure of Beta spike revealed by cryoEM is that all the trimers adopt an open conformation This is in contrast to our earlier study, under the same conditions, that showed 83% of Wuhan spike particles were in the closed form (Fig. 3a)[8]. We have demonstrated that the emergence of Alpha spike, which is completely cleaved, and Beta spike, which we have not observed to adopt the closed conformation, represent two related recent steps in viral adaptation to the human host They follow D614G substitution which was acquired early in the pandemic and acted to increase the spike stability[12–15]. We suggest that modifications in the spike glycoprotein during evolution of the SARS-CoV-2 virus in humans may have made the virus more infectious by promotion of the open forms of spike, increasing the stability of the pre-fusion-conformation of the receptor-bound trimeric spike, and by tighter receptor binding
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