Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants

SARS-CoV-2 from alpha to epsilon As battles to contain the COVID-19 pandemic continue, attention is focused on emerging variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus that have been deemed variants of concern because they are resistant to antibodies elicited by infection or vaccination or they increase transmissibility or disease severity. Three papers used functional and structural studies to explore how mutations in the viral spike protein affect its ability to infect host cells and to evade host immunity. Gobeil et al. looked at a variant spike protein involved in transmission between minks and humans, as well as the B1.1.7 (alpha), B.1.351 (beta), and P1 (gamma) spike variants; Cai et al. focused on the alpha and beta variants; and McCallum et al. discuss the properties of the spike protein from the B1.1.427/B.1.429 (epsilon) variant. Together, these papers show a balance among mutations that enhance stability, those that increase binding to the human receptor ACE2, and those that confer resistance to neutralizing antibodies. —VV

T he COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (1), has led to millions of lives lost and devastating socioeconomic disruptions worldwide. Although the mutation rate of the coronavirus is relatively low because of the proofreading activity of its replication machinery (2), several variants of concern have emerged-including the B.1.1.7 lineage first identified in the United Kingdom, the B.1.351 lineage in South Africa, and the B.1.1.28 lineage in Brazil-within a period of several months (3)(4)(5). These variants not only appear to spread more efficiently than the virus from the initial outbreak [i.e., the strain Wuhan-Hu-1; (1)] but also may be more resistant to immunity elicited by the Wuhan-Hu-1 strain after either natural infection or vaccination (6)(7)(8). The B.1.1.7 variant is of particular concern because it has been reported to be more deadly (9,10). Thus, understanding the underlying mechanisms of the increased transmissibility, risk of mortality, and immune resistance of new variants may facilitate development of intervention strategies to control the crisis.
SARS-CoV-2 is an enveloped positive-stranded RNA virus that depends on fusion of viral and target cell membranes to enter a host cell. This first key step of infection is catalyzed by the virus-encoded trimeric spike (S) protein, which is also a major surface antigen and thus an important target for development of diagnostics, vaccines, and therapeutics. The S protein is synthesized as a single-chain precursor and is subsequently cleaved by a furin-like protease into the receptor-binding fragment S1 and the fusion fragment S2 [ fig. S1 and (11)]. Binding of the viral receptor angiotensinconverting enzyme 2 (ACE2) on the host cell surface to the receptor-binding domain (RBD) of S1, together with a second proteolytic cleavage by another cellular protease in S2 [S2′ site; fig. S1 and (12)], induces dissociation of S1 and irreversible refolding of S2 into a postfusion structure, ultimately leading to membrane fusion (13,14). In the prefusion conformation, S1 folds into four domains-NTD (N-terminal domain), RBD, and two CTDs (C-terminal domains)-that wrap around the prefusion S2 structure. The RBD can adopt two distinct conformations: "up" for a receptor-accessible state and "down" for a receptor-inaccessible state (15). Rapid progress in structural biology of the S protein has advanced our knowledge of the SARS-CoV-2 entry process (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28). We have previously identified two structural elements, the FPPR (fusion peptide proximal re-gion) and the 630 loop, which appear to modulate the S protein stability as well as the RBD conformation and thus the receptor accessibility (22,28).
The S protein is the basis of almost all the first-generation COVID-19 vaccines, which were developed using the Wuhan-Hu-1 sequence (29,30). Several have received emergency use authorization by various regulatory agencies throughout the world because of their impressive protective efficacy and minimal side effects (31,32). These vaccines appear to have somewhat lower efficacy against the B.1.351 variant than against its parental strain (6)(7)(8)33), and this variant became completely resistant to many convalescent serum samples in vitro (8). How to address genetic diversity has therefore become a high priority for developing next-generation vaccines. In this study, we have characterized the full-length S proteins from the B.1.1.7 and B.1.351 variants and determined their structures by cryo-electron microscopy (cryo-EM), providing a structural basis for understanding the molecular mechanisms of the enhanced infectivity of B.1.1.7 and the immune evasion of B.1.351.

Biochemical and antigenic properties of the intact S proteins from the new variants
To characterize the full-length S proteins with the sequences derived from natural isolates of the B.1.1.7 (hCoV-19/England/MILK-C504CD/ 2020) and B.1.351 (hCoV-19/South Africa/KRISP-EC-MDSH925100/2020) variants (fig. S1), we first transfected human embryonic kidney (HEK) 293 cells with the respective expression constructs and compared their membrane fusion activities with those of the full-length S constructs of their parental strains [Wuhan-Hu-1: D614 (Asp at position 614) and its early D614G variant: G614 (Asp-to-Gly mutation at position 614) (34)]. All S proteins expressed at comparable levels ( fig. S2A), and the cells producing these S proteins fused efficiently with ACE2-expressing cells ( fig. S2B). Consistent with our previous findings (22,28), the G614 and B.1.351 variant S constructs showed slightly higher fusion activity than the D614 and B.1.1.7 variants, but the differences diminished when the transfection level increased.
To produce the full-length S proteins, we added a C-terminal strep-tag to the B.1.1.7 and B.1.351 S ( fig. S3A) and expressed and purified these proteins under the conditions established for producing the D614 and G614 S trimers (22,28). The B.1.1.7 protein eluted in three distinct peaks, representing the prefusion S trimer, postfusion S2 trimer, and dissociated S1 monomer, respectively (22), consistent with Coomassie-stained SDS-polyacrylamide gel electrophoresis (SDS-PAGE) analysis ( fig. S3B). Nonetheless, the prefusion trimer was the predominant form, accounting for >70% of the total protein, indicating that this trimer is more to AHC (Anti-human IgG Fc Capture) biosensors and dipped into the wells containing each purified S protein at different concentrations. Binding kinetics were evaluated using a 1:1 Langmuir model except for dimeric ACE2 and antibody G32B6 targeting the RBD-2, which were analyzed by a bivalent binding model. The sensorgrams are in black and the fits in red. Binding constants are also summarized here and in table S1. All experiments were repeated at least twice with essentially identical results. K D , dissociation constant; n.a., not available; RU, response unit.
stable than D614, where the prefusion trimer was only <25%. Like the G614 trimer (28), B.1.351 protein eluted in a single major peak, corresponding to the prefusion S trimer (fig. S3B), with no obvious peaks for dissociated S1 and S2. SDS-PAGE analysis showed that the prefusion trimer peaks contained primarily the cleaved S1/S2 complex for both the proteins, with the cleavage level moderately higher for B.1.351 than for B.1.1.7. These results indicate that the B.1.351 and G614 S proteins have almost identical biochemical properties, whereas the B.1.1.7 trimer is slightly less stable.
To assess antigenic properties of the prefusion variant S trimers, we measured their binding to soluble ACE2 and S-directed monoclonal antibodies isolated from COVID-19 convalescent individuals by bio-layer interferometry (BLI). These antibodies target various epitopic regions on the S trimer, as defined by clusters of competing antibodies and designated RBD-1, RBD-2, RBD-3, NTD-1, NTD-2, and S2 [ fig. S4A; (35)]. All but the last two clusters contain neutralizing antibodies. The B.1.1.7 variant bound stronger to the receptor than did its G614 parent, regardless of the ACE2 oligomeric state (Fig. 1, fig. S4B, and table S1). The B.1.351 trimer had higher affinity for monomeric ACE2, but slightly lower affinity for dimeric ACE2, than the G614 trimer. In both cases, affinity for ACE2 of the B.1.351 protein was lower than that of the B. reduce ACE2 affinity to a level close to that of the G614 protein, consistent with the previous data (36,37). All selected monoclonal antibodies bound G614 S with reasonable affinities, and the B.1.1.7 variant showed a similar pattern but with substantially stronger binding to almost all the antibodies (Fig. 1, fig. S4B, and table S1). By contrast, the B.1.351 variant completely lost binding to the two RBD-2 antibodies, G32B6 and C12A2, as well as to the two NTD-1 antibodies, C12C9 and C83B6, whereas the affinities for the rest of the antibodies were the same as those of the G614 trimer. The BLI data were also consistent with the binding results with the membrane-bound S trimers measured by flow cytometry (fig. S5).
We next assessed the neutralization potency of the antibodies and the trimeric ACE2 construct in blocking infection of these variants in an HIV-based pseudovirus assay. For most antibodies, the neutralization potency correlated with their binding affinity for the membranebound or purified S proteins ( fig. S6 and table S2). C81D6 and C163E6 recognize two nonneutralizing epitopes, located in the NTD and S2, respectively, and they did not neutralize any of the pseudoviruses. The B.1.1.7 virus is the most sensitive to the trimeric ACE2 and the RBD-up-targeting C63C7, suggesting that the B.1.1.7 trimer may prefer the RBD-up conformation. Thus, the detergent-solubilized S proteins adopt a physiologically relevant conformation, and mutations in B.1.351 have a greater impact on the antibody sensitivity of the virus than those in B.1.1.7.
Structures of the full-length S trimers from the B.1.1.7 and B.1.351 variants We determined the cryo-EM structures of the full-length S trimers with the unmodified sequences of the B.1.1.7 and B.1.351 variants. Cryo-EM images were acquired on a Titan Krios electron microscope equipped with a Gatan K3 direct electron detector. We used RELION (38) for particle picking, two-dimensional (2D) classification, 3D classification, and refinement (figs. S7 to S10), and cryoSPARC (39) for validation. 3D classification identified five distinct classes for the B.1.1.7 S trimer-representing one closed prefusion conformation, three one-RBD-up conformations, and one two-RBD-up conformation-and two different classes for the B.1.351 trimer, representing a closed conformation and a one-RBD-up conformation. These structures were refined to 2.9-to 4.3-Å resolution (figs. S7 to S10 and table S3).
The overall architectures of the full-length variant S proteins are very similar to that of the G614 S trimer in the corresponding conformation [figs. S11 and S12; (28)]. In the closed, three-RBD-down structure, the four domains of S1-NTD, RBD, CTD1, and CTD2-wrap around the prefusion S2 trimer. In the one-RBD-up conformation, the RBD position has no effect on the central core region of S2, but two NTDs, the immediately adjacent one and the one from the same protomer, shift away from the threefold axis and open up the trimer. The furin cleavage site at the S1/S2 boundary (residues 682 to 685) in these structures remains disordered, and the structures therefore cannot explain the difference in the cleavage level between the B. For the B.1.1.7 S trimer, most particles used for refinement were in the RBD-up conformation (Fig. 2, A to E). We have proposed that the FPPR (residues 828 to 853) and 630 loop (residues 620 to 640) modulate the stability and fusogenic structural rearrangements of the S protein (22,28). In the closed conformation of the B.1.1.7 trimer, all three FPPR and three 630 loops are disordered (Fig. 2F), which otherwise would help clamp down the RBDs. This explains why the B.1.1.7 trimer is more likely than its parental G614 variant to populate the RBD-up conformation, because the FPPRs and 630 loops are structured in the G614 trimer (28). In the one-RBD-up conformation, one 630 loop on the opposite side of the up RBD becomes fully structured, inserting between neighboring NTD and CTDs in the same configuration found in the G614 trimer (28). The second 630 loop is partially ordered, whereas the third one remains disordered. A similar pattern is found for three FPPRs, although the structured FPPR adopts a conformation distinct from the one seen in our previous structures of the full-length S proteins (22,28). Overall, the arrangement of these structural elements appears to stabilize the cleaved S trimer and to prevent the premature S1 dissociation in the one-RBD-up conformation. The three one-RBD-up structures differ only by the degree to which the up RBD and the adjacent NTD of its neighboring protomer shift away from the central threefold axis (fig. S13A). We have suggested that the two-RBD-up conformation might be unstable (22,28), leading to S1 dissociation and irreversible S2 refolding. If this suggestion is valid, the small class of the two-RBD-up particles probably contains mainly uncleaved S trimers.
The two classes for the B.1.351 S trimer represent the closed prefusion and one-RBD-up states, respectively (Fig. 2, G and H). We superposed the structures of the B.1.1.7 trimer onto the G614 trimer in the closed conformation, aligning them by the S2 structure (Fig. 3A). An outward rotation of all three S1 subunits in B.1.1.7 leads to a slightly more open conformation. This rotation in B.1.1.7 widens the gap between the NTD and the CTDs of the same protomer ( fig. S13B). In the G614 trimer, this gap accommodates the ordered 630 loop that reinforces CTD2 and prevents S1 shedding (28). The widened gap in the variant loosens the grip on the 630 loop, accounting for the absence of ordered features in this part of the B.1.1.7 map. There are two mutations that may be responsible for these structural differences. First, Ala 570 in CTD1 packs against one side of the FPPR in the G614 trimer (Fig. 3B). The A570D (Ala 570 →Asp) mutation, with a larger side chain, may weaken the packing and destabilize the FPPR. Moreover, in the one-RBD-up conformation of the B.  Other mutations in B.1.1.7 cluster in the NTD, including deletions of His 69 , Val 70 , and Tyr 145 (Fig. 3D). The first two residues are in a disordered loop in all these S structures, and the structural impact of their deletion is unclear. Tyr 145 is also near a loop (residues 144 to 155), and its deletion apparently causes only some local changes of the loop. The absence of structural changes in the B.1.1.7 NTD is consistent with the absence of effects on its sensitivity to the various NTD-directed antibodies (35). Additional mutations [N501Y, T716I (Thr 716 →Ile), and D1118H (Asp 1118 →His)] caused minimal local changes ( fig. S14, A to C).

Structural impact of the mutations in the B.1.351 variant
The overall structures of the B.1.351 and G614 trimers were essentially the same for the corre-sponding states, except for some loop regions in the NTD (Fig. 4A and fig. S15). Three mutations-K417N, E484K, and N501Y-at the ACE2 binding site do not produce any major structural rearrangements (Fig. 4B). The most notable differences are in the NTD, which contains three point mutations [L18F(Leu 18 →Phe), D80A (Asp 80 →Ala), and D215G (Asp 215 →Gly)] and a three-residue deletion (L242del, A243del, and L244del). The L18F and D80A changes lead to reconfiguration of the N-terminal segment despite the disulfide between Cys 15 and Cys 136 that partly anchors the N-terminal peptide (Fig. 4C). D215G appears to have the least structural impact because Asp 215 is a solventexposed residue that may compensate for the surface charge from the neighboring, wellexposed Arg 214 .
The most consequential changes are probably from the triple-residue deletion, because these nonpolar residues, located on the edge of the NTD core structure formed by four stack-ing b sheets, are replaced with polar residues His 245 -Arg 246 -Ser 247 . This replacement causes a shift of the nearby loop (residues 144 to 155) and must also reconfigure the adjacent disordered loop (residues 246 to 260), both of which form part of the NTD neutralizing epitopes (40). Furthermore, Arg 246 is pointing toward the side chain of Arg 102 near the segment 172 to 188, forcing this loop to rearrange. As shown in Fig. 4D, the 172-to-188 segment wraps around the edge of the NTD core, packing against Leu 242 -Ala 243 -Leu 244 at the edge of the b sheet in the G614 trimer. The tripleresidue deletion rearranges the 172-to-188 segment with a movement up to 17 Å (Leu 180 ). By substantially altering the conformational preferences of this component of the molecular surface, these mutations likely affect binding of any antibody that has part of its footprint in this region. The additional mutation A701V (Ala 701 →Val) is located in the surface-exposed region of S2 and caused minimal structural changes ( fig. S14D).

Discussion
Transmissibility and immune evasion are independent selective forces driving emergence of viral genetic diversity. The changes of most concern in the SARS-CoV-2 S protein would be those that simultaneously enhance transmission, augment disease severity, and evade immune recognition in previously exposed hosts. Our data suggest that the most problematic combination of such mutations is not yet present in the existing variants examined here.
In the B.1.1.7 virus, mutations A570D and S982A lead to an outward shift of the CTD1, thereby relaxing the FPPR and 630 loop, which help retain the RBD in its "down" position in the parental strain. The mutations increase the frequency with which the S trimer samples the RBD-up conformation, allowing B.1.1.7 to better present the receptor binding motif (RBM) to ACE2 on the host cells. Once one RBD flips up, the fully or partially ordered 630 loops of the neighboring protomers stabilize the CTD2, which folds together with the N-terminal segment of S2, and thus prevent the premature S1 dissociation. N501Y in the ACE2 binding site of the RBD also increases the affinity of that domain for the receptor, probably because of the hydrophobic interaction of Tyr 501 with Tyr 41 of ACE2 (36) and a possible cation-p interaction with ACE2 Lys 353 (fig. S16). The combination of enhanced RBM presentation and additional local interactions might allow the B.1.1.7 virus to infect cell types with lower ACE2 levels than those of the nasal and bronchial epithelial cells that the virus typically infects; an expanded cell tropism could account for the increased risk of mortality in patients infected with this variant (9,10). minimal changes in the sensitivity of the B.1.1.7 variant to the potently neutralizing antibodies [tables S1 and S2; (33)].
In the B.1.351 virus, the S protein largely retains the structure of the G614 trimer with almost identical biochemical stability. N501Y, K417N, and E484K in the RBD have not caused major structural changes, but the loss of salt bridges between Lys 417 and ACE2 Asp 30 and Glu 484 and ACE2 Lys 31 mitigates the increased receptor affinity imparted by N501Y ( fig. S16). K417N and E484K probably lead to loss of binding and neutralization by antibodies that target the RBD-2 epitopes (fig. S4A). The accompanying mutations in the NTD remodel the antigenic surface and greatly reduce the potency of neutralizing antibodies against NTD-1 epitopes. The B.1.351 variant was probably selected under a certain level of immune pressure, because it altered two major neutralizing sites on the S trimer simultaneously with only a slight compromise in its ability to engage a host cell.
The global range of SARS-CoV-2 and the daily vast number of replication events make emergence of new variants inevitable and substantially increases the viral genetic diversity. In many cases, antibody resistance may compromise viral fitness, as in the B.1.351 variant, which resists neutralization by RBD-directed antibodies but also loses the enhanced affinity and transmissibility imparted by N501Y, as a consequence of the immune-escape mutations. It is also possible to combine immune evasion and virulence through continuous viral evolution, such as a B.1.1.7 variant that contains the E484K mutation (B.1.1.7+E484K) (41). Such a combination will bring greater challenges for vaccine development compared with the beginning of the pandemic. If SARS-CoV-2 becomes seasonal, innovative strategies already developed against other human pathogens-such HIV-1, hepatitis C virus, and influenza virus-may be applicable to on-going control of the COVID-19 pandemic. The B.1.351 S trimer, which has superior biochemical stability and new epitopes, should be an excellent starting point for developing next-generation vaccines designed to elicit broadly neutralizing antibody responses. Glu484 Glu484 Lys417 Lys417 Asn188 Asn188 Glu169 Glu169 Glu169 N-terminus

144-155 loop
Cys15-Cys136 Cys15-Cys136 contributions: B.C., Y.C., J.Z., and T.X. conceived the project. Y.C. and H.P. expressed and purified the full-length S proteins. T.X. performed BLI and cell-cell fusion experiments. J.Z. and Y.C. prepared cryo grids and performed EM data collection with contributions from S.M.S. and R.M.W. J.Z. and Y.C. processed the cryo-EM data and built and refined the atomic models with help from S.R. C.L.L. and M.S.S. performed the neutralization assays using the HIV-based pseudoviruses. H.Z., K.A., and W.Y. performed the flow cytometry experiments. P.T., A.G., and D.R.W. produced anti-S monoclonal antibodies. S.L. and J.L. created all the expression constructs. S.R.-V. contributed to cell culture and protein production. All authors analyzed the data. B.C., Y.C., J.Z., and T.X. wrote the manuscript with input from all other authors.
Competing interests: W.Y. serves on the scientific advisory boards of Hummingbird Bioscience and GO Therapeutics and is a consultant to GV20 Oncotherapy. All other authors declare no competing interests. Data and materials availability: The atomic structure coordinates are deposited in the RCSB Protein Data Bank (PDB) under accession numbers 7N1Q, 7N1T, 7N1U, 7N1V, 7N1W, 7N1X, and 7N1Y; and the electron microscopy maps have been deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers EMD-24121, EMD-24122, EMD-24123, EMD-24124, EMD-24125, EMD-24126, and EMD-24127. All materials generated during the current study are available from the corresponding author under a materials transfer agreement with Boston Children's Hospital. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/ by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.