Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies

Abstract

Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively, show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of the spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented an immune response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies, such as 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape.

Keywords: B.1.351 and B.1.1.7 variants; COVID-19; SARS-CoV-2; cryo-EM; low-frequency immune response; neutralizing antibody; receptor-binding domain.

Graphical abstract

Figure 1

Antibody 1–57 utilizes a hydrophilic pocket to accommodate mutation E484K in emerging strains (A) Cryo-EM reconstruction for spike complex with antibody 1–57 from two orthogonal views; a single conformation with all RBDs down is observed. NTD is shown in orange, RBD in green, glycans in red, antibody heavy chain in blue, and light chain in gray. (B) Domain level view of 1–57 in complex with RBD, with the emerging mutants highlighted in red. (C) Details of antibody 1–57 recognition of RBD showing the overall interface (left panel), recognition by CDR H3 (middle panel), and recognition by CDR L1 and L2 (right panel). CDR H1, H2, H3 are colored in shades of blue; CDR L1, L2, and L3 are colored in shades of gray. E484 is highlighted in bright red (right panel). Nitrogen atoms are colored in blue, oxygen atoms in red; hydrogen bonds (distance <3.2 Å) are represented as dashed lines. (D) Expanded view of the E484 environment at the interface with 1–57 (left panel) and modeling of K484 (right panel) suggest a mechanism of antibody 1–57 accommodation of the E484K mutation; colored as in (B). See also Table S1 and Figure S2.

Figure 2

Structural basis of antibody 2–7 accommodation of mutation N501Y in emerging strains (A) Cryo-EM reconstruction for spike complex with antibody 2–7 from two orthogonal views; a single conformation with one RBD down and two RBDs up is observed. NTD is shown in orange, RBD in green, glycans in red, antibody heavy chain in magenta, and light chain in gray. (B) Domain level view of 2–7 in complex with RBD, with the emerging mutants highlighted in red. (C) Details of antibody 2–7 recognition of RBD showing the overall interface (left panel), recognition by CDR H2 (middle panel), and recognition by CDR L1 and L3 (right panel). CDR H1, H2, and H3 are colored in shades of magenta; CDR L1, L2, and L3 are colored in shades of gray. N501 is highlighted in bright red (right panel). (D) Expanded view of the N501 environment at the interface with 2–7 (left panel) and modeling of Y501 (right panel) suggest a mechanism of antibody 2–7 accommodation of the N501Y mutation; colored as in (B). See also Table S1 and Figure S3.

Figure 3

Antibodies 2–7 and 1–57 exemplify rare responses, suggesting that mutations against these antibodies have low selection pressure (A) Analysis of 52 known RBD-directed neutralizing antibodies indicates that 2–7 and 1–57 approach RBD with angles distinct from prevalent antibody classes. (B) Per residue frequency recognized by the 52 antibodies. VH1-2 and VH3-53 antibody classes recognize RBD residues with high targeting frequency; 1–57 and 2–7 recognize RBD residues with low targeting frequencies. See also Figure S4.

Figure 4

Prevalent emerging mutations appear to arise at epitopes of prevalent neutralizing response, suggesting that resistance mutants might arise less frequently to rare responses, such as antibodies 1–57 and 2–7 (A) Most frequent mutations and positions observed in circulating SARS-CoV-2 strains. (B) Location of prevalent RBD mutations and antibody footprints. (C) Correlation between per residue antibody recognition frequency and the top 50 RBD position mutations. (D) Correlation between mutation effect on ACE2 binding and its frequency. The blue dashed line, R value, and p value represent the fit after removing the two “outliers,” K417N and F486L mutations. See also Figure S4.