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. 2022 Jun 28;13(3):e0358021.
doi: 10.1128/mbio.03580-21. Epub 2022 Apr 25.

Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain

Clara G Altomare  1 , Daniel C Adelsberg  1 , Juan Manuel Carreno  1 , Iden A Sapse  1 , Fatima Amanat  1   2 , Ali H Ellebedy  3   4   5 , Viviana Simon  1   6   7   8 , Florian Krammer  1   8 , Goran Bajic  1
Affiliations

Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain

Clara G Altomare et al. mBio. .

Abstract

Structural characterization of infection- and vaccination-elicited antibodies in complex with antigen provides insight into the evolutionary arms race between the host and the pathogen and informs rational vaccine immunogen design. We isolated a germ line-encoded monoclonal antibody (mAb) from plasmablasts activated upon mRNA vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and determined its structure in complex with the spike glycoprotein by electron cryomicroscopy (cryo-EM). We show that the mAb engages a previously uncharacterized neutralizing epitope on the spike N-terminal domain (NTD). The high-resolution structure reveals details of the intermolecular interactions and shows that the mAb inserts its heavy complementarity-determining region 3 (HCDR3) loop into a hydrophobic NTD cavity previously shown to bind a heme metabolite, biliverdin. We demonstrate direct competition with biliverdin and that, because of the conserved nature of the epitope, the mAb maintains binding to viral variants B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta), and B.1.1.529 (omicron). Our study describes a novel conserved epitope on the NTD that is readily targeted by vaccine-induced antibody responses. IMPORTANCE We report the first structure of a vaccine-induced antibody to SARS-CoV-2 spike isolated from plasmablasts 7 days after vaccination. The genetic sequence of the antibody PVI.V6-14 suggests that it is completely unmutated, meaning that this type of B cell did not undergo somatic hypermutation or affinity maturation; this cell was likely already present in the donor and was activated by the vaccine. This is, to our knowledge, also the first structure of an unmutated antibody in complex with its cognate antigen. PVI.V6-14 binds a novel, conserved epitope on the N-terminal domain (NTD) and neutralizes the original viral strain. PVI.V6-14 also binds the newly emerged variants B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta), and B.1.1.529 (omicron). Given that this antibody was likely already present in the donor prior to vaccination, we believe that this antibody class could potentially "keep up" with the new variants, should they continue to emerge, by undergoing somatic hypermutation and affinity maturation.

Keywords: adaptive immunity; coronavirus; electron microscopy; monoclonal antibodies; vaccine.

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Conflict of interest statement

The authors declare a conflict of interest. The Icahn School of Medicine at Mount Sinai has filed patent applications relating to SARS-CoV-2 serological assays and NDV-based SARS-CoV-2 vaccines which list Florian Krammer as co-inventor. Viviana Simon and Fatima Amanat are also listed on the serological assay patent application as co-inventors. Mount Sinai has spun out a company, Kantaro, to market serological tests for SARS-CoV-2. Florian Krammer has consulted for Merck and Pfizer (before 2020), and is currently consulting for Pfizer, Seqirus and Avimex. The Krammer laboratory is also collaborating with Pfizer on animal models of SARS-CoV-2. Ali Ellebedy has consulted for InBios and Fimbrion Therapeutics (before 2021) and is currently a consultant for Mubadala Investment Company. The Ellebedy laboratory received funding under sponsored research agreements that are unrelated to the data presented in the current study from Emergent BioSolutions and from AbbVie.

Figures

FIG 1
FIG 1
PVI.V6-14 mAb recognizes a novel epitope on the SARS-CoV-2 spike NTD. Shown is a cryo-EM structure model of the SARS-CoV-2 spike trimer (the three protomers are in hues of blue, and glycans are in gray) with PVI.V6-14 Fab (the heavy chain [HC] is in purple, and the light chain [LC] is in pink) bound to the NTD (A), with a 90°-rotated view (B). Two Fabs are bound per trimer in the final reconstruction.
FIG 2
FIG 2
PVI.V6-14 mAb binds the spike NTD primarily through its HCDR3 loop. Shown are two different views of the details of the intermolecular interactions between PVI.V6-14 and the NTD that are dominated by the HCDR3 loop. NTD-interacting amino acid residues are shown in gold, with residue number labels underscored.
FIG 3
FIG 3
PVI.V6-14 binds viral variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta), and B.1.1.529 (omicron) but not P.1 (gamma). (A) Binding of PVI.V6-14 IgG to WA1/2020, (gray), B.1.1.7 (alpha) (blue), B.1.351 (beta) (green), P.1 (gamma) (red), B.1.617.2 (delta) (yellow), and B.1.1.529 (omicron) (black) NTDs of SARS-CoV-2 spike. The area under the curve (AUC) was calculated by subtracting the average of blank values plus 3 times the standard deviation of the blank values. Shown are means from a representative experiment performed in triplicates. Anti-polyhistidine IgG was used as positive control across the ELISA plates. (B) Table recapitulating the VOC amino acid mutations. (C and D) Structural mapping of the VOC mutations onto the NTD in complex with PVI.V6-14 Fab. The structure explains the mAb dependence on the R190 residue in the NTD and the diminished binding to the P.1 VOC. The color scheme is the same as the one described above for panel A.
FIG 4
FIG 4
Biliverdin directly competes with PVI.V6-14. (A) Structural superposition of the biliverdin-bound NTD (PDB accession number 7B62) with the PVI.V6-14-bound NTD (this study) (PDB accession number 7RBU). Biliverdin is shown in green, and the PVI.V6-14 HCDR3 loop is shown in purple sticks. NTD-interacting amino acid residues are shown in gold, with residue number labels underscored. (B) Biolayer interferometry (BLI)-based competition assay of biliverdin with PVI.V6-14 on the recombinant NTD. RU, response units. (C) Neutralization assay with an authentic SARS-CoV-2 isolate of NTD binding PVI.V6-14 and RBD binding 2C08 mAb with and without biliverdin (bv). PVI.V6-14 directly competes with biliverdin, while 2C08 neutralization activity is unaffected by biliverdin. (D) Remdesivir neutralization control.
FIG 5
FIG 5
Structural comparison of PVI.V6-14 and P008_056. (A) Atomic models of the PVI.V6-14- and P008_056-bound SARS-CoV-2 spike. While both Fabs compete with biliverdin, their epitopes and angles of approach are different. (B) Structural superposition of PVI.V6-14 and P008_056 Fab-NTD complexes showing that the binding of the two classes of antibodies is mutually exclusive. (C) Structural superposition of the PVI.V6-14 (purple)-, P008_056 (blue)-, and biliverdin (green)-bound NTD. Major structural rearrangements are localized to the 245–255, 145–155, and 175–185 loops. The PVI.V6-14 NTD conformation is similar to the biliverdin-bound one.
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