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[Preprint]. 2024 Mar 1:2024.02.28.582613.
doi: 10.1101/2024.02.28.582613.

Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination

Jordan Clark  1   2 , Irene Hoxie  1   2 , Daniel C Adelsberg  1 , Iden A Sapse  1 , Robert Andreata-Santos  1   2   3 , Jeremy S Yong  1   2 , Fatima Amanat  1 , Johnstone Tcheou  1   2 , Ariel Raskin  1   2 , Gagandeep Singh  1   2 , Irene González-Domínguez  1 , Julia E Edgar  4 , Stylianos Bournazos  4 , Weina Sun  1 , Juan Manuel Carreño  1   2 , Viviana Simon  1   2   5   6   7 , Ali H Ellebedy  8   9   10 , Goran Bajic  1 , Florian Krammer  1   2   5
Affiliations

Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination

Jordan Clark et al. bioRxiv. .

Update in

Abstract

Neutralizing antibodies correlate with protection against SARS-CoV-2. Recent studies, however, show that binding antibody titers, in the absence of robust neutralizing activity, also correlate with protection from disease progression. Non-neutralizing antibodies cannot directly protect from infection but may recruit effector cells thus contribute to the clearance of infected cells. Also, they often bind conserved epitopes across multiple variants. We characterized 42 human mAbs from COVID-19 vaccinated individuals. Most of these antibodies exhibited no neutralizing activity in vitro but several non-neutralizing antibodies protected against lethal challenge with SARS-CoV-2 in different animal models. A subset of those mAbs showed a clear dependence on Fc-mediated effector functions. We determined the structures of three non-neutralizing antibodies with two targeting the RBD, and one that targeting the SD1 region. Our data confirms the real-world observation in humans that non-neutralizing antibodies to SARS-CoV-2 can be protective.

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Conflict of interest statement

Conflict of interest statement The Icahn School of Medicine at Mount Sinai has filed patent applications relating to SARS-CoV-2 serological assays, NDV-based SARS-CoV-2 vaccines influenza virus vaccines and influenza virus therapeutics which list Florian Krammer as co-inventor. Dr. Simon is also listed on the SARS-CoV-2 serological assays patent. Mount Sinai has spun out a company, Kantaro, to market serological tests for SARS-CoV-2 and another company, Castlevax, to develop SARS-CoV-2 vaccines. Florian Krammer is co-founder and scientific advisory board member of Castlevax. Florian Krammer has consulted for Merck, Curevac, Seqirus and Pfizer and is currently consulting for 3rd Rock Ventures, GSK, Gritstone and Avimex. The Krammer laboratory is also collaborating with Dynavax on influenza vaccine development. The Ellebedy laboratory has received funding under sponsored research agreements from Moderna, Emergent BioSolutions, and AbbVie. A.H.E. has received consulting and speaking fees from InBios International, Inc, Fimbrion Therapeutics, RGAX, Mubadala Investment Company, AstraZeneca, Moderna, Pfizer, GSK, Danaher, Third Rock Ventures, Goldman Sachs, and Morgan Stanley; is the founder of ImmuneBio Consulting and a recipient of royalties from licensing agreements with Abbvie and Leyden Laboratories B.V.

Figures

Figure 1.
Figure 1.. Characterization of mAb binding and neutralization against SARS-CoV-2 variants.
(A-D) Binding of RBD-specific (A), NTD-specific (B), S2-specific (C), and unknown epitope-specific (D) SARS-CoV-2 mAbs to the spike proteins of SARS-CoV-2 variants. Neutralizing mAbs are denoted with red Ns. (E) Neutralizing activity of the neutralizing mAbs against authentic SARS-CoV-2 variants.
Figure 2.
Figure 2.. Investigating the protection elicited by the mAbs using lethal animal challenge models.
(A-D) Maximum weight loss and survival of BALB/cAnNHsd mice treated with RBD-specific (A), NTD-specific (B), S2-specific (C), and unknown epitope-specific (D) SARS-CoV-2 mAbs prior to lethal challenge with mouse-adapted SARS-CoV-2. (E) Hamster weight loss following treatment with the 6 most protective mAbs and challenge with wild type SARS-CoV-2. Neutralizing mAbs are shown as crosses, while non-neutralizing mAbs are shown as circles. In (A-D), the vertical bars in the maximum weight loss graphs indicates the mean with standard deviation. P values are shown only for statistically significant comparisons as determined by a Kruskal-Wallis with Dunn’s multiple comparisons test.
Figure 3.
Figure 3.. Mouse lung titers following mAb treatment and SARS-CoV-2 challenge.
(A-D) murine lung titers 3 dpi after treatment with RBD-specific (A), NTD-specific (B), S2-specific (C), and unknown epitope-specific (D) SARS-CoV-2 mAbs and challenge with mouse adapted SARS-CoV-2. (E-H) lung titers 5 dpi after treatment with RBD-specific (E), NTD-specific (F), S2-specific (G), and unknown epitope-specific (H) SARS-CoV-2 mAbs and challenge with mouse adapted SARS-CoV-2. Neutralizing mAbs are shown as crosses, while non-neutralizing mAbs are shown as circles. P values are shown only for groups with titers statistically significant compared to the negative control, as determined by an ordinary one-way ANOVA with Dunnett’s multiple comparisons test with a single pooled variance.
Figure 4.
Figure 4.. Cryo-EM structures of PVI.V6-12, PVI.V3-21, and PVI.V5-4 in complex with SARS-CoV-2 spike.
(A) and (B) Global, modest-resolution cryo-EM maps of PVI.V6-12 and PVI.V3-21 Fabs in complex with spike. The structures identify the binding epitopes on the spike RBD. Fabs are colored green, RBD sienna, and the rest of spike blue. (C) Cryo-EM map of PVI.V5-4 in complex with spike at 3.67Å nominal resolution. The structure defines the PVI.V5-4 epitope on the sub-domain 1 (SD1). Spike S1 including RBD, SD1, and SD2 domains are colored sienna, S2 dark grey, and PVI.5-4 variable heavy and light chains blue and green, respectively. (D) Cartoon representation of the atomic model of PVI.V5-4 in complex with spike SD1. Major interactions are defined by the antibody HCDR3, HCDR2, and LCDR3 loops. N318 glycan is shown for context. € Surface representation of PVI.V5-4 epitope on spike SD1. The Fab interacting loops are shown as cartoon, and individual interacting residues are labeled and shown as sticks. The spike interacting residues are underlined. N318 glycan is shown for context.
Figure 5.
Figure 5.. Characterization of the Fc-mediated activity of the mAbs.
(A) FcγRIIIa reporter activity of the RBD, NTD, S2, and unknown epitope binding mAbs. (B) FcγRIIa reporter activity of the RBD, NTD, S2, and unknown epitope binding mAbs. (C) Binding of complement protein C1q to the Fc portion of the mAbs in the presence of wild type SARS-CoV-2 spike protein. Dotted lines denote the limit of detection.
Figure 6.
Figure 6.. Investigating the protection elicited by Fc-silent mutant mAbs.
(A) FcγRIIIa reporter activity of the seven most protective mAbs and their LALA and LALAPG mutant counterparts. (B) FcγRIIa reporter activity of the wild type, LALA, and LALAPG mAbs. (C) Binding of complement protein C1q by the wild type, LALA, and LALAPG mAbs in the presence of wild type SARS-CoV-2 spike protein. Dotted lines denote the limit of detection. (D) Weight loss and survival of BALB/cAnNHsd mice treated the seven most protective mAbs and their LALA and LALAPG counterparts following lethal challenge with mouse-adapted SARS-CoV-2.
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