Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations

Dussupt, Vincent; Sankhala, Rajeshwer S.; Mendez-Rivera, Letzibeth; Townsley, Samantha; Schmidt, Fabian; Wieczorek, Lindsay; Lal, Kerri G.; Donofrio, G.; Tran, Ursula; Jackson, Nathaniel D.; Zaky, Weam I.; Zemil, Michelle; Tritsch, Sarah R.; Chen, Wei‐Hung; Martinez, Elizabeth; Ahmed, Aslaa; Choe, Misook; Chang, William C.; Hajduczki, Agnes; Jian, Ningbo; Peterson, Caroline E.; Rees, Phyllis A.; Rutkowska, Magdalena; Slike, Bonnie M.; Selverian, Christopher N; Swafford, Isabella; Teng, I-Ting; Thomas, Paul; Zhou, Tongqing; Smith, Catherine Arnott; Currier, Jeffrey R.; Kwong, Peter D.; Rolland, Morgane; Davidson, Edgar; Doranz, Benjamin J.; Mores, Christopher N.; Hatziioannou, Théodora; Reiley, William W.; Bieniasz, Paul D.; Paquin‐Proulx, Dominic; Gromowski, Gregory D.; Polonis, Victoria R.; Michael, Nelson L.; Modjarrad, Kayvon; Joyce, Michael; Krebs, Shelly J.

doi:10.1038/s41590-021-01068-z

Cited by 44 publications

(89 citation statements)

References 67 publications

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“…In contrast, the overall neutralizing activity among anti-RBD antibodies obtained from the same time points from this cohort was significantly higher in all cases (58%, 68%, 75% respectively) (Figure 2C, (Robbiani et al, 2020; Wang et al, 2021c)). Anti-NTD neutralizing antibodies were significantly enriched in IGVH1-24, IGVH3-33 and IGVH3-30 all of which are enriched among neutralizing antibodies that target the NTD supersite (Figure 2D and Table S4, (Amanat et al, 2021; Cerutti et al, 2021b; Chi et al, 2020; Dussupt et al, 2021; Haslwanter et al, 2021; Li et al, 2021; Liu et al, 2021; McCallum et al, 2021a; Planas et al, 2021b; Suryadevara et al, 2021b; Voss et al, 2021)). IGVH1-24 was frequently associated with IGVL1-51 which is also over-represented among neutralizers compared to the database (Table S4).…”

Section: Resultsmentioning

confidence: 99%

“…Nearly all anti-NTD antibodies characterized to date were obtained using the intact S protein to capture specific memory B cells. Neutralizing anti-NTD antibodies obtained by this method represent a small subset of the total anti-S antibodies and in most cases, they target a single carbohydrate flanked epitope that faces away from the cell membrane and is mutated in several variants of concern including Omicron (Amanat et al, 2021; Cerutti et al, 2021b; Chi et al, 2020; Dussupt et al, 2021; Haslwanter et al, 2021; Li et al, 2021; Liu et al, 2021; McCallum et al, 2021a; Planas et al, 2021b; Suryadevara et al, 2021b; Voss et al, 2021). To focus on NTD we used a combination of soluble Wuhan-Hu-1 and Gamma NTD proteins to identify memory B cells producing antibodies specific for this domain.…”

Section: Resultsmentioning

confidence: 99%

“…Less is known about anti-NTD antibody responses. In contrast to RBD, the anti-NTD neutralizing antibodies obtained to date primarily target a single supersite consisting of variable loops flanked by glycans (Amanat et al, 2021; Cerutti et al, 2021b; Chi et al, 2020; Dussupt et al, 2021; Haslwanter et al, 2021; Li et al, 2021; Liu et al, 2021; McCallum et al, 2021a; Planas et al, 2021b; Suryadevara et al, 2021b; Voss et al, 2021). Residues in the supersite are mutated in several variants of concern including Beta, Gamma and Omicron, the latter of which carries 3 deletions, 4 amino acid substitutions and an insertion in the NTD that render antibodies to the supersite infective (Callaway, 2021; Faria et al, 2021; Tegally et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Conserved Neutralizing Epitopes on the N-Terminal Domain of Variant SARS-CoV-2 Spike Proteins

Wang

Muecksch

Cho

et al. 2022

Preprint

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SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor binding domain (RBD) and the N-terminal domain (NTD) of the spike trimer (S) constitute the two major neutralizing targets for the antibody system. Neutralizing antibodies targeting the RBD bind to several different sites on this domain. In contrast, most neutralizing antibodies to NTD characterized to date bind to a single supersite, however these antibodies were obtained by methods that were not NTD specific. Here we use NTD specific probes to focus on anti-NTD memory B cells in a cohort of pre-omicron infected individuals some of which were also vaccinated. Of 275 NTD binding antibodies tested 103 neutralized at least one of three tested strains: Wuhan-Hu-1, Gamma, or PMS20, a synthetic variant which is extensively mutated in the NTD supersite. Among the 43 neutralizing antibodies that were further characterized, we found 6 complementation groups based on competition binding experiments. 58% targeted epitopes outside the NTD supersite, and 58% neutralized either Gamma or Omicron, but only 14% were broad neutralizers. Three of the broad neutralizers were characterized structurally. C1520 and C1791 recognize epitopes on opposite faces of the NTD with a distinct binding pose relative to previously described antibodies allowing for greater potency and cross-reactivity with 7 different variants including Beta, Delta, Gamma and Omicron. Antibody C1717 represents a previously uncharacterized class of NTD-directed antibodies that recognizes the viral membrane proximal side of the NTD and SD2 domain, leading to cross-neutralization of Beta, Gamma and Omicron. We conclude SARS-CoV-2 infection and/or Wuhan-Hu-1 mRNA vaccination produces a diverse collection of memory B cells that produce anti-NTD antibodies some of which can neutralize variants of concern. Rapid recruitment of these cells into the antibody secreting plasma cell compartment upon re-infection likely contributes to the relatively benign course of subsequent infections with SARS-CoV-2 variants including Omicron.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Conserved Neutralizing Epitopes on the N-Terminal Domain of Variant SARS-CoV-2 Spike Proteins

Wang

Muecksch

Cho

et al. 2022

Preprint

Self Cite

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“… Human IgG B cells of convalescent pts RBD/NTD - - 73 h11B11 Humanized IgG4 Mouse ACE2 - - 74 WRAIR-2125, etc. Human IgG1 B cells of convalescent pts RBD/NTD Potent neutralizing activity against all major SARS-CoV-2 variants - 75 910–30 Human IgG1 B cells of a convalescent pt RBD - - 76 hSARS2-02 hSARS2-38 Chimeric IgG1 Mouse RBD - - 77 2–36 Human IgG1 B cells of infected pts RBD Cross-reactivity against SARS-CoV-1, SARS-CoV-2, and all current SARS-CoV-2 variants - 20 , 78 58G6, etc. Human IgG B cells of convalescent pts RBD - - 79 MW06 Human IgG1 …”

Section: Sars-cov-2 and Conventional Igg Mabsmentioning

confidence: 99%

Therapeutic antibodies for COVID-19: is a new age of IgM, IgA and bispecific antibodies coming?

Zhang

Sun

2022

mAbs

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Early humoral immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are dominated by IgM and IgA antibodies, which greatly contribute to virus neutralization at mucosal sites. Given the essential roles of IgM and IgA in the control and elimination of SARS-CoV-2 infection, the mucosal immunity could be exploited for therapeutic and prophylactic purposes. However, almost all neutralizing antibodies that are authorized for emergency use and under clinical development are IgG antibodies, and no vaccine has been developed to boost mucosal immunity for SARS-CoV-2 infection. In addition to IgM and IgA, bispecific antibodies (bsAbs) combine specificities of two antibodies in one molecule, representing an important alternative to monoclonal antibody cocktails. Here, we summarize the latest advances in studies on IgM, IgA and bsAbs against SARS-CoV-2. The current challenges and future directions in vaccine design and antibody-based therapeutics are also discussed.

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“…To respond to global efforts combating the SARS-CoV-2 virus, we previously designed and produced constructs incorporating an N-terminal purification tag, a site-specific protease-cleavage site, the antigen of interest, and a C-terminal sequence targeted by biotin ligase that allow for tag-based purification and in-process biotinylation. Through this strategy, we have produced wildtype SARS-CoV-2 spike ectodomain and subdomain probes allowing for the identification of potent neutralizing antibodies and nanobodies that target the receptor binding domain (RBD) or the N-terminal domain (NTD) of SARS-CoV-2 [14–19], the characterization of antibody binding affinities and specificities, and the quantification of immune responses against spike and its subdomains in nonhuman primates to inform vaccine development [20, 21] and to find correlates of elicited responses with neutralization [22]. Moreover, with the rise of SARS-CoV-2 VOCs, we found that probes incorporating mutations defined by the variants could be helpful in the characterization of the impact of VOC mutations on vaccine effectiveness [23–25].…”

Section: Introductionmentioning

confidence: 99%

Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron

Teng

Nazzari

Choe

et al. 2021

Preprint

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Since the outbreak of the COVID-19 pandemic, widespread infections have allowed SARS-CoV-2 to evolve in human, leading to the emergence of multiple circulating variants. Some of these variants show increased resistance to vaccines, convalescent plasma, or monoclonal antibodies. In particular, mutations in the SARS-CoV-2 spike have drawn attention. To facilitate the isolation of neutralizing antibodies and the monitoring the vaccine effectiveness against these variants, we designed and produced biotin-labeled molecular probes of variant SARS-CoV-2 spikes and their subdomains, using a structure-based construct design that incorporated an N-terminal purification tag, a specific amino acid sequence for protease cleavage, the variant spike-based region of interest, and a C-terminal sequence targeted by biotin ligase. These probes could be produced by a single step using in-process biotinylation and purification. We characterized the physical properties and antigenicity of these probes, comprising the N-terminal domain (NTD), the receptor-binding domain (RBD), the RBD and subdomain 1 (RBD-SD1), and the prefusion-stabilized spike ectodomain (S2P) with sequences from SARS-CoV-2 variants of concern or of interest, including variants Alpha, Beta, Gamma, Epsilon, Iota, Kappa, Delta, Lambda, Mu, and Omicron. We functionally validated probes by using yeast expressing a panel of nine SARS-CoV-2 spike-binding antibodies and confirmed sorting capabilities of variant probes using yeast displaying libraries of plasma antibodies from COVID-19 convalescent donors. We deposited these constructs to Addgene to enable their dissemination. Overall, this study describes a matrix of SARS-CoV-2 variant molecular probes that allow for assessment of immune responses, identification of serum antibody specificity, and isolation and characterization of neutralizing antibodies.

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Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations

Cited by 44 publications

References 67 publications

Conserved Neutralizing Epitopes on the N-Terminal Domain of Variant SARS-CoV-2 Spike Proteins

Conserved Neutralizing Epitopes on the N-Terminal Domain of Variant SARS-CoV-2 Spike Proteins

Therapeutic antibodies for COVID-19: is a new age of IgM, IgA and bispecific antibodies coming?

Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron

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