Profiling B cell immune responses to identify neutralizing antibodies from convalescent COVID-19 patients

Abstract The pandemic Coronavirus Disease 2019 (COVID-19) causes noticeable morbidity and mortality worldwide. In addition to vaccine and antiviral drug therapy, the use of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) neutralizing antibodies for treatment purposes is a viable alternative. In this study, we aimed to profile the humoral responses and identify neutralizing antibodies against SARS-CoV-2 using high-throughput single-cell sequencing that tailored to B cell receptor sequencing. From two convalescent patients with high serum titer against SARS-COV-2, we identified seven antibodies specifically binding to SARS-CoV-2. Among these, the most potent antibody, P4A1 was demonstrated to block the binding of spike protein to its receptor angiotensin-converting enzyme 2 (ACE2), and prevent the viral infection in neutralization assays with pseudovirus as well as live virus at nM to sub-nM range. Moreover, antibody P4A1 can also bind strongly to spike protein with N354D/D364Y, R408I, W436R, V367F or D614G mutations respectively, suggesting that the antibody alone or in combination with other antibodies that recognize different variations of SARS-CoV-2, may provide a broad spectrum therapeutic option for COVID-19 patients. Authors Lisu Huang, Bingqing Shen, Yu Guo, and Shu Shen contributed equally to this work.

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Profiling B cell immune responses to identify neutralizing antibodies from convalescent COVID-19 patients

10.21203/rs.3.rs-38173/v1 ◽

2020 ◽

Author(s):

Lisu Huang ◽

Bingqing Shen ◽

Yu Guo ◽

Shu Shen ◽

Heyu Huang ◽

...

Keyword(s):

B Cell ◽

Neutralizing Antibodies ◽

Therapeutic Option ◽

Antiviral Drug ◽

Cell Receptor ◽

High Serum ◽

Spike Protein ◽

Live Virus ◽

Angiotensin Converting Enzyme 2 ◽

Humoral Responses

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The N-terminal domain of spike glycoprotein mediates SARS-CoV-2 infection by associating with L-SIGN and DC-SIGN

10.1101/2020.11.05.369264 ◽

2020 ◽

Cited By ~ 3

Author(s):

Wai Tuck Soh ◽

Yafei Liu ◽

Emi E. Nakayama ◽

Chikako Ono ◽

Shiho Torii ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Cell Receptor ◽

Spike Protein ◽

Primary Host ◽

Angiotensin Converting Enzyme 2 ◽

Lectin Receptor ◽

Terminal Domain ◽

Host Cell Receptor ◽

Protein Serum

The widespread occurrence of SARS-CoV-2 has had a profound effect on society and a vaccine is currently being developed. Angiotensin-converting enzyme 2 (ACE2) is the primary host cell receptor that interacts with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Although pneumonia is the main symptom in severe cases of SARS-CoV-2 infection, the expression levels of ACE2 in the lung is low, suggesting the presence of another receptor for the spike protein. In order to identify the additional receptors for the spike protein, we screened a receptor for the SARS-CoV-2 spike protein from the lung cDNA library. We cloned L-SIGN as a specific receptor for the N-terminal domain (NTD) of the SARS-CoV-2 spike protein. The RBD of the spike protein did not bind to L-SIGN. In addition, not only L-SIGN but also DC-SIGN, a closely related C-type lectin receptor to L-SIGN, bound to the NTD of the SARS-CoV-2 spike protein. Importantly, cells expressing L-SIGN and DC-SIGN were both infected by SARS-CoV-2. Furthermore, L-SIGN and DC-SIGN induced membrane fusion by associating with the SARS-CoV-2 spike protein. Serum antibodies from infected patients and a patient-derived monoclonal antibody against NTD inhibited SARS-CoV-2 infection of L-SIGN or DC-SIGN expressing cells. Our results highlight the important role of NTD in SARS-CoV-2 dissemination through L-SIGN and DC-SIGN and the significance of having anti-NTD neutralizing antibodies in antibody-based therapeutics.

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Influenza Virus Resistance to Human Neutralizing Antibodies

mBio ◽

10.1128/mbio.00213-12 ◽

2012 ◽

Vol 3 (4) ◽

Author(s):

James E. Crowe

Keyword(s):

Influenza Virus ◽

B Cell ◽

Neutralizing Antibodies ◽

Cell Receptor ◽

B Cell Receptor ◽

Influenza Viruses ◽

Surface Proteins ◽

Progeny Virus ◽

Human Antibody ◽

Functional Surface

ABSTRACT The human antibody repertoire has an exceptionally large capacity to recognize new or changing antigens through combinatorial and junctional diversity established at the time of V(D)J recombination and through somatic hypermutation. Influenza viruses exhibit a relentless capacity to escape the human antibody response by altering the amino acids of their surface proteins in hypervariable domains that exhibit a high level of structural plasticity. Both parties in this high-stakes game of shape shifting drive structural evolution of their functional proteins (the B cell receptor/antibody on one side and the viral hemagglutinin and neuraminidase proteins on the other) using error-prone polymerase systems. It is likely that most of the genetic mutations that occur in these systems are deleterious, resulting in the failure of the B cell or virus with mutations to propagate in the immune repertoire or viral quasispecies. A subset of mutations is tolerated in functional surface proteins that enter the B cell or virus progeny pool. In both cases, selection occurs in the population of mutated and unmutated species. In cases where the functional avidity of the B cell receptor is increased significantly, that clone may be selected for preferential expansion. In contrast, an influenza virus that “escapes” the inhibitory effect of secreted antibodies may represent a high proportion of the progeny virus in that host. The recent paper by O’Donnell et al. [C. D. O’Donnell et al., mBio 3(3):e00120-12, 2012] identifies a mechanism for antibody resistance that does not require escape from binding but rather achieves a greater efficiency in replication.

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An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

Science ◽

10.1126/science.abe3255 ◽

2020 ◽

pp. eabe3255 ◽

Cited By ~ 7

Author(s):

Michael Schoof ◽

Bryan Faust ◽

Reuben A. Saunders ◽

Smriti Sangwan ◽

Veronica Rezelj ◽

...

Keyword(s):

Cell Receptor ◽

Affinity Maturation ◽

Host Cells ◽

Spike Protein ◽

Airway Epithelia ◽

Angiotensin Converting Enzyme 2 ◽

Inactive Conformation ◽

Binding Domains ◽

Host Cell Receptor ◽

Yeast Surface

The SARS-CoV-2 virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryogenic electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.

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CTLA-4 Blockade, during HIV Virus-Like Particles Immunization, Alters HIV-Specific B-Cell Responses

Vaccines ◽

10.3390/vaccines8020284 ◽

2020 ◽

Vol 8 (2) ◽

pp. 284 ◽

Cited By ~ 1

Author(s):

Phoebe E. Lewis ◽

Ethan C. Poteet ◽

Dongliang Liu ◽

Changyi Chen ◽

Celia C. LaBranche ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

T Cell Activation ◽

Neutralizing Antibodies ◽

Cell Activation ◽

Cell Activity ◽

High Serum ◽

Virus Like Particles ◽

Hiv Virus ◽

Specific Igg

Studies have shown that blockade of CTLA-4 promoted the expansion of germinal center B-cells in viral infection or immunization with model antigens. Few studies have evaluated the immunological consequences of CTLA-4 blockade during immunization against relevant vaccine candidates. Here, we investigated the effects of CTLA-4 blockade on HIV virus-like particles (VLPs) vaccination in a C57BL/6J mouse model. We found that CTLA-4 blockade during HIV VLP immunization resulted in increased CD4+ T-cell activation, promoted the expansion of HIV envelope (Env)-specific follicular helper T cell (Tfh) cells, and significantly increased HIV Gag- and Env-specific IgG with higher avidity and antibody-dependent cellular cytotoxicity (ADCC) capabilities. Furthermore, after only a single immunization, CTLA-4 blockade accelerated T-cell dependent IgG class switching and the induction of significantly high serum levels of the B-cell survival factor, A proliferation-inducing ligand (APRIL). Although no significant increase in neutralizing antibodies was observed, increased levels of class-switched Env- and Gag-specific IgG are indicative of increased polyclonal B-cell activation, which demonstrated the ability to mediate and enhance ADCC in this study. Altogether, our findings show that CTLA-4 blockade can increase the levels of HIV antigen-specific B-cell and antigen-specific Tfh cell activity and impact humoral immune responses when combined with a clinically relevant HIV VLP-based vaccine.

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

Nature Immunology ◽

10.1038/s41590-021-01068-z ◽

2021 ◽

Author(s):

Vincent Dussupt ◽

Rajeshwer S. Sankhala ◽

Letzibeth Mendez-Rivera ◽

Samantha M. Townsley ◽

Fabian Schmidt ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Low Dose ◽

Viral Escape ◽

Spike Protein ◽

Receptor Binding Domain ◽

Viral Inactivation ◽

Angiotensin Converting Enzyme 2 ◽

Therapeutic Monoclonal Antibodies ◽

Potent Protection

AbstractPrevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.

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Introduction of two prolines and removal of the polybasic cleavage site leads to optimal efficacy of a recombinant spike based SARS-CoV-2 vaccine in the mouse model

10.1101/2020.09.16.300970 ◽

2020 ◽

Author(s):

Fatima Amanat ◽

Shirin Strohmeier ◽

Raveen Rathnasinghe ◽

Michael Schotsaert ◽

Lynda Coughlan ◽

...

Keyword(s):

Mouse Model ◽

Cleavage Site ◽

Neutralizing Antibodies ◽

Vaccine Development ◽

Middle Eastern ◽

Host Cells ◽

Spike Protein ◽

Optimized Design ◽

Angiotensin Converting Enzyme 2 ◽

Viral Target

AbstractThe spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as the prime target for vaccine development. The spike protein mediates both binding to host cells and membrane fusion and is also so far the only known viral target of neutralizing antibodies. Coronavirus spike proteins are large trimers that are relatively instable, a feature that might be enhanced by the presence of a polybasic cleavage site in the SARS-CoV-2 spike. Exchange of K986 and V987 to prolines has been shown to stabilize the trimers of SARS-CoV-1 and the Middle Eastern respiratory syndrome coronavirus spikes. Here, we test multiple versions of a soluble spike protein for their immunogenicity and protective effect against SARS-CoV-2 challenge in a mouse model that transiently expresses human angiotensin converting enzyme 2 via adenovirus transduction. Variants tested include spike protein with a deleted polybasic cleavage site, the proline mutations, a combination thereof, as well as the wild type protein. While all versions of the protein were able to induce neutralizing antibodies, only the antigen with both a deleted cleavage site and the PP mutations completely protected from challenge in this mouse model.ImportanceA vaccine for SARS-CoV-2 is urgently needed. A better understanding of antigen design and attributes that vaccine candidates need to have to induce protective immunity is of high importance. The data presented here validates the choice of antigens that contain the PP mutation and suggests that deletion of the polybasic cleavage site could lead to a further optimized design.

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Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients

10.1101/2020.12.28.424622 ◽

2020 ◽

Author(s):

Haitao Xiang ◽

Yingze Zhao ◽

Xinyang Li ◽

Peipei Liu ◽

Longlong Wang ◽

...

Keyword(s):

Immune Responses ◽

B Cell ◽

Neutralizing Antibodies ◽

Cell Receptor ◽

Cell Immune Response ◽

Next Generation Sequencing Technology ◽

Network Analyses ◽

Cell Clones ◽

Gene Usage ◽

Therapeutic Development

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patient’s immunological status, and found dramatic changes in the IGH within the patients’ immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones during 2-3 weeks of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34 and IGHV4-39 in COVID-19 patients were more abundant than that of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.

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Protein Footprinting, Conformational Dynamics and Interface-Adjacent Neutralization ‘Hotspots’ in the SARS-CoV-2 Spike Protein Receptor Binding Domain / Human ACE2 Interaction

10.26434/chemrxiv.13385387 ◽

2020 ◽

Author(s):

Dominic Narang ◽

Matthew Balmer ◽

D. Andrew James ◽

Derek Wilson

Keyword(s):

Receptor Binding ◽

Neutralizing Antibodies ◽

Conformational Dynamics ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Angiotensin Converting Enzyme 2 ◽

Additional Information ◽

Protein Receptor ◽

Hdx Ms

This study provides an HDX-MS based analysis of the interaction between the SARS-CoV-2 spike protein and the human Angiotensin Converting Enzyme 2. <div><br></div><div>- The data agree exactly with the X-ray co-crystal structure of this complex, but provide additional information based on shifts in dynamics that are observed just outside the interface. </div><div><br></div><div>- These dynamic changes occur specifically in regions that are the primary targets of neutralizing antibodies that target spike protein, suggesting that the neutralization mechanism may result from suppression of dynamic shifts in the spike Receptor Binding Domain (RBD) that are necessary for favorable binding thermodynamics in the spike / ACE2 interaction.</div>

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Can Levamisole be used in the treatment of COVID-19 patients presenting with diarrhea?

The Journal of Infection in Developing Countries ◽

10.3855/jidc.13101 ◽

2020 ◽

Vol 14 (08) ◽

pp. 844-846

Author(s):

Oğuz Abdullah Uyaroğlu ◽

Gülay Sain Güven ◽

İbrahim Güllü

Keyword(s):

Antiviral Drug ◽

Cell Receptor ◽

Host Cells ◽

Converting Enzyme ◽

Immunomodulatory Effects ◽

Angiotensin Converting Enzyme 2 ◽

Beneficial Effects ◽

The World ◽

Glandular Cells ◽

A Cell

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China, on Jan 7, 2020. Over the following months, the virus rapidly spread throughout the world. Coronavirus Disease 2019 (COVID-19) can involve the gastrointestinal tract, including symptoms like nausea, vomiting and diarrhea and shedding of the SARS-CoV-2 in feces. Angiotensin-converting enzyme 2 (ACE2) protein, which has been proven to be a cell receptor for SARS-CoV-2, is expressed in the glandular cells of gastric, duodenal, and rectal epithelia, supporting the entry of SARS-CoV-2 into the host cells. According to the literature, rates of COVID-19 patients reporting diarrhea were between 7 - 14%. Diarrhea in the course of COVID-19 disease can cause dehydration and hospitalization. Although no antiviral drug was specifically designed for the treatment of diarrhea, several molecules could have beneficial effects by reducing viral replication. In this letter, we discussed the Levamisole, which is an anthelmintic agent with immunomodulatory effects, could be used effectively both for antiviral therapy and especially in COVID-19 patients with diarrhea.

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