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Principal Investigator: Tongqing Zhou
Organization: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Fiscal Year: 2023
Award: $245,592
Funding agency: National Institute of Allergy and Infectious Diseases
The continued emergence of SARS-CoV-2 Omicron sub-variants evaded neutralization by antibodies elicited against the viral spike protein of early variants. To map or evaluate the antibody responses and antibody repertoire elicited by current vaccines or infection, we developed molecular probes based on new variants of concern. Utilizing these probes, our study characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. A technique was created for acquiring antibody sequences capable of quickly generating and evaluating monoclonal antibodies from numerous probes sorted B cells isolated through flow cytometry. In response to infection by any variant, comparable cross-binding antibody reactions were triggered, demonstrating a consistent ranking of dominant epitopes. Moreover, there was a consistent employment of convergent V genes and similar B cell clones visible across all infecting variants. These shared responses, even amid variations in the antigen, might explain the persistent effectiveness of vaccines relying on an initial single variant.
Our collaborator selected two synthetic DARPin-derived proteins-FSR16m and FSR22-for the possible treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FSR16m and FSR22 are trimeric proteins composed of DARPin SR16m or SR22 fused with a T4 foldon. Despite being selected using a spike protein derived from a now historical SARS-CoV-2 strain, both FSR16m and FSR22 demonstrate a wide-ranging ability to neutralize various SARS-CoV-2 strains. They effectively inhibit the activity of authentic B.1.351, B.1.617.2, and BA.1.1 viruses. To elucidate the neutralization mechanism, we performed cryo-EM structural analysis which revealed that these DARPins (Designed Ankyrin Repeat Proteins) recognize a specific segment within the receptor-binding domain (residues 456, 475, 486, 487, and 489) that overlaps a critical region of the angiotensin-converting enzyme 2 (ACE2)-binding surface. Intranasal administration of FSR16m protected K18-hACE2 transgenic mice exposed to B.1.617.2. Given the potent and extensive neutralization capabilities of FSR16m and FSR22, these agents hold substantial promise as candidates for both preventing and treating SARS-CoV-2 infections.
In a third study, we employed a yeast display technology that maintains natural antibody pairing, combined with next-generation sequencing (NGS) and extensive bioinformatic analysis. The goal is to comprehensively investigate the subdomain specificity of natural human antibodies from two convalescent donors. Utilizing this advanced screening approach, the study maps the cross-reactive responses of antibodies generated by the two donors against various SARS-CoV-2 variants and other betacoronaviruses. The neutralization potency of a subset of cross-reactive antibodies generated in this study is tested, revealing that most antibodies from these patients do not possess neutralizing capabilities. A comparison of specific and non-specific antibodies is conducted by analyzing somatic hypermutation on a repertoire-wide scale for the two individuals. Remarkably, the extent of somatic hypermutation is found to be unique for each patient. The insights gained from this research provide functional understanding of cross-reactive antibodies, which could prove invaluable in devising strategies to combat emerging SARS-CoV-2 variants and divergent betacoronaviruses.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><2019-nCoV variant><2019-nCoV variant forms><2019-nCoV variant strains><ACE2><ANK Domain><ANK Repeat><Angiotensin Receptor><Ankyrin Repeat><Ankyrin Repeat Domain><Antibodies><Antibody Repertoire><Antibody Response><Antibody Specificity><Antigenic Determinants><Antigens><B blood cells><B cell><B cells><B-Cells><B-Lymphocytes><B-cell><B.1.1.529><B.1.351><B.1.617.2><Binding><Binding Determinants><Binding Sites><Bio-Informatics><Bioinformatics><COVID-19 antibody><COVID-19 infection><COVID-19 therapy><COVID-19 treatment><COVID-19 variant><COVID-19 variant forms><COVID-19 variant strains><COVID-19 virus><COVID-19 virus infection><COVID19 infection><COVID19 therapy><COVID19 treatment><COVID19 virus><Cell Isolation><Cell Segregation><Cell Separation><Cell Separation Technology><Clinical Treatment Moab><Clone Cells><CoV-2><CoV2><Combining Site><Complex><Cryo-electron Microscopy><Cryoelectron Microscopy><Delta variant><Electron Cryomicroscopy><Employment><Epitopes><Exposure to><Flow Cytofluorometries><Flow Cytofluorometry><Flow Cytometry><Flow Microfluorimetry><Flow Microfluorometry><Generalized Growth><Genes><Genetic Alteration><Genetic Change><Genetic defect><Goals><Growth><Human><Ig Somatic Hypermutation><Immunoglobulin Somatic Hypermutation><Individual><Infection><Intranasal Administration><Intranasal Drug Administration><K-18><K-18 conjugate><K18><K18 combination><Maps><Modern Man><Molecular Interaction><Molecular Probes><Monoclonal Antibodies><Mutation><NGS Method><NGS system><Omicron variant><Patients><Process><Property><Proteins><Reaction><Reactive Site><Research><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 B.1.1.529><SARS-CoV-2 B.1.351><SARS-CoV-2 B.1.617.2><SARS-CoV-2 antibody><SARS-CoV-2 beta><SARS-CoV-2 delta><SARS-CoV-2 infection><SARS-CoV-2 omicron><SARS-CoV-2 omicron variant><SARS-CoV-2 therapy><SARS-CoV-2 treatment><SARS-CoV-2 variant><SARS-CoV-2 variant forms><SARS-CoV-2 variant strains><SARS-CoV2><SARS-CoV2 antibody><SARS-CoV2 infection><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Serology><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 infection><Severe acute respiratory syndrome related corona virus 2><Site><Sorting><South Africa strain><South Africa variant><South African strain><South African 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acute respiratory syndrome coronavirus 2 treatment><severe acute respiratory syndrome coronavirus 2 variant><severe acute respiratory syndrome coronavirus 2 variant forms><severe acute respiratory syndrome coronavirus 2 variant strains><somatic hypermutation><treat COVID-19><treat COVID19><treat SARS-CoV-2><treat coronavirus disease 2019><treat severe acute respiratory syndrome coronavirus 2><vaccine effectiveness><variants of concern><β CoV><β coronavirus><βCoV>