Automated and virus variant-programmable surrogate test qualitatively compares to the gold standard SARS-CoV-2 neutralization assay DOI Creative Commons

Dina Ali,

Maggie L. Bartlett,

Christopher D. Heger

et al.

npj Viruses, Journal Year: 2024, Volume and Issue: 2(1)

Published: Dec. 30, 2024

Abstract The ongoing emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants underscores the need for rapid, adaptable, high-throughput testing. However, assays neutralizing antibodies, which are a good measure viral protection, usually require cell culture and either infectious SARS-CoV-2 or pseudotyped particles. To circumvent challenges cell-based assays, surrogate virus neutralization tests (sVNTs) inhibition binding spike (S) protein receptor domain (RBD) to its receptor, human angiotensin-converting enzyme (hACE2) by antibodies. Here we tested prototype automated microfluidic cartridge-based sVNT platform using wild-type (WT) B.1.617.2 (Delta) variant RBDs. This showed high correlation with biospecimens collected post-COVID-19 vaccination post-SARS-CoV-2 infection as well pre-pandemic negative sera. Thus, this assay, takes less than 80 min, is relatively simple, safe, accurate alternative traditional VNTs.

Language: Английский

Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-COV-2 Variants DOI Open Access

Lingyan Cui,

Tingting Li,

Wenhui Xue

et al.

Published: April 10, 2024

Currently, SARS-CoV-2 has evolved into various variants, including the numerous highly mutated Omicron sub-lineages, significantly increasing immune evasion ability. The development raises concerns about possibly diminished effectiveness of available vaccines and antibody-based therapeutics. Here, we describe those representative categories broadly neutralizing antibodies (bnAbs) that retain prominent against emerging variants sub-lineages. molecular characteristics, epitope conservation, resistance mechanisms these are further detailed, aiming to offer suggestion or direction for therapeutic antibodies, facilitate vaccine design with broad-spectrum potential.

Language: Английский

Citations

6
Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants DOI Creative Commons

Lingyan Cui,

Tingting Li,

Wenhui Xue

et al.

Viruses, Journal Year: 2024, Volume and Issue: 16(6), P. 900 - 900

Published: June 1, 2024

Currently, SARS-CoV-2 has evolved into various variants, including the numerous highly mutated Omicron sub-lineages, significantly increasing immune evasion ability. The development raises concerns about possibly diminished effectiveness of available vaccines and antibody-based therapeutics. Here, we describe those representative categories broadly neutralizing antibodies (bnAbs) that retain prominent against emerging variants sub-lineages. molecular characteristics, epitope conservation, resistance mechanisms these are further detailed, aiming to offer suggestion or direction for therapeutic antibodies, facilitate design with broad-spectrum potential.

Language: Английский

Citations

6
Discovery, recognized antigenic structures, and evolution of cross-serotype broadly neutralizing antibodies from porcine B-cell repertoires against foot-and-mouth disease virus DOI Creative Commons
Fengjuan Li,

Sheng-Ze Wu,

Lv Lv

et al.

PLoS Pathogens, Journal Year: 2024, Volume and Issue: 20(10), P. e1012623 - e1012623

Published: Oct. 15, 2024

It is a great challenge to isolate the broadly neutralizing antibodies (bnAbs) against foot-and-mouth disease virus (FMDV) due its existence as seven distinct serotypes without cross-protection. Here, by vaccination of pig with FMDV O and A whole antigens, we obtained 10 bnAbs O, and/or Asia1 dissecting 216 common clonotypes two specific porcine B-cell receptor (BCR) gene repertoires containing total 12720 B cell clones, indicating induction cross-serotype after sequential antigens. The majority (9/10) were derived from terminally differentiated cells different clonal lineages, which convergently targeted conserved "RGDL" motif on structural protein VP1 mimicking recognition inhibit viral attachment cells. Cryo-EM complex structures revealed that other bnAb pOA-2 specifically targets novel inter-pentamer antigen structure surrounding three-fold axis, highly determinant at residue 68 VP2. This unique binding pattern enabled neutralization destabilizing particle. evolutionary analysis demonstrated origin an intermediate B-cell, emphasizing crucial role somatic hypermutations (SHMs) in balancing breadth potency neutralization. However, excessive SHMs may deviate trajectory broad study provides strategy uncover mutable pathogens antigenic explore protective vaccine.

Language: Английский

Citations

4
Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies DOI Creative Commons

Ohan Mazigi,

David B. Langley, Jake Y. Henry

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(1)

Published: Jan. 2, 2025

The emergence of SARS-CoV-2 variants concern (VOCs) has greatly diminished the neutralizing activity previously FDA-approved monoclonal antibodies (mAbs), including that antibody cocktails and first-generation broadly such as S309 (Sotrovimab). In contrast, targeting cryptic conformational epitopes receptor binding domain (RBD) have demonstrated broad against emerging variants, but exert only moderate activity, which so far hindered clinical development. Here, we utilize in vitro display technology to identify affinity-mature class 6 epitope, accessible “up” conformation spike trimer. Increasing affinity into low picomolar range endowed potent neutralization VOCs protection hACE2 mice from viral challenge. Cryoelectron microscopy crystal structures two affinity-matured (4C12-B12 4G1-C2) complex with RBD highlighted modes distal mutational hotspots commonly overserved VOCs, providing direct structural insights observed resistance. Moreover, further demonstrate rather than being an artifact selection, are common IgG1 + memory B cell repertoire convalescent patients can be induced human V-gene transgenic through immunization. Our results highlight importance very high (picomolar) development vaccines suggest threshold provision long-lasting immunity SARS-CoV-2.

Language: Английский

Citations

0
Contrastive Learning Enables Epitope Overlap Predictions for Targeted Antibody Discovery DOI Creative Commons
Clinton Holt, Alexis K. Janke, Parastoo Amlashi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Computational epitope prediction remains an unmet need for therapeutic antibody development. We present three complementary approaches predicting relationships from amino acid sequences. First, we analyze ∼18 million pairs targeting ∼250 protein families and establish that a threshold of >70% CDRH3 sequence identity among antibodies sharing both heavy light chain V-genes reliably predicts overlapping-epitope pairs. Next, develop supervised contrastive fine-tuning framework large language models which results in embeddings better correlate with information than those pre-trained models. Applying this learning approach to SARS-CoV-2 receptor binding domain antibodies, achieve 82.7% balanced accuracy distinguishing same-epitope versus different-epitope demonstrate the ability predict relative levels structural overlap on functional bins (Spearman ρ = 0.25). Finally, create AbLang-PDB, generalized model broad range families. AbLang-PDB achieves five-fold improvement average precision compared sequence-based methods, effectively amount ( 0.81). In discovery campaign searching HIV-1 broadly neutralizing 8ANC195, 70% computationally selected candidates demonstrated specificity, 50% showing competitive 8ANC195. Together, computational presented here provide powerful tools epitope-targeted discovery, while demonstrating efficacy improving epitope-representation.

Language: Английский

Citations

0
Early 2022 breakthrough infection sera from India target the conserved cryptic class 5 epitope to counteract immune escape by SARS-CoV-2 variants DOI Creative Commons
Indrani Das Jana, Kawkab Kanjo, Subhanita Roy

et al.

Journal of Virology, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

ABSTRACT During the coronavirus disease 2019 (COVID-19) pandemic, vast majority of epitope mapping studies have focused on sera from mRNA-vaccinated populations high-income countries. In contrast, here, we report an analysis 164 serum samples isolated patients with breakthrough infection in India during early 2022 who received two doses ChAdOx viral vector vaccine. Sera were screened for neutralization breadth against wild-type (WT), Kappa, Delta, and Omicron BA.1 viruses. Three highest potency selected mapping, using charged scanning mutagenesis coupled yeast surface display next-generation sequencing. The mapped primarily targeted recently identified class 5 cryptic and, to a lesser extent, 1 4 epitopes. is completely conserved across all severe acute respiratory syndrome 2 (SARS-CoV-2) variants most sarbecoviruses. Based these observations, additional 26 characterized, showed broad neutralizing activity, including XBB.1.5. This contrast results obtained individuals receiving multiple original updated mRNA vaccines, where impaired XBB later concern (VOCs) observed. Our study demonstrates that vaccine highly exposed population sufficient drive substantial emerging upcoming concern. These data highlight important role hybrid immunity conferring protection inform future strategies protect rapidly mutating IMPORTANCE Worldwide implementation vaccines parallel emergence newer shaped humoral immune response population-specific manner. While characterizing this monitoring progression at level, it also imperative developing effective countermeasures form novel therapeutics. has implemented world’s second largest COVID-19 vaccination encountered large number post-vaccination “breakthrough” infections. From cohort infection, whose broadly different SARS-CoV-2 variants. Interestingly, target epitope, which was not previous population-level conducted Western rare remains variants, emerged ones SARS-like coronaviruses may cause outbreaks, thus representing potential vaccines.

Language: Английский

Citations

0
Structural Immunology of SARS‐CoV‐2 DOI Creative Commons
Meng Yuan, Ian A. Wilson

Immunological Reviews, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 27, 2024

The SARS-CoV-2 spike (S) protein has undergone significant evolution, enhancing both receptor binding and immune evasion. In this review, we summarize ongoing efforts to develop antibodies targeting various epitopes of the S protein, focusing on their neutralization potency, breadth, escape mechanisms. Antibodies receptor-binding site (RBS) typically exhibit high neutralizing potency but are frequently evaded by mutations in variants. contrast, conserved regions, such as S2 stem helix fusion peptide, broader reactivity generally lower potency. However, several broadly have demonstrated exceptional efficacy against emerging variants, including latest omicron subvariants, underscoring potential vulnerable sites RBS-A RBS-D/CR3022. We also highlight public classes different protein. targeted present opportunities for germline-targeting vaccine strategies. Overall, developing escape-resistant, potent effective vaccines remains crucial combating future This review emphasizes importance identifying key utilizing antibody affinity maturation inform therapeutic design.

Language: Английский

Citations

3
Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins DOI Creative Commons
Sameer Kumar, Souradip Dasgupta,

Mohammad M. Sajadi

et al.

Viruses, Journal Year: 2024, Volume and Issue: 16(3), P. 407 - 407

Published: March 6, 2024

Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting trimeric spike (S) proteins of SARS-CoV-2. Vaccines therapeutic design strategies must impart characteristics virion S from historical emerging variants onto practical constructs such as soluble, stabilized trimers. The virus is a heterotrimer two subunits: S1, which includes receptor binding domain (RBD) that binds cell surface ACE2, S2, mediates membrane fusion. Previous studies suggest antigenic, structural, functional may differ current soluble surrogates. For example, it was reported certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind SARS-CoV-2 but do not neutralize virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions examine reactivity broadly non-neutralizing anti-S human (mAbs) isolated in 2020. Binding efficiency assessed by FCS with trimers, pseudoviruses inactivated wild-type virions representing 2020 date. Anti-glycan mAbs were tested compared. We find both specific anti-glycan exhibit variable efficient range stabilized, Across mAbs, efficiencies positively correlated pseudoviruses. generally lower than or Among potency did correlate any target. No activity detected antibodies. Notably, released membranes detergent treatment gained more HIV-neutralizing lost all mAbs. Collectively, data surfaces present appreciable amounts nonfunctional favoring former structures latter. solubilized represents structure bound while engineered trimers composite reactive mAb types. detection disparate antigenicity immunoreactivity profiles virion-associated highlight value single-virus analyses designing future antiviral

Language: Английский

Citations

1
Broadening sarbecovirus neutralization with bispecific antibodies combining distinct conserved targets on the receptor binding domain DOI Creative Commons
Denise Guerra, Laura Radić, Mitch Brinkkemper

et al.

Human Vaccines & Immunotherapeutics, Journal Year: 2024, Volume and Issue: 20(1)

Published: Aug. 20, 2024

Monoclonal neutralizing antibodies (mAbs) are considered an important prophylactic against SARS-CoV-2 infection in at-risk populations and a strategy to counteract future sarbecovirus-induced disease. However, most mAbs isolated so far neutralize only few sarbecovirus strains. Therefore, there is growing interest bispecific (bsAbs) which can simultaneously target different spike epitopes thereby increase breadth prevent viral escape. Here, we generate characterize panel of 30 novel broadly reactive bsAbs using efficient controlled Fab-arm exchange protocol. We specifically combine some the broadest described far, conserved on receptor binding domain (RBD). Several show superior cross-binding neutralization compared parental cocktails sarbecoviruses from diverse clades, including recent variants. BsAbs include mAb COVA2–02 among potent broad combinations. As result, study unknown epitope that this targets distinct region at base RBD, could be when designing next-generation bsAb constructs contribute better pandemic preparedness.

Language: Английский

Citations

1
Broadening sarbecovirus neutralization with bispecific antibodies combining distinct conserved targets on the receptor binding domain DOI Open Access
Denise Guerra, Laura Radić, Mitch Brinkkemper

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 9, 2024

Monoclonal neutralizing antibodies (mAbs) are considered an important prophylactic against SARS-CoV-2 infection in at-risk populations and a strategy to counteract future sarbecovirus-induced disease. However, most mAbs isolated so far neutralize only few sarbecovirus strains. Therefore, there is growing interest bispecific (bsAbs) which can simultaneously target different spike epitopes thereby increase breadth prevent viral escape. Here, we generate characterize panel of 30 novel broadly reactive bsAbs using efficient controlled Fab-arm exchange protocol. We specifically combine some the broadest described far, conserved on receptor binding domain (RBD). Several show superior cross-binding neutralization compared parental sarbecoviruses from diverse clades, including recent variants. BsAbs include mAb COVA2-02 among potent broad combinations. As result, study unknown epitope that this targets distinct region at base RBD, could be when designing next-generation bsAb constructs contribute better pandemic preparedness.

Language: Английский

Citations

0