scholarly journals Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2

2022 ◽  
Author(s):  
Nell Saunders ◽  
Delphine Planas ◽  
William Henry Bolland ◽  
Christophe Rodriguez ◽  
Slim Fourati ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Neutralization Sensitivity ◽  
Terminal Domain ◽  
Spike Function

SARS-CoV-2 lineages are continuously evolving. As of December 2021, the AY.4.2 Delta sub-lineage represented 20 % of sequenced strains in UK and has been detected in dozens of countries. It has since then been supplanted by the Omicron variant. AY.4.2 displays three additional mutations (T95I, Y145H and A222V) in the N-terminal domain (NTD) of the spike when compared to the original Delta variant (B.1.617.2) and remains poorly characterized. Here, we analyzed the fusogenicity of the AY.4.2 spike and the sensitivity of an authentic AY.4.2 isolate to neutralizing antibodies. The AY.4.2 spike exhibited similar fusogenicity and binding to ACE2 than Delta. The sensitivity of infectious AY.4.2 to a panel of monoclonal neutralizing antibodies was similar to Delta, except for the anti-RBD Imdevimab, which showed incomplete neutralization. Sensitivity of AY.4.2 to sera from individuals having received two or three doses of Pfizer or two doses of AstraZeneca vaccines was reduced by 1.7 to 2.1 fold, when compared to Delta. Our results suggest that mutations in the NTD remotely impair the efficacy of anti-RBD antibodies. The temporary spread of AY.4.2 was not associated with major changes in spike function but rather to a partially reduced neutralization sensitivity.

scholarly journals Breakthrough Virus Neutralization Resistance as a Correlate of Protection in a Nonhuman Primate Heterologous Simian Immunodeficiency Virus Vaccine Challenge Study

2015 ◽  
Vol 89 (24) ◽  
pp. 12388-12400 ◽  
Author(s):  
Fang-Hua Lee ◽  
Rosemarie Mason ◽  
Hugh Welles ◽  
Gerald H. Learn ◽  
Brandon F. Keele ◽  
...  
Keyword(s):  
Simian Immunodeficiency Virus ◽  
Nonhuman Primate ◽  
Neutralizing Antibodies ◽  
Sieve Analysis ◽  
Neutralization Sensitivity ◽  
Immune Correlates ◽  
Vaccine Trials ◽  
Genetic Signature ◽  
Immunodeficiency Virus ◽  
Sieve Analyses

ABSTRACTComprehensive assessments of immune correlates of protection in human immunodeficiency virus (HIV) vaccine trials are essential to vaccine design. Neutralization sieve analysis compares the neutralization sensitivity of the breakthrough transmitted/founder (TF) viruses from vaccinated and control animals to infer the molecular mechanisms of vaccine protection. Here, we report a robust neutralization sieve effect in a nonhuman primate simian immunodeficiency virus (SIV) vaccine trial (DNA prime/recombinant adenovirus type 5 [rAd5] boost) (VRC-10-332) that demonstrated substantial protective efficacy and revealed a genetic signature of neutralization resistance in the C1 region ofenv. We found significant enrichment for neutralization resistance in the vaccine compared to control breakthrough TF viruses when tested with plasma from vaccinated study animals, plasma from chronically SIV-infected animals, and a panel of SIV-specific monoclonal antibodies targeting six discrete Env epitopes (P< 0.008 for all comparisons). Neutralization resistance was significantly associated with the previously identified genetic signature of resistance (P< 0.0001), and together, the results identify virus neutralization as a correlate of protection. These findings further demonstrate thein vivorelevance of our previousin vitroanalyses of the SIVsmE660 challenge stock, which revealed a broad range of neutralization sensitivities of its component viruses. In sum, this report demonstrates proof-of-concept that phenotypic sieve analyses can elucidate mechanistic correlates of immune protection following vaccination and raises a cautionary note for SIV and SHIV (simian-human immunodeficiency virus) vaccine studies that employ challenge strains with envelope glycoproteins that fail to exhibit neutralization resistance profiles typical of TF viruses.IMPORTANCEWith more than 2 million new infections annually, the development of an effective vaccine against HIV-1 is a global health priority. Understanding immunologic correlates of protection generated in vaccine trials is critical to advance vaccine development. Here, we assessed the role of vaccine-elicited neutralizing antibodies in a recent nonhuman primate study of a vaccine that showed significant protection against simian immunodeficiency virus (SIV) challenge and suggested a genetic signature of neutralization sensitivity. We found that breakthrough viruses able to establish infection in vaccinated animals were substantially more resistant to antibody-mediated neutralization than were viruses from controls. These findings suggest that vaccine-elicited neutralizing antibodies selectively blocked the transmission of more sensitive challenge viruses. Sieve analysis also corroborated a genetic signature of neutralization sensitivity and highlighted the impact of challenge swarm diversity. Our findings suggest an important role for neutralization sieve analyses as an informative component of comprehensive immune-correlates analyses.

scholarly journals SARS-CoV-2 immune evasion by variant B.1.427/B.1.429

2021 ◽  
Author(s):  
Matthew McCallum ◽  
Jessica Bassi ◽  
Anna De Marco ◽  
Alex Chen ◽  
Alexandra C Walls ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Immune Evasion ◽  
Neutralizing Antibodies ◽  
Natural Infection ◽  
Clinical Stage ◽  
Viral Evolution ◽  
Structural Rearrangement ◽  
Peptide Cleavage ◽  
Terminal Domain ◽  
Novel Variant

SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.

scholarly journals Distinct evolution of infection-enhancing and neutralizing epitopes in the spike protein of SARS-CoV-2 variants (from alpha to omicron) : a structural and molecular epidemiology study

2021 ◽  
Author(s):  
Patrick GUERIN ◽  
Nouara YAHI ◽  
Fodil AZZAZ ◽  
Henri CHAHINIAN ◽  
Jean-Marc SABATIER ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Structural Dynamics ◽  
Neutralizing Antibodies ◽  
Mass Vaccination ◽  
Spike Protein ◽  
Epidemiology Study ◽  
Gamma Delta ◽  
Los Alamos ◽  
Terminal Domain ◽  
Neutralizing Epitopes

Abstract Infection-enhancing antibodies may limit the efficiency of Covid-19 vaccines. We analyzed the evolution ofneutralizing and facilitating epitopes in 1,860,489 SARS-CoV-2 genomes stored in the Los Alamos databasefrom June to November 2021. The structural dynamics of these epitopes was determined by molecular modelingof the spike protein on a representative panel of SARS-CoV-2 variants. D614, which belongs to an antibody-dependent-enhancement (ADE) epitope common to SARS-CoV-1 and SARS-CoV-2, has mutated to D614G in2020, which could explain why ADE has not been detected following mass vaccination. A second epitopelocated in the N-terminal domain (NTD), specific of SARS-CoV-2, is highly conserved among most variants. Incontrast, the neutralizing epitope of the NTD showed extensive variations in SARS-CoV-2 variants. The balancebetween facilitating and neutralizing antibodies is in favor of neutralization for the Wuhan strain, alpha and betavariants, but not for gamma, delta, lambda, and mu. The recently emerging omicron variant is atypic as itsmutational profiles affects both neutralization and ADE epitopes. Overall, our data reveal that the evolution ofSARS-CoV-2 has dramatically affected the ADE/neutralization balance. Future vaccines should consider thesefindings to design new formulations adapted to SARS-CoV-2 variants and lacking ADE epitopes in the spikeprotein.

scholarly journals Homologous and heterologous serological response to the N-terminal domain of SARS-CoV-2

2021 ◽  
Author(s):  
Huibin Lv ◽  
Owen Tak-Yin Tsang ◽  
Ray T. Y. So ◽  
Yiquan Wang ◽  
Meng Yuan ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Global Economy ◽  
Vaccine Development ◽  
Serological Response ◽  
Receptor Binding Domain ◽  
Plasma Samples ◽  
Mice Model ◽  
Terminal Domain ◽  
Major Antigen ◽  
Serology Testing

SUMMARYThe increasing numbers of infected cases of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses serious threats to public health and the global economy. Most SARS-CoV-2 neutralizing antibodies target the receptor binding domain (RBD) and some the N-terminal domain (NTD) of the spike protein, which is the major antigen of SARS-CoV-2. While the antibody response to RBD has been extensively characterized, the antigenicity and immunogenicity of the NTD protein are less well studied. Using 227 plasma samples from COVID-19 patients, we showed that SARS-CoV-2 NTD-specific antibodies could be induced during infection. As compared to the serological response to SARS-CoV-2 RBD, the SARS-CoV-2 NTD response is less cross-reactive with SARS-CoV. Furthermore, neutralizing antibodies are rarely elicited in a mice model when NTD is used as an immunogen. We subsequently demonstrate that NTD has an altered antigenicity when expressed alone. Overall, our results suggest that while NTD offers an alternative strategy for serology testing, it may not be suitable as an immunogen for vaccine development.

scholarly journals HIV-1 co-receptor usage and variable loop contact impacts V3 loop bnAb susceptibility

2019 ◽  
Author(s):  
Ludy Registre ◽  
Yvetane Moreau ◽  
Sila Toksoz Ataca ◽  
Surya Pulukuri ◽  
Timothy J. Henrich ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Neutralizing Antibodies ◽  
Sequence Data ◽  
Neutralizing Antibody ◽  
V3 Loop ◽  
Neutralization Sensitivity ◽  
Receptor Usage ◽  
Variable Loop ◽  
Ccr5 Receptor ◽  
Hiv 1

ABSTRACTIn clinical trials, HIV-1 broadly neutralizing antibodies (bnAbs) effectively lower plasma viremia and delay virus reemergence after antiretroviral treatment is stopped among infected individuals that have undetectable virus levels. Presence of less neutralization susceptible strains prior to treatment, however, decreases the efficacy of these antibody-based treatments. The HIV-1 envelope glycoprotein harbors extensive genetic variation, and thus, neutralization sensitivity often cannot be predicted by sequence analysis alone. Sequence-based prediction methods are needed because phenotypic-based assays are labor intensive and not sensitive. Based on the finding that phenotypically confirmed CXCR4- as compared to exclusive CCR5-utilizing strains are less neutralization sensitive, especially to variable loop 1 and 2 (V1-V2) and V3 loop bnAbs, we show that an algorithm that predicts receptor usage identifies envelopes with decreased V3 loop bnAb susceptibility. Homology modeling suggests that the primary V3 loop bnAb epitope is equally accessible among CCR5- and CXCR4-using strains although variants that exclusively use CXCR4 have V3 loop protrusions that interfere with CCR5 receptor interactions. On the other hand, homology modeling also shows that envelope V1 loop orientation interferes with V3 loop directed bnAb binding, and this accounts for decreased neutralization sensitivity in some but not all cases. Thus, there are likely different structural reasons for the co-receptor usage restriction and the differential bnAb susceptibility. Algorithms that use sequence data to predict receptor usage and antibody-envelope homology models can be used to identify variants with decreased sensitivity to V3 loop and potentially other bnAbs.AUTHOR SUMMARYHIV-1 broadly neutralizing antibody (bnAb) therapies are effective, but the pre-existence of less susceptible variants may lead to therapeutic failure. Sequence-based methods are needed to predict pre-treatment variants’ neutralization sensitivity. HIV-1 strains that use the CXCR4 as compared to the CCR5 receptor are less neutralization susceptible, especially to V1-V2 and V3 loop bnAbs. A sequence-based algorithm that predicts receptor usage can identify envelope variants with decreased V3 loop bnAb susceptibility. While the inability to utilize the CCR5 receptor maps to a predicted protrusion in the envelope V3 loop, this viral determinant does not directly influence V3 loop bnAb sensitivity. Furthermore, homology modeling predicted contact between the envelope V1 loop and an antibody also impact V3 loop bnAb susceptibility in some but not all cases. An algorithm that predicts receptor usage and homology modeling can be used to predict sensitivity to bnAbs that target the V3 loop and potentially other envelope domains. These sequence-based methods will be useful as HIV-1 bnAbs enter the clinical arena.

scholarly journals N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

2021 ◽  
Author(s):  
Matthew McCallum ◽  
Anna De Marco ◽  
Florian Lempp ◽  
M. Alejandra Tortorici ◽  
Dora Pinto ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Protective Immunity ◽  
Selective Pressure ◽  
Memory B Cells ◽  
Host Cells ◽  
Receptor Binding Domain ◽  
Effector Functions ◽  
Terminal Domain ◽  
Frequent Mutations ◽  
A Site

SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.

scholarly journals Therapeutic antibodies, targeting the SARS-CoV-2 spike N-terminal domain, protect lethally infected K18-hACE2 mice

2021 ◽  
Author(s):  
Tal Noy-Porat ◽  
Adva Mechaly ◽  
Yinon Levy ◽  
Efi Makdasi ◽  
Ron Alcalay ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Phage Display Library ◽  
Host Cells ◽  
Terminal Domain ◽  
Isolation And Characterization ◽  
Recent Emergence ◽  
Therapeutic Monoclonal Antibodies

AbstractSince the onset of the current COVID-19 pandemic, high priority is given to the development of neutralizing antibodies, as a key approach for the design of therapeutic strategies to countermeasure and eradicate the disease. Previously, we reported the development of human therapeutic monoclonal antibodies (mAbs) exhibiting very high protective ability. These mAbs recognize epitopes on the spike receptor binding domain (RBD) of SARS-CoV-2 that is considered to represent the main rout of receptor engagement by the SARS-CoV-2 virus. The recent emergence of viral variants emphasizes the notion that efficient antibody treatments need to rely on mAbs against several distinct key epitopes in order to circumvent the occurrence of therapy escape-mutants. Here we report the isolation and characterization of 12 neutralizing mAbs, identified by screening a phage-display library constructed from lymphatic cells collected from severe COVID-19 patients. The antibodies target three distinct epitopes on the spike N-terminal domain (NTD) of SARS-CoV-2, one of them defining a major site of vulnerability of the virus. Extensive characterization of these mAbs suggests a neutralization mechanism which relies both on amino-acid and N-glycan recognition on the virus, and involvement of receptors other than the hACE2 on the target cell. Two of the selected mAbs, which demonstrated superior neutralization potency in vitro, were further evaluated in vivo, demonstrating their ability to fully protect K18-hACE2 transgenic mice even when administered at low doses and late after infection. The study demonstrates the high potential of the mAbs for therapy of SARS-CoV-2 infection and underlines the possible role of the NTD in mediating infection of host cells via alternative cellular portals other than the canonical ACE2 receptor.

scholarly journals More Is Always Better Than One: The N-Terminal Domain of the Spike Protein as Another Emerging Target for Hampering the SARS-CoV-2 Attachment to Host Cells

2021 ◽  
Vol 22 (12) ◽  
pp. 6462
Author(s):  
Sonia Di Gaetano ◽  
Domenica Capasso ◽  
Pietro Delre ◽  
Luciano Pirone ◽  
Michele Saviano ◽  
...  
Keyword(s):  
Small Molecules ◽  
Neutralizing Antibodies ◽  
Recent Literature ◽  
Rna Virus ◽  
Binding Domain ◽  
Host Cells ◽  
Virus Attachment ◽  
Terminal Domain ◽  
Putative Target ◽  
Better Than

Although the approved vaccines are proving to be of utmost importance in containing the Coronavirus disease 2019 (COVID-19) threat, they will hardly be resolutive as new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, a single-stranded RNA virus) variants might be insensitive to the immune response they induce. In this scenario, developing an effective therapy is still a dire need. Different targets for therapeutic antibodies and diagnostics have been identified, among which the SARS-CoV-2 spike (S) glycoprotein, particularly its receptor-binding domain, has been defined as crucial. In this context, we aim to focus attention also on the role played by the S N-terminal domain (S1-NTD) in the virus attachment, already recognized as a valuable target for neutralizing antibodies, in particular, building on a cavity mapping indicating the presence of two druggable pockets and on the recent literature hypothesizing the presence of a ganglioside-binding domain. In this perspective, we aim at proposing S1-NTD as a putative target for designing small molecules hopefully able to hamper the SARS-CoV-2 attachment to host cells.

scholarly journals A Recombinant Protein SARS-CoV-2 Candidate Vaccine Elicits High-titer Neutralizing Antibodies in Macaques.

2021 ◽  
Author(s):  
Gary Baisa ◽  
David Rancour ◽  
Keith Mansfield ◽  
Monika Burns ◽  
Lori Martin ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
High Titer ◽  
Binding Domain ◽  
Pseudotyped Virus ◽  
Receptor Binding Domain ◽  
Binding Assays ◽  
Neutralizing Activity ◽  
Terminal Domain

Abstract BackgroundVaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. MethodsWe assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain or an extended C-terminal domain containing the receptor-binding domain and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. ResultsA robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the N-terminal domain alone lacked this activity. Crucially, sera from animals immunized with the extended receptor binding domain but not the N-terminal domain had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. ConclusionsThese data support the utility of spike subunit-based antigens as a vaccine for use in humans.

scholarly journals A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques.

2020 ◽  
Author(s):  
Gary Baisa ◽  
David Rancour ◽  
Keith Mansfield ◽  
Monika Burns ◽  
Lori Martin ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
High Titer ◽  
Pseudotyped Virus ◽  
Binding Assays ◽  
Neutralizing Activity ◽  
Terminal Domain ◽  
Vitro Binding ◽  
Cynomolgus Macaques ◽  
Human Igg1

Vaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. We assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain (NTD) or an extended C-terminal domain containing the receptor-binding domain (RBD) and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either each antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. A robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and was maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the NTD alone lacked this activity. Crucially, sera from animals immunized with the RBD but not the NTD had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. These data support the utility of spike subunit-based antigens as a vaccine for use in humans.

Sign in / Sign up

Export Citation Format

Share Document