SARS-CoV-2 antibody avidity responses in natural infection and vaccination

Background: In ongoing SARS CoV-2 pandemic, understanding antibody responses have played a key role in measuring extent of exposure, protection from reinfection, vaccine efficacy and serodiagnosis. Antibody avidity is total binding strength of immunoglobulin G (IgG) toward its target epitope. High antibody avidity has been correlated with effective neutralization of the SARSCoV-2 virus. However, the data on avidity responses against COVID-19 infection and vaccination are limited. Objective(s): To understand the avidity responses among sera of naturally infected, recovered COVID-19 patients;naive Covaxin, Covishield vaccinees and breakthrough infections. Material(s) and Method(s): In this study, we utilized an in-house developed SARS-CoV-2 anti-spike receptor binding domain (SRBD) IgG ELISA to optimize the avidity assay. A panel of anti-SARS-CoV- 2 SRBD IgG positive serum samples were treated with known concentration of a chaotropic agent (urea) for disruption of the noncovalent interactions of the antigen-antibody complex. This disruption causes low avidity antibodies to dissociate which gives the percentage of high avidity antibodies present in a serum sample. Additionally, the optimized assay was used to understand the avidity responses among sera belonging to individuals naturally infected and recovered after COVID-19, naive Covaxin and Covishield vaccinees;followed by breakthrough infections. Result(s) and Conclusion(s): The anti-SRBD avidity progressively elevated over a period of twelve months. Moreover, overall antibody avidity responses were similar in the case of natural infection and naive two doses of Covaxin and Covishield vaccinated individuals. However, avidity responses were high among individuals with a breakthrough infection as compared to naive vaccinees.

Nanopore single-molecule analysis of biomarkers: Providing possible clues to disease diagnosis

Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic COVID-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.Copyright © 2023 Elsevier B.V.

Exploring the role of framework mutations in enabling breadth of a cross-reactive antibody (CR3022) against the SARS-CoV-2 RBD and its variants of concern.

Cross-reactive and broadly neutralizing antibodies against surface proteins of diverse strains of rapidly evolving viral pathogens like SARS-CoV-2 can prevent infection and therefore are crucial for the development of effective universal vaccines. While antibodies typically incorporate mutations in their complementarity determining regions during affinity maturation, mutations in the framework regions have been reported as players in determining properties of broadly neutralizing antibodies against HIV and the Influenza virus. We propose an increase in the cross-reactive potential of CR3022 against the emerging SARS- CoV-2 variants of concern through enhanced conformational flexibility. In this study, we use molecular dynamics simulations, in silico mutagenesis, structural modeling, and docking to explore the role of light chain FWR mutations in CR3022, a SARS-CoV anti-spike (S)-protein antibody cross-reactive to the S-protein receptor binding domain of SARS-CoV-2. Our study shows that single substitutions in the light chain framework region of CR3022 with conserved epitopes across SARS-CoV strains allow targeting of diverse antibody epitope footprints that align with the epitopes of recently-categorized neutralizing antibody classes while enabling binding to more than one strain of SARS-CoV-2. Our study has implications for rapid and evolution-based engineering of broadly neutralizing antibodies and reaffirms the role of framework mutations in effective change of antibody orientation and conformation via improved flexibility.Communicated by Ramaswamy H. Sarma.

Requirement for booster doses in healthy, cancer and immunosuppressed patients infected with the ancestral or variant SARS-CoV-2

Introduction: Current SARS-CoV-2 vaccines are effective at preventing COVID-19 or limiting disease severity in healthy individuals, but effectiveness is lower among patients with cancer or immunosuppression. Vaccine effectiveness wanes with time and varies by vaccine type. Moreover, current vaccines are based on the ancestral SARS-CoV-2 spike protein sequence, and emerging viral variants evade vaccine induced immunity. Booster doses partially overcome these issues, but there are limited clinical data on the durability of protection afforded by boosters - especially against SARS-CoV-2 variants. Methods: Here we describe a mechanistic mathematical model for vaccination-induced immunity in patients with cancer and use it to predict vaccine effectiveness taking into account current and possible future viral, host and vaccine characteristics. Crucially, this allows predictions over time frames currently not reported in the clinical literature. The model incorporates the infection of lung epithelium by SARS-CoV-2, the response of innate and adaptive immune cells to infection, the production of pro-and anti-inflammatory cytokines, the activation of the coagulation cascade. The model further accounts for the interactions between the virus, immune cells and tumor cells as well as for vaccination-induced immunity and anti-cancer therapies. Results: Model predictions were validated with available clinical data. The model predicts that for healthy individuals vaccinated and boosted with mRNA-1273, BNT-162b2a, and Ad26.COV2.S, robust immunogenicity against the ancestral and delta variant extends beyond a year. Immunogenicity is enhanced following booster vaccination in patients with cancer on various anti-cancer therapies and for patients without cancer on immunosuppressive agents. However, our model predicts that more than one booster dose will be required for patients with cancer, or on immunosuppression, to maintain protective immunity against current and hypothetical future variants. SARS-CoV2 variants with enhanced binding to target cells, reduced affinity for vaccine-generated antibodies or reduced immunogenicity resulted in lower antibody levels and more severe disease compared with variants with enhanced viral replication or internalization rates. Conclusion: For patients with cancer and immunosuppressed individuals, SARS-CoV2 variants with enhanced ability to bind to target cells, altered antibody affinity or reduced immunogenicity could lead to breakthrough infections even after a single booster dose. Our mathematical model is useful for anticipating and planning future vaccinations in patients with cancer.

Towards diagnostic and therapeutic avenues against SARS-CoV-2 by combining CryoEM and molecular simulations

Molecular simulations have been instrumental in identifying the structure-function relationships of biomolecules in the atomic level as well as providing a means for structure-based drug discovery, thereby explaining and guiding experimental findings. The increase in computational power, the new physics and machine-learning-based algorithms is significantly driving the boost in the field and gives access to addressing biomolecular phenomena of increasing length and timescales. In this talk I will discuss examples where using state-of-the-art integrative structural biology methods that inject Cryo-EM experimental data into the simulation, we can reveal accurate protein-functional dynamics of the SARS-CoV-2 spike protein in an atomistic level. In this way we can a) reveal virus vulnerabilities by identifying cryptic binding sites exposed during the S protein conformational transition related to the recognition to the host cell and b) provide with the molecular motion and energetics of protein-antibody complexes which enables to suggest mutations that increase the spike-antibody affinity. These predictions are validated in further CryoEM experiments.

The prominent role of a CDR1 somatic hypermutation for convergent IGHV3-53/3-66 antibodies in binding to SARS-CoV-2.

In the fight against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), monoclonal antibodies (mAbs) serve as key strategies for the rapid prevention and treatment of COVID-19. However, analysis to fully characterize functional SARS-CoV-2 mAbs is still needed. In this study, by interrogating 1,695 published or patented mAbs of human origin and validated SARS-CoV-2-binding potency, we found a highly preferential usage of IGHV3-53/3-66 germline genes that was then revealed as a distinct selectivity of SARS-CoV-2-induced humoral immunity across other coronaviruses. Moreover, among the rare somatic hypermutations, we identified a novel mutation signature of F27 to I, L, or V with high frequency, which was located in the CDR1 region of the heavy chain among IGHV3-53/3-66-encoded antibodies. This convergent mutation contributed to improving SARS-CoV-2 binding affinity and may advance our knowledge of the humoral immunity to SARS-CoV-2.

Microfluidic Antibody Affinity Profiling Reveals the Role of Memory Reactivation and Cross-Reactivity in the Defense Against SARS-CoV-2.

Recent efforts in understanding the course and severity of SARS-CoV-2 infections have highlighted both potentially beneficial and detrimental effects of cross-reactive antibodies derived from memory immunity. Specifically, due to a significant degree of sequence similarity between SARS-CoV-2 and other members of the coronavirus family, memory B-cells that emerged from previous infections with endemic human coronaviruses (HCoVs) could be reactivated upon encountering the newly emerged SARS-CoV-2, thus prompting the production of cross-reactive antibodies. Determining the affinity and concentration of these potentially cross-reactive antibodies to the new SARS-CoV-2 antigens is therefore particularly important when assessing both existing immunity against common HCoVs and adverse effects like antibody-dependent enhancement (ADE) in COVID-19. However, these two fundamental parameters cannot easily be disentangled by surface-based assays like enzyme-linked immunosorbent assays (ELISAs), which are routinely used to assess cross-reactivity. Here, we have used microfluidic antibody affinity profiling (MAAP) to quantitatively evaluate the humoral immune response in COVID-19 convalescent patients by determining both antibody affinity and concentration against spike antigens of SARS-CoV-2 directly in nine convalescent COVID-19 patient and three pre-pandemic sera that were seropositive for common HCoVs. All 12 sera contained low concentrations of high-affinity antibodies against spike antigens of HCoV-NL63 and HCoV-HKU1, indicative of past exposure to these pathogens, while the affinity against the SARS-CoV-2 spike protein was lower. These results suggest that cross-reactivity as a consequence of memory reactivation upon an acute SARS-CoV-2 infection may not be a significant factor in generating immunity against SARS-CoV-2.

Evolution of anti-sars-cov-2 igg antibody and igg avidity post pfizer and moderna mrna vaccinations

Introduction: Messenger RNA (mRNA) based vaccines (Pfizer/BioNTech and Moderna) have shown to be highly effective at providing immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Aims: To study the duration of immunity, evolution of IgG antibody levels and IgG avidity (an index of antibody-antigen binding strength), and differences in immune responses between (mRNA) based vaccines. Methods: We performed a prospective study of 72 subjects without a history of SARS-CoV-2 who received both doses of either the Pfizer (n=55) or Moderna (n=17) mRNA vaccine. Anti-spike protein receptor binding domain (RBD) IgG antibody levels and IgG avidity indices were measured longitudinally using a qualitative finger stick MidaSpot™ rapid test at the point-of-care and a quantitative dry blood spot-based pGOLD™ laboratory test over ∼ 4 months post-vaccination. Results: On average, anti-RBD IgG antibody levels peaked at ∼2 weeks after second vaccination dose and declined thereafter, while antibody avidity increased suggesting antibody maturation (Figure). Moderna vaccine recipients exhibited higher side effect severity, higher peak anti-RBD IgG antibody levels and higher avidity up to the 90 days point, when compared to Pfizer vaccine recipients. Nevertheless, the differences in antibody and avidity levels diminished at ∼ 120 days post-vaccination, in line with the similar efficacy of the two vaccines. A qualitative MidaSpot finger stick rapid test detected 100% anti-SARS-CoV-2 RBD positivity for fully vaccinated subjects in both Pfizer and Moderna cohorts and turning negative greater than 90 days post-vaccination for 9% of subjects in the Pfizer cohort whose quantitative anti-IgG fell below the 25-percentile levels. Conclusions: Longitudinal quantitative measurements of anti-RBD antibody and avidity levels provide insight to immune responses and could aid the assessment of immunity and vaccine effectiveness.

Affinity of anti-spike antibodies in SARS-CoV-2 patient plasma and its effect on COVID-19 antibody assays.

BACKGROUND: Measuring anti-spike protein antibodies in human plasma or serum is commonly used to determine prior exposure to SARS-CoV-2 infection and to assess the anti-viral protection capacity. According to the mass-action law, a lesser concentration of tightly binding antibody can produce the same quantity of antibody-antigen complexes as higher concentrations of lower affinity antibody. Thus, measurements of antibody levels reflect both affinity and concentration. These two fundamental parameters cannot be disentangled in clinical immunoassays, and so produce a bias which depends on the assay format. METHODS: To determine the apparent affinity of anti-spike protein antibodies, a small number of antigen-coated magnetic microparticles were imaged by fluorescence microscopy after probing antigen-antibody equilibria directly in patient plasma. Direct and indirect anti-SARS-CoV-2 immunoassays were used to measure antibody levels in the blood of infected and immunised individuals. FINDINGS: We observed affinity maturation of antibodies in convalescent and vaccinated individuals, showing that higher affinities are achieved much faster by vaccination. We demonstrate that direct and indirect immunoassays for measuring anti-spike protein antibodies depend differently on antibody affinity which, in turn, affects accurate interpretation of the results. INTERPRETATION: Direct immunoassays show substantial antibody affinity dependence. This makes them useful for identifying past SARS-CoV-2 exposure. Indirect immunoassays provide more accurate quantifications of anti-viral antibody levels. FUNDING: The authors are all full-time employees of Abbott Laboratories. Abbott Laboratories provided all operating funds. No external funding sources were used in this study.