SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individualsDadonaite, Burrell, Logue
et alJ Virol (2025)
Abstract: The immune response to viral infection is shaped by past exposures to related virus strains, a phenomenon known as imprinting. For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), much of the population has been imprinted by a viral spike from an early strain, either through vaccination or infection during the early stages of the COVID-19 pandemic. As a consequence of this imprinting, infection with more recent SARS-CoV-2 strains primarily boosts cross-reactive antibodies elicited by the imprinting strain. Here we compare the neutralizing antibody specificities of imprinted individuals versus infants infected with a recent strain. Specifically, we use pseudovirus-based deep mutational scanning to measure how spike mutations affect neutralization by the serum antibodies of adults and children imprinted by the original vaccine versus infants with a primary infection by an XBB* variant. While the serum neutralizing activity of the imprinted individuals primarily targets the spike receptor-binding domain (RBD), the serum neutralizing activity of infants infected with only XBB* mostly targets the spike N-terminal domain. In these infants, secondary exposure to the XBB* spike via vaccination shifts more of the neutralizing activity toward the RBD, although the specific RBD sites targeted are different from imprinted adults. The dramatic differences in neutralization specificities among individuals with different exposure histories likely impact SARS-CoV-2 evolution.IMPORTANCEWe show that a person's exposure history to different SARS-CoV-2 strains strongly affects which regions on the viral spike that their neutralizing antibodies target. In particular, infants who have just been infected once with a recent viral strain make neutralizing antibodies that target different regions of the viral spike than adults or children who have been exposed to both older and more recent strains. This person-to-person heterogeneity means that the same viral mutation can have different impacts on the antibody immunity of different people.
Computational electrostatic engineering of nanobodies for enhanced SARS-CoV-2 receptor binding domain recognitionIqbal, Asim, Khan
et alFront Mol Biosci (2025) 12, 1512788
Abstract: This study presents a novel computational approach for engineering nanobodies (Nbs) for improved interaction with receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Using Protein Structure Reliability reports, RBD (7VYR_R) was selected and refined for subsequent Nb-RBD interactions. By leveraging electrostatic complementarity (EC) analysis, we engineered and characterized five Electrostatically Complementary Nbs (ECSb1-ECSb5) based on the CeVICA library's SR6c3 Nb. Through targeted modifications in the complementarity-determining regions (CDR) and framework regions (FR), we optimized electrostatic interactions to improve binding affinity and specificity. The engineered Nbs (ECSb3, ECSb4, and ECSb5) demonstrated high binding specificity for AS3, CA1, and CA2 epitopes. Interestingly, ECSb1 and ECSb2 selectively engaged with AS3 and CA1 instead of AS1 and AS2, respectively, due to a preference for residues that conferred superior binding complementarities. Furthermore, ECSbs significantly outperformed SR6c3 Nb in MM/GBSA results, notably, ECSb4 and ECSb3 exhibited superior binding free energies of -182.58 kcal.mol-1 and -119.07 kcal.mol-1, respectively, compared to SR6c3 (-105.50 kcal.mol-1). ECSbs exhibited significantly higher thermostability (100.4-148.3 kcal·mol⁻1) compared to SR6c3 (62.6 kcal·mol⁻1). Similarly, enhanced electrostatic complementarity was also observed for ECSb4-RBD and ECSb3-RBD (0.305 and 0.390, respectively) relative to SR6c3-RBD (0.233). Surface analyses confirmed optimized electrostatic patches and reduced aggregation propensity in the engineered Nb. This integrated EC and structural engineering approach successfully developed engineered Nbs with enhanced binding specificity, increased thermostability, and reduced aggregation, laying the groundwork for novel therapeutic applications targeting the SARS-CoV-2 spike protein.Copyright © 2025 Iqbal, Asim, Khan, Sultan and Ali.
In-house assays for detecting anti-SARS-CoV-2 antibodies in serum and urine: Correlation with COVID-19 severity from a cohort study in QatarVaikath, Al-Nesf, Majbour
et alJ Infect Public Health (2025) 18 (6), 102744
Abstract: Serological assays targeting antibodies against key viral proteins, including the Spike (S1), Receptor Binding Domain (RBD), and Nucleocapsid, play a critical role in understanding immunity and supporting diagnostic efforts during COVID-19 pandemic, and afterward. This study aimed to develop and validate in-house assays for detecting anti-SARS-CoV-2 antibodies in serum and urine.ELISA-based assay was developed to detect IgG and IgM antibodies against SARS-CoV-2. The assay was examined in serum and urine samples of two different cohort of patients affected by COVID-19 disease with different severity and compared to age and sex matched control group. Neutralizing antibody activity was evaluated using an RBD-ACE2 binding inhibition assay. Additionally, a Sengenics protein microarray platform was employed to assess epitope-specific antibody responses.The in-house ELISA assay reliably detected antibodies in both 163 serum and 64 urine samples compared to 50 serum samples from healthy control, with strong correlations observed between antibody levels in the two biofluids. Neutralizing antibody levels correlated positively with disease severity, highlighting their clinical relevance. The performance of the in-house assays was comparable to commercial kits, and the Sengenics microarray provided detailed insights into antibody profiles, identifying dominant epitopes within the Nucleocapsid core domain and RBD.The developed in-house assay demonstrated robust performance and versatility, offering a cost-effective and scalable alternative to commercial kits. Their ability to detect antibodies in both serum and urine highlighted their potential as non-invasive diagnostic tools. These findings contribute to advancing sero-diagnostic capabilities, improving understanding of immune responses to SARS-CoV-2, and supporting global efforts to monitor and manage COVID-19 effectively.Copyright © 2025. Published by Elsevier Ltd.
Impact of pre-existing immunity on humoral and cellular responses to CoronaVac in SARS-CoV-2 variants: A focus on common human CoronavirusesPinpathomrat, Seeyankem, Sophonmanee
et alAsian Pac J Allergy Immunol (2025)
Abstract: The global COVID-19 pandemic, caused by SARS-CoV-2, has highlighted the importance of understanding immune responses elicited by vaccines.This study evaluated antibody and T cell responses to the inactivated CoronaVac vaccine, as well as the role of pre-existing immunity to common human coronaviruses (HCoVs) in shaping vaccine-induced immunity.We enrolled 64 participants (17 males and 47 females) and measured IgG levels against HCoVs before and after vaccination. T cell responses were analysed by stimulating peripheral blood mononuclear cells (PBMCs) with wild-type, Delta, and Omicron spike peptides.We found pre-existing antibodies against HCoV-229E, HCoV-HKU1, HCoV-NL63, and HCoV-OC43 were present before vaccination. Notably, a positive correlation was observed between pre-existing antibodies to HCoV-229E and HCoV-HKU1 and anti-RBD IgG levels post-vaccination. Pre-existing CD4+ T cell responses were observed for the wild-type strain before vaccination, with a significant reduction in IFN-γ secretion after Delta re-stimulation and partial restoration after Omicron re-stimulation. IL-4 production by CD4+ T cells was significantly reduced upon re-stimulation with Delta and Omicron compared to wild-type. CD8+ T cells again showed a reduction of IL-4 production after Delta re-stimulation compared to the original strain.This work demonstrate that CoronaVac induces robust humoral and cellular immune responses, though variant-specific responses vary. Pre-existing immunity to certain HCoVs may influence vaccine-induced antibody responses, underscoring the importance of monitoring immunity to emerging SARS-CoV-2 variants and informing future vaccine design.
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