Search Results (1,445)

Background: Monoclonal antibodies (mAbs) initially played a major role in outpatient COVID-19 management by providing rapid passive immunity and reducing progression to severe disease. However, continuous SARS-CoV-2 evolution progressively compromised the effectiveness of several anti-spike products. This narrative review summarizes the trajectory of COVID-19 mAbs across three phases: early clinical efficacy, loss of efficacy due to immune escape, and future directions. Methods: We conducted a narrative review focusing on mechanisms of action, pivotal clinical trials, and real-world effectiveness of neutralizing anti-spike mAbs and host-directed immunomodulatory mAbs. Emphasis was placed on the impact of variants—especially Omicron—on susceptibility and clinical use, as well as on emerging next-generation platforms. Results: First-generation neutralizing mAbs substantially reduced the hospitalization rates during the Alpha and Delta waves, while immunomodulatory mAbs became standard options for the hyperinflammatory phase in hospitalized patients. With the emergence of Omicron and its sub-lineages, extensive immune escape led to marked reductions in neutralization for many earlier anti-spike agents and consequent restrictions in use. Later-generation approaches targeting more conserved epitopes provided temporary solutions but were also challenged by ongoing antigenic drift. Host-directed immunomodulators retained clinical relevance because their mechanism is independent of viral spike mutations. Conclusions: The clinical role of monoclonal antibodies in COVID-19 has been dynamic and increasingly constrained by viral evolution. Future strategies should prioritize broadly neutralizing antibodies targeting conserved epitopes, innovative delivery platforms, and integration with real-time surveillance to preserve clinical utility in the endemic phase and improve preparedness for future outbreaks. Full article

Background: Although prolonged inflammatory symptoms are an infrequent and problematic adverse effect of vaccination that can occur in some people, the transient activation of acute phase reactants (APRs) is expected with adjuvanted vaccines and helps to potentiate immune responses. Methods: This experiment examined the association between vaccine reactogenicity and immunogenicity in monkeys immunized with an adjuvanted recombinant protein including a receptor binding domain–human IgG1-Fc fusion protein (RBD-Fc) sequenced from the ancestral Wuhan strain of SARS-CoV-2. The acute inflammatory reaction to immunization was assessed by determining the decline in serum iron levels at 24 h and the increase in the neutrophil-to-lymphocyte ratio (NLR) as the adherent neutrophil pool trafficked into circulation. Results: Robust primary and secondary antibody responses were elicited. Larger decreases in serum iron and higher NLRs were associated with a stronger inhibition of RBD binding with angiotensin-converting enzyme (ACE2) when five early viral variants of SARS-CoV-2 were tested, including Wuhan, Alpha, Beta, Gamma and Delta. Inhibition of ACE2-RBD binding was less evident when the Omicron variant was tested. Individual variation in the APR was also predictive of the persistence of cell-mediated immunity based on the number of interferon-expressing mononuclear cells activated by viral antigen in ELISpot assays. Conclusions: Rapid antibody responses to primary immunization and large secondary responses to booster immunizations were elicited by this adjuvanted recombinant RBD-Fc vaccine, and our analysis affirmed the view that a transient APR can enhance antibody binding with antigen proteins. Full article

Background: SARS-CoV-2 reinfections increased substantially after the emergence of Omicron variants. Methods: We conducted a cross-sectional study of 2095 individuals with prior Omicron BA.2 infection in Shanghai, China, during the early post-zero-COVID period. Data on demographics, infection history, and lifestyle factors were collected via questionnaire, and blood samples were obtained for ancestral RBD-blocking antibody measurement. Results: Meeting WHO physical activity recommendations (≥600 MET-min/week) was associated with lower reinfection odds (OR = 0.59, 95% CI: 0.46–0.74, p < 0.001). The overall median ancestral RBD-blocking antibody level was 263.93 U/mL (IQR: 36.41–331.87). Older age was associated with lower ancestral RBD-blocking antibody levels (β = –0.0038 per year, 95% bootstrap CI: –0.0057 to –0.0019, p < 0.001). All vaccinated groups had significantly higher ancestral RBD-blocking antibody levels than unvaccinated individuals: partially vaccinated (β = 0.4440, 95% CI: 0.1569 to 0.6830, p < 0.001), fully vaccinated (β = 0.8516, 95% CI: 0.7464 to 0.9595, p < 0.001), homologous booster (β = 1.0297, 95% CI: 0.9408 to 1.1223, p < 0.001), and heterologous booster (β = 1.0838, 95% CI: 0.9387 to 1.2226, p < 0.001). Time since last immune event was inversely associated with ancestral RBD-blocking antibody levels (β = –0.0232 per month, 95% CI: –0.0385 to –0.0077, p = 0.0031). Conclusions: In this cross-sectional study, meeting WHO physical activity recommendations was associated with 41% lower odds of SARS-CoV-2 reinfection, although reverse causality cannot be ruled out. All vaccinated groups had higher ancestral RBD-blocking antibody levels than unvaccinated individuals. Older age and longer time since last immune event were associated with lower ancestral RBD-blocking antibody levels. These associations need confirmation in prospective, well-powered studies. Full article

This study explored the use of bubble-type settings to control COVID-19 transmissibility during microscale production of emulsified sausage products. Using AnyLogic 8.7.6 and the Wells–Riley model, the effects of virus variants (Wuhan, Delta, Omicron) and screeners (masks, ventilation) on the probability of infection (POI) were simulated. Results showed that virus variants, screeners, and their interactions significantly affected the POI. Implementing control measures—such as efficient masks and increased ventilation—within bubble-type settings can effectively reduce COVID-19 infection risks during microscale sausage production, demonstrating the model’s potential in evaluating preventive measures for small-scale food manufacturing environments. Full article

We present a robust, data-efficient framework for early outbreak assessment using multiscale analysis and Computational Singular Perturbation (CSP). This framework overcomes the shortcomings of the standard compartmental epidemiological models, which often struggle with parameter identifiability during the early stages of a pandemic, limiting their predictive utility considerably when data is sparse. Rather than relying on curve-fitting population profiles, which are sensitive to uncertainty, our approach isolates the dominant “explosive time scale that characterizes the outbreak’s intensity and duration. Using a calibrated SEIRD model, CSP allows for the identification of the paths that drive the process during the outbreak phase and the critical transition from accelerating to decelerating growth, which serves as a reliable precursor to the epidemic peak. This framework is assessed against the 4th, 5th, and 6th waves of the COVID-19 pandemic in Greece during 2021, covering periods dominated by the Delta and Omicron variants. Using only early-stage data from short calibration windows, CSP diagnostic tools revealed distinct dynamical drivers for each wave; e.g., a transition from the 4th wave that was driven by transmission intensity (Delta variant dominance) to the 6th wave that was driven by rapid exposure-to-infection turnover and reduced opposition from recovery mechanisms (Omicron variant dominance). Furthermore, it is demonstrated that the timing of the outbreak’s weakening can be accurately predicted, demonstrating robustness with results obtained from longer observation windows. These findings position multiscale analysis as a powerful, pathogen-agnostic early-warning system, capable of disentangling complex epidemic mechanisms and assessing intervention efficacy in real-time. Full article

Background: Wastewater-based surveillance (WBS) has emerged as a valuable tool for population-level monitoring of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmission, yet the interplay between sampling strategies and disease prevalence in shaping detection performance remains ambiguous. We investigated how grab and composite sampling influence SARS-CoV-2 ribonucleic acid (RNA) detection dynamics and predictive lag times across high- and low-prevalence communities in Selangor, Malaysia. Methods: A 28-week longitudinal study was conducted in Selangor, Malaysia, comparing grab and composite wastewater sampling in communities with high and low Coronavirus disease 2019 (COVID-19) prevalence. SARS-CoV-2 RNA in 348 samples was quantified using digital Reverse Transcription Polymerase Chain Reaction (RT-dPCR), and viral lineages were characterized by Nanopore sequencing. Detection sensitivity and lead times relative to reported cases were evaluated. Results: In low-prevalence settings, grab sampling showed higher detection sensitivity than composite sampling (92.0% vs. 70.0%), whereas both methods achieved similarly high detection in high-prevalence areas (>97.0%). Lag-time analysis indicated that grab sampling in high-prevalence settings was significantly associated with case trends at potential two-week lead (p = 0.024), while composite sampling in low-prevalence settings showed the strongest association at a potential one-week lead (p = 0.0022). Overall, lag structures varied by both sampling strategy and prevalence context. Both sampling approaches captured the replacement of Omicron sublineages (XBB.1.5, XBB.1.9.1, XBB.1.16) and identified additional circulating variants, including EG.5, that were not captured in the available clinical sequencing dataset during the same period. Conclusions: These findings reveal that local transmission intensity is associated with the utility of different sampling designs. Context-specific optimization of WBS sampling strategies enhances sensitivity, reduces detection lag, and strengthens early warning and genomic-tracking capacity in public health surveillance frameworks. Full article

Mucosal immunity, including antibodies like immunoglobulin A (IgA), function as the body’s first line of defense in the respiratory tract, particularly against viruses. An anti-rS protein IgA enzyme-linked immunosorbent assay (ELISA) was developed using the Omicron XBB.1.5 subvariant of SARS-CoV-2 and was validated to demonstrate the suitability of the method for testing saliva from SARS-CoV-2 vaccine clinical trials. This assay successfully met acceptance criteria for inter-/intra-assay precision, specificity, selectivity, linearity, lower/upper limits of quantitation, and assay robustness. The IgA in saliva was stable for up to 7 freeze/thaw cycles, for up to 48 h at 24 °C, up to 7 days at 4 °C, up to 3 weeks at −20 °C, and up to 1 year at −80 °C. After validation using Omicron XBB.1.5 rS protein, cross-reactivity was demonstrated with the SARS-CoV-2 variant JN.1. This validated IgA assay can be a valuable tool to assess mucosal IgA levels in SARS-CoV-2 clinical trials. Full article

The surface spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key target for the development of Coronavirus Disease 2019 (COVID-19) vaccines. Nevertheless, the mutations in the S protein, particularly in its receptor-binding domain region, have resulted in a reduced or complete loss of immunogenicity and/or protective efficacy in early vaccines against the Omicron variant and subvariants. Accordingly, continuous efforts are required to develop effective vaccines against multiple Omicron subvariants to reduce current and future threats. In this study, we designed an mRNA vaccine targeting the S protein of a recent Omicron-XEC subvariant (XEC-S-mRNA) and assessed its immunogenicity, including its broad neutralizing activity, and its protective efficacy against multiple Omicron subvariants. Our results demonstrated that the lipid nanoparticle-formulated mRNA vaccine formed an appropriate particle size with strong stability and successful antigen expression. It elicited durable cellular immune responses and broad neutralizing antibodies against multiple early and recent Omicron subvariants, thereby cross-protecting transgenic mice from challenge with a heterologous Omicron strain (KP.3). Moreover, the vaccine-induced neutralizing antibodies alone were sufficient to prevent Omicron-KP.3 infection. Overall, this study shows promise for further development of the candidate vaccine against current and future Omicron infections. Full article

Understanding how clinical symptoms relate to immune responses during major variant transitions remains important for informing post-pandemic surveillance and vaccination strategies. This study compared symptom patterns and SARS-CoV-2-specific anti-RBD IgM and anti-S1 IgG antibody responses among vaccinated individuals infected during the pre-Omicron and Omicron-dominant periods, representing a key phase in the evolution of SARS-CoV-2 population immunity. A retrospective analysis of 216 confirmed COVID-19 cases was performed by evaluating 11 predefined symptoms together with anti-RBD IgM and anti-S1 IgG levels measured at Day-14 after symptom onset, corresponding to the period when humoral antibody responses are detectable following SARS-CoV-2 infection. Participants with breakthrough infection during the Omicron-dominant period reported fewer symptoms overall compared to the pre-Omicron period, with a median of three versus four symptoms, respectively. Cough was the most common symptom during the Omicron period (82.1%), followed by sore throat (81.4%) and fever (78.6%). In contrast, loss of taste or smell was significantly more frequent in the pre-Omicron period (64.8% versus 22.9%, p < 0.05). IgG levels were significantly higher during the Omicron period than during the pre-Omicron period, increasing by 42.3%, reflecting enhanced antibody responses likely driven by repeated exposure. A consistent association between cough and elevated IgG levels was observed in both periods (p < 0.05), suggesting an association between symptom presentation and the magnitude of the early humoral response. These findings suggest that while clinical symptom profiles evolved across a major SARS-CoV-2 variant transition, certain symptom–antibody relationships remained consistent. Such associations may provide insight into how clinical manifestations relate to immune responses in populations with pre-existing immunity and may support interpretation of symptomatic infection during ongoing SARS-CoV-2 circulation. Full article

The aim of this study was to evaluate the association between baseline clinical and CT characteristics and to identify factors associated with intensive care unit (ICU) admission in hospitalized COVID-19 patients. This retrospective study included 176 adult patients with laboratory-confirmed SARS-CoV-2 infection hospitalized at the COVID Hospital of the Clinical Hospital Center Kosovska Mitrovica during 2021–2022 (Delta and Omicron variants). Patients were divided into two groups according to intensive care unit requirement: those treated in a general inpatient ward (No ICU) and those requiring ICU admission (ICU group). Demographic and clinical characteristics, lifestyle factors, CT findings, CT severity score (CTSS) values, and therapeutic interventions were compared between groups. Of the total cohort, 113 patients (64%) were hospitalized in a general inpatient ward, while 63 (36%) required intensive care unit admission. Independent predictors of ICU admission identified in the multivariate logistic regression analysis were obesity (B = 2.96, p < 0.001), dyspnea (B = 1.51, p = 0.041), higher CT severity score (B = 0.68, p < 0.001), and lower glucose levels (B = −0.27, p = 0.014). Furthermore, for each one-point increase in the CTSS, the odds of ICU admission nearly doubled (OR = 1.97). Total CT score values above the cut-off point (15.0) demonstrated significant reliability in discriminating the need for ICU transfer in patients with COVID-19. These findings suggest that combined clinical and radiological assessment at hospital admission may facilitate early identification of patients at high risk of requiring ICU care, with the CT severity score representing the strongest radiological predictor. Full article

The continued evolution of SARS-CoV-2 has enabled an escape from most monoclonal antibodies, yet a subset of broadly neutralizing antibodies targeting three newly identified super-conserved RBD epitopes—SCORE-A, SCORE-B, and SCORE-C—retains remarkable activity against even the most recent JN.1-derived sublineages. Here, we employed an integrated computational framework combining conformational dynamics, mutational scanning, MM-GBSA binding energetics, and frustration profiling to dissect the molecular mechanisms by which XGI antibodies achieve broad neutralization and resistance to immune escape. Structural analysis revealed that all three SCORE epitopes share a common architecture: a highly conserved, minimally frustrated core that provides stable anchoring, flanked by peripheral regions that accommodate antibody-specific variations. Conformational dynamics showed that SCORE-A antibodies (XGI-183) rigidify the lateral epitope while leaving the RBM partially mobile; SCORE-B antibodies (XGI-198, XGI-203) clamp the RBM apex, directly blocking ACE2; and SCORE-C antibodies (XGI-171) allosterically loosen the RBM loop, impairing receptor engagement indirectly. Mutational scanning identified a hierarchical hotspot organization where primary hotspots (e.g., K356, T500, Y380, T385) are evolutionarily constrained and minimally frustrated, while secondary hotspots (e.g., V503, Y508, S383) are neutrally frustrated and represent the principal sites of immune-driven mutations. MM-GBSA decomposition revealed that van der Waals-driven hydrophobic packing dominates binding, with electrostatic interactions providing auxiliary stabilization. Critically, frustration analysis demonstrated that immune escape hotspots reside precisely in zones of neutral frustration—“energetic playgrounds” that permit mutational exploration without destabilizing the RBD—while minimally frustrated cores are evolutionarily locked. The comparative analysis of conformational versus mutational frustration distributions revealed a unifying principle: aligned neutral frustration yields permissive, escape-prone interfaces; decoupling enables the targeting of constrained cores; and the convergence of minimal frustration in both distributions creates invulnerable interfaces. These findings establish that broad neutralization arises not from ultra-high-affinity anchors but from strategic energy distribution across rigid, evolutionarily informed interfaces, providing a roadmap for designing next-generation therapeutics that target the invulnerable cores of viral surface proteins. Full article

The evolution and spatial dissemination of SARS-CoV-2 Omicron subvariants have been characterized by rapid lineage replacement and complex transmission dynamics influenced by regional connectivity. This study presents a comprehensive discrete phylogeographic analysis of 90,136 SARS-CoV-2 sequences collected in Poland from 2022 to 2024 to reconstruct the dispersal dynamics of major Omicron lineages, including BA.1, BA.2, BA.5, CH.1, XBB.1, and JN.1. Utilizing Bayesian statistical frameworks, we identified significant viral transitions between the 16 Polish voivodeships and established variant-specific dominance windows ranging from 2 to 4 months. Our findings reveal a highly dynamic epidemic landscape with shifting regional epicenters. The initial BA.1 wave was primarily driven by the Mazovian voivodeship, accounting for 36.1% of outward migration events. This pattern shifted dramatically with the rise in BA.2, which was centered in the industrial Silesian region in the south-west, a densely populated area with strong economic ties to neighboring countries, potentially reflecting a different introduction or transmission dynamic. Furthermore, the epidemic landscape continued to reconfigure during the BA.5 wave, marked by the emergence of new transmission hubs in eastern border regions such as Lublin. Subsequent lineages exhibited distinct geographic signatures: BA.5 spread broadly along the Baltic-central corridor, CH.1 was centered in the north-east, XBB.1 re-emerged in the west-central region of Greater Poland, and JN.1 was driven overwhelmingly by Lesser Poland. These transitions highlight that regional transmission hubs are transient and influenced by local factors such as population density, cross-border mobility, and socio-economic connectivity. This study underscores the critical value of dense genomic surveillance in identifying evolving dispersal routes to inform adaptive, region-specific public health interventions. Full article

Highly mutated Omicron sub-lineages JN.1 and NB.1.8.1 harbor extensive spike changes, but their impact in preterm infants is poorly documented. We report a preterm male infant with three hospitalizations in seven weeks: severe SARS-CoV-2 ARDS at 40 days of life (DOL 40) requiring ventilation caused by JN.1.16, HCoV-OC43 infection at DOL 65, and a mild SARS-CoV-2 reinfection at DOL 87 due to NB.1.8.1, the first detection of this variant in Tunisia. Spike analysis showed a shared JN.1 backbone but distinct N-terminal and receptor-binding domain changes, supporting intra-Omicron reinfection driven by antigenic divergence and immature immunity and underscoring the value of pediatric genomic surveillance, including phylogenetic placement of case genomes within local Omicron diversity. Full article