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12 pages, 397 KB  
Article
Humoral Response to the Third Dose of SARS-CoV-2 Vaccine Among Dialysis Patients: A Breakthrough Infection Case–Control Study
by Francesca Colavita, Concetta Castilletti, Giulia Matusali, Silvia Accordini, Salvatore De Masi, Roberto Da Cas, Natasha Gianesini, Giovanni Baglio, Massimo Francalancia, Giuseppe Traversa, Flavia Chiarotti, Silvia Meschi, Elvira Bianco, Mario Salomone, Alfonso Mele, Piergiorgio Messa, Carmine Zoccali, Francesca Menniti Ippolito and the COVIDVaxDia Study Group
Vaccines 2025, 13(9), 935; https://doi.org/10.3390/vaccines13090935 (registering DOI) - 1 Sep 2025
Abstract
Background: COVID-19 vaccination and subsequent booster doses became critical components of public health strategies to control the pandemic and reduce disease severity, especially in fragile individuals. Among these, subjects undergoing dialysis represent one of the highly vulnerable populations. Methods: We conducted a multicenter [...] Read more.
Background: COVID-19 vaccination and subsequent booster doses became critical components of public health strategies to control the pandemic and reduce disease severity, especially in fragile individuals. Among these, subjects undergoing dialysis represent one of the highly vulnerable populations. Methods: We conducted a multicenter case–control study among dialysis patients between March 2021 and May 2022 (study population n = 3264). We evaluated anti-S/RBD-IgG and anti-SARS-CoV-2 neutralizing antibodies before (T3) and after (T4) the third dose in individuals with a COVID-19 diagnosis after the third dose (cases) and in those who did not report infection (controls). Results: The study included 187 cases and 150 controls. Serological analysis showed a significant increase (p < 0.001) in anti-SARS-CoV-2 antibody levels after the third vaccine dose (from T3 to T4) in both groups. At T3, with the same number of days between the second dose and T3, the antibody levels detected were significantly lower in cases as compared to controls. At T4, we observed similar antibody titers in the two groups. Notably, the mean difference in time from the third dose to T4 was significantly greater in controls (73.0 days vs. 36.7, p < 0.001), suggesting a reduced antibody waning in controls. Accordingly, multivariate analysis showed that the risk of infection was considerably reduced by the pre-third-dose antibody levels. Conclusions: This study reinforces the critical role of the humoral response in preventing infections in the vulnerable population of dialysis patients. Regular monitoring of antibody levels and timely administration of booster doses are essential to optimize protection in this group. Full article
(This article belongs to the Section COVID-19 Vaccines and Vaccination)
14 pages, 1644 KB  
Article
Exploring TREC and KREC Levels in Nursing Home Residents and Staff and Their Association with SARS-CoV-2 Antibody Response After Vaccination
by Eline Meyers, Natalja Van Biesen, Liselore De Rop, Tine De Burghgraeve, Marina Digregorio, Laëtitia Buret, Samuel Coenen, Beatrice Scholtes, Jan Y. Verbakel, Stefan Heytens and Piet Cools
Vaccines 2025, 13(8), 874; https://doi.org/10.3390/vaccines13080874 - 19 Aug 2025
Viewed by 483
Abstract
Background: T-cell receptor excision circles (TRECs) and kappa-deleting recombination excision circles (KRECs) are markers of recent thymic and bone marrow output, respectively. As they have previously been associated with immunosenescence, we aimed to investigate their association with anti-spike SARS-CoV-2 (S1RBD) IgG antibody response [...] Read more.
Background: T-cell receptor excision circles (TRECs) and kappa-deleting recombination excision circles (KRECs) are markers of recent thymic and bone marrow output, respectively. As they have previously been associated with immunosenescence, we aimed to investigate their association with anti-spike SARS-CoV-2 (S1RBD) IgG antibody response after COVID-19 vaccination in nursing home residents (NHRs) and staff (NHS). Methods: We measured TREC and KREC levels and S1RBD IgG antibody levels from dried blood spots (DBSs) using in-house qPCRs and a commercial ELISA kit, respectively, in 200 participants (50 NHRs and 150 NHS). DBSs were collected in April 2021, approximately two months after primary course COVID-19 vaccination (BNT162b2). We assessed the association between TREC and KREC as dependent variables and age, sex, infection-priming status, and post-vaccination S1RBD-specific IgG concentrations as independent variables by simple and multiple linear regression. Results: TREC and KREC levels were significantly lower in NHRs compared with NHS and were negatively correlated with age (p < 0.001). Neither TREC nor KREC levels were significantly associated with SARS-CoV-2 antibody concentrations (p > 0.05). Conclusions: In our study population, TREC and KREC levels decreased with age and were statistically significantly lower in NHRs than NHS. They were, however, not associated with the antibody response after COVID-19 vaccination. Yet, additional research is warranted to explore their potential relevance in cellular immune responses or in combination with other biomarkers of immune function. Full article
(This article belongs to the Special Issue Understanding Immune Responses to COVID-19 Vaccines)
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16 pages, 1623 KB  
Article
Glycosylated SARS-CoV-2 RBD Antigens Expressed in Glycoengineered Yeast Induce Strong Immune Responses Through High Antigen–Alum Adsorption
by Ai Li, Tiantian Wang, Bin Zhang, Xuchen Hou, Peng Sun, Hao Wang, Huifang Xu, Min Tan, Xin Gong, Jun Wu and Bo Liu
Biomolecules 2025, 15(8), 1172; https://doi.org/10.3390/biom15081172 - 15 Aug 2025
Viewed by 356
Abstract
Glycosylation plays a pivotal role in regulating the functions and immunogenicity of antigens. Targeting the receptor-binding domain (RBD) of the spike protein (S protein) of SARS-CoV-2, we examined the impact of different glycoforms on RBD antigen immunogenicity and the underlying mechanisms. IgG-specific antibody [...] Read more.
Glycosylation plays a pivotal role in regulating the functions and immunogenicity of antigens. Targeting the receptor-binding domain (RBD) of the spike protein (S protein) of SARS-CoV-2, we examined the impact of different glycoforms on RBD antigen immunogenicity and the underlying mechanisms. IgG-specific antibody titers and pseudovirus neutralization were compared in mice immunized with RBD antigens bearing different glycoforms, which were prepared using glycoengineering-capable Pichia pastoris and mammalian cell expression systems with distinct glycosylation pathways. The glycosylation impacted the surface charges of the RBD antigen, and influenced its adsorption onto alum. This may further lead to variations in the antigen’s immunogenicity. The high-mannose variant of the RBD antigen (H-MAN/RBD) expressed in wild-type Pichia pastoris induced significantly higher IgG-specific antibody titers and pseudovirus neutralization activity compared with the complex RBD variant (Complex/RBD) expressed in mammalian cells (293F) or glycoengineering-capable Pichia pastoris. The rate of H-MAN/RBD adsorption onto aluminum hydroxide (alum) adjuvant was significantly higher than that of Complex/RBD. It was assumed that H-MAN/RBD might carry more negative charges because of its phosphomannose-modified surfaces, leading to a higher rate of adsorption onto the positively charged alum and enhancing the immune response. To assess the impact of phosphomannose modification on antigen immunogenicity, a yeast strain was engineered to prepare a low-mannose RBD antigen (L-MAN/RBD); additionally, a yeast strain was constructed to generate a low-phosphomannose-modified RBD antigen (L-MAN-P/RBD). In conclusion, phosphomannose modification substantially enhanced the immunogenicity of RBD by altering the surface charges of the RBD antigen and facilitating its adsorption onto alum. These findings offer novel insights and strategies for vaccine design and immunotherapeutic approaches. Full article
(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
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16 pages, 875 KB  
Article
Profile of Selected MicroRNAs as Markers of Sex-Specific Anti-S/RBD Response to COVID-19 mRNA Vaccine in Health Care Workers
by Simona Anticoli, Maria Dorrucci, Elisabetta Iessi, Salvatore Zaffina, Rita Carsetti, Nicoletta Vonesch, Paola Tomao and Anna Ruggieri
Int. J. Mol. Sci. 2025, 26(15), 7636; https://doi.org/10.3390/ijms26157636 - 7 Aug 2025
Viewed by 734
Abstract
Sex-based immunological differences significantly influence the outcome of vaccination, yet the molecular mediators underpinning these differences remain largely elusive. MicroRNAs (miRNAs), key post-transcriptional regulators of gene expression, have emerged as critical modulators of innate and adaptive immune responses. In this study, we investigated [...] Read more.
Sex-based immunological differences significantly influence the outcome of vaccination, yet the molecular mediators underpinning these differences remain largely elusive. MicroRNAs (miRNAs), key post-transcriptional regulators of gene expression, have emerged as critical modulators of innate and adaptive immune responses. In this study, we investigated the expression profile of selected circulating miRNAs as potential biomarkers of sex-specific humoral responses to the mRNA COVID-19 vaccine in a cohort of health care workers. Plasma samples were collected longitudinally at a defined time point (average 71 days) post-vaccination and analyzed using RT-qPCR to quantify a panel of immune-relevant miRNAs. Anti-spike (anti-S) IgG titers were measured by chemiluminescent immunoassays. Our results revealed sex-dependent differences in miRNA expression dynamics, with miR-221-3p and miR-148a-3p significantly overexpressed in vaccinated female HCWs and miR-155-5p overexpressed in vaccinated males. MiR-148a-3p showed a significant association with anti-S/RBD (RBD: receptor binding domain) IgG levels in a sex-specific manner. Bioinformatic analysis for miRNA targets indicated distinct regulatory networks and pathways involved in innate and adaptive immune responses, potentially underlying the differential immune activation observed between males and females. These findings support the utility of circulating miRNAs as minimally invasive biomarkers for monitoring and predicting sex-specific vaccine-induced immune responses and provide mechanistic insights that may inform tailored vaccination strategies. Full article
(This article belongs to the Special Issue Molecular Research on Immune Response to Virus Infection and Vaccines)
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19 pages, 977 KB  
Article
Physical-Hydric Properties of a Planosols Under Long-Term Integrated Crop–Livestock–Forest System in the Brazilian Semiarid
by Valter Silva Ferreira, Flávio Pereira de Oliveira, Pedro Luan Ferreira da Silva, Adriana Ferreira Martins, Walter Esfrain Pereira, Djail Santos, Tancredo Augusto Feitosa de Souza, Robson Vinício dos Santos and Milton César Costa Campos
Forests 2025, 16(8), 1261; https://doi.org/10.3390/f16081261 - 2 Aug 2025
Viewed by 330
Abstract
The objective of this study was to evaluate the physical-hydric properties of a Planosol under an Integrated Crop–Livestock–Forest (ICLF) system in the Agreste region of Paraíba, Brazil, after eight years of implementation, and to compare them with areas under a conventional cropping system [...] Read more.
The objective of this study was to evaluate the physical-hydric properties of a Planosol under an Integrated Crop–Livestock–Forest (ICLF) system in the Agreste region of Paraíba, Brazil, after eight years of implementation, and to compare them with areas under a conventional cropping system and secondary native vegetation. The experiment was conducted at the experimental station located in Alagoinha, in the Agreste mesoregion of the State of Paraíba, Brazil. The experimental design adopted was a randomized block design (RBD) with five treatments and four replications (5 × 4 + 2). The treatments consisted of: (1) Gliricidia (Gliricidia sepium (Jacq.) Steud) + Signal grass (Urochloa decumbens) (GL+SG); (2) Sabiá (Mimosa caesalpiniaefolia Benth) + Signal grass (SB+SG); (3) Purple Ipê (Handroanthus avellanedae (Lorentz ex Griseb.) Mattos) + SG (I+SG); (4) annual crop + SG (C+SG); and (5) Signal grass (SG). Two additional treatments were included for statistical comparison: a conventional cropping system (CC) and a secondary native vegetation area (NV), both located near the experimental site. The CC treatment showed the lowest bulk density (1.23 g cm−3) and the lowest degree of compaction (66.3%) among the evaluated treatments, as well as a total porosity (TP) higher than 75% (0.75 m3 m−3). In the soil under the integration system, the lowest bulk density (1.38 g cm−3) and the highest total porosity (0.48 m3 m−3) were observed in the SG treatment at the 0.0–0.10 m depth. High S-index values (>0.035) and a low relative field capacity (RFc < 0.50) and Kθ indicate high structural quality and low soil water storage capacity. It was concluded that the SG, I+SG, SB+SG, and CC treatments presented the highest values of soil bulk and degree of compaction in the layers below 0.10 m. The I+SG and C+SG treatments showed the lowest hydraulic conductivities and macroaggregation. The SG and C+SG treatments had the lowest available water content and available water capacity across the three analyzed soil layers. Full article
(This article belongs to the Special Issue Forest Soil Physical, Chemical, and Biological Properties)
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13 pages, 291 KB  
Article
Assessment of SARS-CoV-2 Infection, Vaccination, and Immunity Status Among a Population of Dentists/Academic Professors in a Clinical Setting: One-Year Findings
by Patricia Manarte-Monteiro, Gabriella Marques, Dina Alves, Mary Duro, Joana Domingues, Sandra Gavinha, Lígia Pereira da Silva and Liliana Teixeira
COVID 2025, 5(8), 120; https://doi.org/10.3390/covid5080120 - 28 Jul 2025
Viewed by 277
Abstract
Background: This study aimed to assess the prevalence of SARS-CoV-2 infection, vaccination, and immune status among a population, both Dentists and University Professors, within a clinical setting at one and at 12 months after COVID-19 vaccination. Methods: A cross-sectional study involving 47 professionals [...] Read more.
Background: This study aimed to assess the prevalence of SARS-CoV-2 infection, vaccination, and immune status among a population, both Dentists and University Professors, within a clinical setting at one and at 12 months after COVID-19 vaccination. Methods: A cross-sectional study involving 47 professionals (aged 27–52) was conducted in the University Fernando Pessoa. Participants completed an online survey on SARS-CoV-2 infection status and vaccination, received and provided plasma samples for serological analysis. The protocol was approved by the UFP-Ethics Committee. Anti-S1-RBD SARS-CoV-2 IgM and IgG antibody titration values (AU/mL) were measured, by enzyme-linked-immunosorbent assay (ELISA), with reactive immunoglobulins (Ig) seropositivity for values ≥1 AU/mL. Results: SARS-CoV-2 infection rate increased from 8.5% in July 2021 to 48.9% in June 2022, with 8.5% experiencing reinfection. Vaccination rate was 91.5% by July 2021 and increased slightly to 93.6% by June 2022; 72.3% of the sample received a third dose. IgG seropositivity increased from 91.5% to 95.7% in June 2022. After one-year, significant associations were found between IgG seropositivity and both participant’s age (p = 0.009; <50 years) and vaccine doses (p = 0.003; 1–3 doses) received. Conclusions: SARS-CoV-2 infection rate, vaccination, and IgG seropositivity rates were high and increased over one year. The age and vaccination status were associated with the immunity status at 12th month follow-up. Findings highlight variability in IgG seroprevalence due to multiple influencing factors, which justifies future studies. Full article
(This article belongs to the Section COVID Clinical Manifestations and Management)
19 pages, 4424 KB  
Article
Humoral and Memory B Cell Responses Following SARS-CoV-2 Infection and mRNA Vaccination
by Martina Bozhkova, Ralitsa Raycheva, Steliyan Petrov, Dobrina Dudova, Teodora Kalfova, Marianna Murdjeva, Hristo Taskov and Velizar Shivarov
Vaccines 2025, 13(8), 799; https://doi.org/10.3390/vaccines13080799 - 28 Jul 2025
Viewed by 827
Abstract
Background: Understanding the duration and quality of immune memory following SARS-CoV-2 infection and vaccination is critical for informing public health strategies and vaccine development. While waning antibody levels have raised concerns about long-term protection, the persistence of memory B cells (MBCs) and T [...] Read more.
Background: Understanding the duration and quality of immune memory following SARS-CoV-2 infection and vaccination is critical for informing public health strategies and vaccine development. While waning antibody levels have raised concerns about long-term protection, the persistence of memory B cells (MBCs) and T cells plays a vital role in sustaining immunity. Materials and Methods: We conducted a longitudinal prospective study over 12 months, enrolling 285 participants in total, either after natural infection or vaccination with BNT162b2 or mRNA-1273. Peripheral blood samples were collected at four defined time points (baseline, 1–2 months, 6–7 months, and 12–13 months after vaccination or disease onset). Immune responses were assessed through serological assays quantifying anti-RBD IgG and neutralizing antibodies, B-ELISPOT, and multiparameter flow cytometry for S1-specific memory B cells. Results: Both mRNA vaccines induced robust B cell and antibody responses, exceeding those observed after natural infection. Memory B cell frequencies peaked at 6 months and declined by 12 months, but remained above the baseline. The mRNA-1273 vaccine elicited stronger and more durable humoral and memory B-cell-mediated immunity compared to BNT162b2, likely influenced by its higher mRNA dose and longer prime-boost interval. Class-switched memory B cells and S1-specific B cells were significantly expanded in vaccine recipients. Natural infection induced more heterogeneous immune memory. Conclusions: Both mRNA vaccination and natural SARS-CoV-2 infection induce a comparable expansion of memory B cell subsets, reflecting a consistent pattern of humoral immune responses across all studied groups. These findings highlight the importance of vaccination in generating sustained immunological memory and suggest that the vaccine platform and dosage influence the magnitude and durability of immune responses against SARS-CoV-2. Full article
(This article belongs to the Special Issue Evaluating the Immune Response to RNA Vaccine)
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28 pages, 5780 KB  
Article
Multiscale Modeling and Dynamic Mutational Profiling of Binding Energetics and Immune Escape for Class I Antibodies with SARS-CoV-2 Spike Protein: Dissecting Mechanisms of High Resistance to Viral Escape Against Emerging Variants
by Mohammed Alshahrani, Vedant Parikh, Brandon Foley and Gennady Verkhivker
Viruses 2025, 17(8), 1029; https://doi.org/10.3390/v17081029 - 23 Jul 2025
Viewed by 752
Abstract
The rapid evolution of SARS-CoV-2 has underscored the need for a detailed understanding of antibody binding mechanisms to combat immune evasion by emerging variants. In this study, we investigated the interactions between Class I neutralizing antibodies—BD55-1205, BD-604, OMI-42, P5S-1H1, and P5S-2B10—and the receptor-binding [...] Read more.
The rapid evolution of SARS-CoV-2 has underscored the need for a detailed understanding of antibody binding mechanisms to combat immune evasion by emerging variants. In this study, we investigated the interactions between Class I neutralizing antibodies—BD55-1205, BD-604, OMI-42, P5S-1H1, and P5S-2B10—and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein using multiscale modeling, which combined molecular simulations with the ensemble-based mutational scanning of the binding interfaces and binding free energy computations. A central theme emerging from this work is that the unique binding strength and resilience to immune escape of the BD55-1205 antibody are determined by leveraging a broad epitope footprint and distributed hotspot architecture, additionally supported by backbone-mediated specific interactions, which are less sensitive to amino acid substitutions and together enable exceptional tolerance to mutational escape. In contrast, BD-604 and OMI-42 exhibit localized binding modes with strong dependence on side-chain interactions, rendering them particularly vulnerable to escape mutations at K417N, L455M, F456L and A475V. Similarly, P5S-1H1 and P5S-2B10 display intermediate behavior—effective in some contexts but increasingly susceptible to antigenic drift due to narrower epitope coverage and concentrated hotspots. Our computational predictions show strong agreement with experimental deep mutational scanning data, validating the accuracy of the models and reinforcing the value of binding hotspot mapping in predicting antibody vulnerability. This work highlights that neutralization breadth and durability are not solely dictated by epitope location, but also by how binding energy is distributed across the interface. The results provide atomistic insight into mechanisms driving resilience to immune escape for broadly neutralizing antibodies targeting the ACE2 binding interface—which stems from cumulative effects of structural diversity in binding contacts, redundancy in interaction patterns and reduced vulnerability to mutation-prone positions. Full article
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17 pages, 6805 KB  
Article
Ferritin Nanocages Exhibit Unique Structural Dynamics When Displaying Surface Protein
by Monikaben Padariya, Natalia Marek-Trzonkowska and Umesh Kalathiya
Int. J. Mol. Sci. 2025, 26(15), 7047; https://doi.org/10.3390/ijms26157047 - 22 Jul 2025
Viewed by 388
Abstract
Ferritin nanocages with spherical shells carry proteins or antigens that enable their use as highly efficient nanoreactors and nanocarriers. Mimicking the surface Spike (S) receptor-binding domain (RBD) from SARS-CoV-2, ferritin nanocages induce neutralizing antibody production or block viral entry. Herein, by implementing molecular [...] Read more.
Ferritin nanocages with spherical shells carry proteins or antigens that enable their use as highly efficient nanoreactors and nanocarriers. Mimicking the surface Spike (S) receptor-binding domain (RBD) from SARS-CoV-2, ferritin nanocages induce neutralizing antibody production or block viral entry. Herein, by implementing molecular dynamics simulation, we evaluate the efficiency in the interaction pattern (active or alternative sites) of H-ferritin displaying the 24 S RBDs with host-cell-receptor or monoclonal antibodies (mAbs; B38 or VVH-72). Our constructed nanocage targeted the receptor- or antibody-binding interfaces, suggesting that mAbs demonstrate an enhanced binding affinity with the RBD, with key interactions originating from its variable heavy chain. The S RBD interactions with ACE2 and B38 involved the same binding site but led to divergent dynamic responses. In particular, both B38 chains showed that asymmetric fluctuations had a major effect on their engagement with the Spike RBD. Although the receptor increased the binding affinity of VVH-72 for the RBD, the mAb structural orientation on the nanocage remained identical to its conformation when bound to the host receptor. Overall, our findings characterize the essential pharmacophore formed by Spike RBD residues over nanocage molecules, which mediates high-affinity interactions with either binding partner. Importantly, the ferritin-displayed RBD maintained native receptor and antibody binding profiles, positioning it as a promising scaffold for pre-fusion stabilization and protective RBD vaccine design. Full article
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12 pages, 747 KB  
Article
Nuclear Factor Erythroid 2-Related Factor 2 and SARS-CoV-2 Infection Risk in COVID-19-Vaccinated Hospital Nurses
by Stefano Rizza, Luca Coppeta, Gianluigi Ferrazza, Alessandro Nucera, Maria Postorino, Andrea Quatrana, Cristiana Ferrari, Rossella Menghini, Susanna Longo, Andrea Magrini and Massimo Federici
Vaccines 2025, 13(7), 739; https://doi.org/10.3390/vaccines13070739 - 9 Jul 2025
Viewed by 455
Abstract
Background/Objectives: The COVID-19 pandemic has caused sickness and death among many health care workers. However, the apparent resistance of health care workers to SARS-CoV-2 infection despite their high-risk work environment remains unclear. To investigate if inflammation and circadian disruption contribute to resistance [...] Read more.
Background/Objectives: The COVID-19 pandemic has caused sickness and death among many health care workers. However, the apparent resistance of health care workers to SARS-CoV-2 infection despite their high-risk work environment remains unclear. To investigate if inflammation and circadian disruption contribute to resistance or diminished susceptibility to the SARS-CoV-2 virus, we retrospectively evaluated a cohort of volunteer hospital nurses (VHNs). Methods: A total of 246 apparently healthy VHNs (mean age 37.4 ± 5.9 years) who had received the BNT162b2 mRNA vaccine were asked to report their sleep quality, according to the Pittsburgh Sleep Quality Index, and number of SARS-CoV-2 infections during the observational study period (from the end of December 2020 to April 2025). The expression of inflammation-associated mediators and circadian transcription factors in peripheral blood mononuclear cells, as well as sleep quality, were examined. Results: Our findings revealed no anthropometric, biochemical, or inflammation-associated parameters but demonstrated significantly greater levels of NFE2L2, also known as nuclear factor erythroid-derived 2-like 2 (NFR2), gene expression in peripheral blood mononuclear cells among VHNs who had never been infected with SARS-CoV-2 (n = 97) than in VHNs with only one (n = 119) or with two or more (n = 35) prior SARS-CoV-2 infections (p < 0.01). This result was confirmed through one-to-one propensity score matching (p < 0.01). Moreover, NRF2 gene expression was not associated with the number of COVID-19 vaccinations (p = 0.598). Finally, NRF2 gene expression was higher among participants who reported better sleep quality (p < 0.01). Conclusions: Our findings suggest possible interactions among NRF2 gene expression, protection against SARS-CoV-2 infection, and the modulation of COVID-19 vaccination efficacy. Full article
(This article belongs to the Special Issue SARS-CoV-2 Pathogenesis, Vaccines and Therapeutics)
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32 pages, 5019 KB  
Article
Syzygium aromaticum Phytoconstituents Target SARS-CoV-2: Integrating Molecular Docking, Dynamics, Pharmacokinetics, and miR-21 rs1292037 Genotyping
by Mustafa Ahmed Muhmood, Faiza Safi, Mohammed Mukhles Ahmed and Safaa Abed Latef Almeani
Viruses 2025, 17(7), 951; https://doi.org/10.3390/v17070951 - 5 Jul 2025
Viewed by 1850
Abstract
Background and aim: The COVID-19 pandemic, caused by SARS-CoV-2, remains a global health crisis despite vaccination efforts, necessitating novel therapeutic strategies. Natural compounds from Syzygium aromaticum (clove), such as eugenol and β-caryophyllene, exhibit antiviral and anti-inflammatory properties, while host genetic factors, including miR-21 [...] Read more.
Background and aim: The COVID-19 pandemic, caused by SARS-CoV-2, remains a global health crisis despite vaccination efforts, necessitating novel therapeutic strategies. Natural compounds from Syzygium aromaticum (clove), such as eugenol and β-caryophyllene, exhibit antiviral and anti-inflammatory properties, while host genetic factors, including miR-21 rs1292037 polymorphism, may influence disease susceptibility and severity. This study investigates the dual approach of targeting SARS-CoV-2 via Syzygium aromaticum phytoconstituents while assessing the role of miR-21 rs1292037 in COVID-19 pathogenesis. Methods: Firstly, molecular docking and molecular dynamics simulations were employed to assess the binding affinities of eugenol and caryophyllene against seven key SARS-CoV-2 proteins—including Spike-RBD, 3CLpro, and RdRp—using SwissDock (AutoDock Vina) and the Desmond software package, respectively. Secondly, GC-MS was used to characterize the composition of clove extract. Thirdly, pharmacokinetic profiles were predicted using in silico models. Finally, miR-21 rs1292037 genotyping was performed in 100 COVID-19 patients and 100 controls, with cytokine and coagulation markers analyzed. Results: Docking revealed strong binding of eugenol to viral Envelope Protein (−5.267 kcal/mol) and caryophyllene to RdRp (−6.200 kcal/mol). ADMET profiling indicated favorable absorption and low toxicity. Molecular dynamics simulations confirmed stable binding of methyl eugenol and caryophyllene to SARS-CoV-2 proteins, with caryophyllene–7Z4S showing the highest structural stability, highlighting its strong antiviral potential. Genotyping identified the TC genotype as prevalent in patients (52%), correlating with elevated IL-6 and D-dimer levels (p ≤ 0.01), suggesting a hyperinflammatory phenotype. Males exhibited higher ferritin and D-dimer (p < 0.0001), underscoring sex-based disparities. Conclusion: The bioactive constituents of Syzygium aromaticum exhibit strong potential as multi-target antivirals, with molecular simulations highlighting caryophyllene’s particularly stable interaction with the 7Z4S protein. Methyl eugenol also maintained consistent binding across several SARS-CoV-2 targets. Additionally, the miR-21 rs1292037 polymorphism may influence COVID-19 severity through its role in inflammatory regulation. Together, these results support the combined application of phytochemicals and genetic insights in antiviral research, pending further clinical verification. Full article
(This article belongs to the Special Issue Recent Advances in Antiviral Natural Products 2025)
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13 pages, 2026 KB  
Article
Pre-Existing Anti-Inflammatory Immune Conditions Influence Early Antibody Avidity and Isotype Profile Following Comirnaty® Vaccination in Mice
by Mariangeles Castillo, María C. Miraglia, Florencia C. Mansilla, Cecilia P. Randazzo, Leticia V. Bentancor, Teresa Freire and Alejandra V. Capozzo
Vaccines 2025, 13(7), 677; https://doi.org/10.3390/vaccines13070677 - 24 Jun 2025
Viewed by 658
Abstract
Background/Objectives: Vaccine immunogenicity is often suboptimal in vulnerable populations such as the elderly, infants, and individuals in low- and middle-income countries. One contributing factor may be pre-existing immunomodulatory conditions, including helminth infections. This study investigates the impact of Fasciola hepatica (F. hepatica [...] Read more.
Background/Objectives: Vaccine immunogenicity is often suboptimal in vulnerable populations such as the elderly, infants, and individuals in low- and middle-income countries. One contributing factor may be pre-existing immunomodulatory conditions, including helminth infections. This study investigates the impact of Fasciola hepatica (F. hepatica) derived molecules on the early humoral response to the COVID-19 mRNA vaccine Comirnaty® in a mouse model. Methods: BALB/c mice were pretreated with a F. hepatica protein extract (FH) or complete Freund’s adjuvant (CFA) prior to vaccination. Cytokine production and antibody responses were assessed at 0, 14, and 21 days post-vaccination (dpv) through serum analysis and ex vivo splenocyte stimulation with the SARS-CoV-2 receptor-binding domain (RBD) or LPS. Results: At 0 dpv, FH-treated mice showed increased serum IL-10, while CFA treatment induced IL-12. FH- but not CFA-treated splenocytes secreted IL-10 upon RBD or LPS stimulation. At 21 dpv, FH-treated mice lacked IFN-γ production but maintained IL-10 and showed elevated IL-4, consistent with a Th2-skewed profile. Although total anti-RBD IgG levels were similar between groups, FH-treated mice exhibited reduced IgG avidity and a higher IgG1/IgG2 ratio. CFA-treated mice showed delayed avidity maturation. Conclusions: Prior exposure to F. hepatica antigens can modulate the early immune response to Comirnaty®, affecting both cellular activation and antibody quality. This altered response may reflect a reduced early protective capacity of the vaccine, which might need to be considered when designing or evaluating vaccination strategies using mRNA vaccines in helminth-endemic regions. Full article
(This article belongs to the Section Vaccine Advancement, Efficacy and Safety)
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26 pages, 2617 KB  
Article
Humoral and Cellular Immune Responses to SARS-CoV-2 in Participants with Head and Neck Cancer
by Luminita Mărutescu, Alexandru Enea, Nefeli-Maria Antoniadis, Marian Neculae, Diana Antonia Costea, Marcela Popa, Elena Dragu, Elena Codrici, Violeta Ristoiu, Bianca Galateanu, Ariana Hudita, Gratiela Gradisteanu Pircalabioru, Abdelali Filali-Mouhim, Serban Vifor Gabriel Bertesteanu, Veronica Lazăr, Carmen Chifiriuc, Raluca Grigore and Petronela Ancuta
Viruses 2025, 17(6), 848; https://doi.org/10.3390/v17060848 - 13 Jun 2025
Viewed by 1056
Abstract
Background: SARS-CoV-2 immunity is understudied in cancer patients. Here, we monitored natural/vaccine-induced SARS-CoV-2 immunity in patients with head and neck cancer (HNC) stratified as vaccinated (mRNA/adenovirus-based vaccines), convalescent, and hybrid immunity. Methods: Plasma/PBMC samples were collected from 49 patients with HNC and 14 [...] Read more.
Background: SARS-CoV-2 immunity is understudied in cancer patients. Here, we monitored natural/vaccine-induced SARS-CoV-2 immunity in patients with head and neck cancer (HNC) stratified as vaccinated (mRNA/adenovirus-based vaccines), convalescent, and hybrid immunity. Methods: Plasma/PBMC samples were collected from 49 patients with HNC and 14 non-oncologic controls recruited between August 2021 and March 2022. Longitudinal follow-up was performed on 25 HNC patients. Plasma antibodies (Abs) against Spike (S1/S2), receptor-binding domain (RBD), and nucleocapsid (NC) of IgG/IgA isotypes and 25 cytokines/chemokines were quantified using MILLIPLEX® technology. The frequency, phenotype, and isotype of circulating SARS-CoV-2-specific B-cells were studied by flow cytometry using RBD tetramers (Tet++). The proliferation of B-cells and CD4+ and CD8+ T-cells in response to Spike/NC peptides was monitored by a carboxyfluorescein succinimidyl ester (CFSE) assay. Results: Plasma SARS-CoV-2 S1/S2/RBD IgG/IgA Abs were detected in all HNC participants at enrollment median time since immunization (TSI) 117 days at levels similar to controls and were significantly higher in convalescent/hybrid versus vaccinated. NC IgG/IgA Abs were only detected after infection. The frequency of Tet++ B-cells, enriched in the CD27+ memory phenotype and IgG/IgA isotype, positively correlated with plasma levels of RBD IgG/IgA Abs and Spike-specific CD4+ T-cell proliferation, regardless of the immunization status and TSI. Spike/NC-specific B-cell proliferation reached the highest levels in convalescent HNC and was positively correlated with NC IgG Abs, but not with the frequency of Tet++ B-cells. Finally, Tet++ B-cell frequencies remained stable between the two subsequent visits (median TSI: 117 versus 341 days), indicating their ability to persist for a relatively long time. Conclusions: This study monitored SARS-CoV-2 humoral/cellular immunity in an HNC cohort relative to non-oncologic participants and demonstrates that SARS-CoV-2-specific B-cells persist beyond 11 months post-immunization. These findings have implications for the management of HNC in the context of SARS-CoV-2 infection and other viral infections. Full article
(This article belongs to the Section Coronaviruses)
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26 pages, 6162 KB  
Article
Ethnic Comparisons of Spike-Specific CD4+ T Cells, Serological Responses, and Neutralizing Antibody Titers Against SARS-CoV-2 Variants
by Fani Pantouli, Vanessa Silva-Moraes and Ted M. Ross
Vaccines 2025, 13(6), 607; https://doi.org/10.3390/vaccines13060607 - 4 Jun 2025
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Abstract
Background/Objectives: To evaluate how immune responses compare among ethnic groups approximately 2 years after receiving a third dose of COVID-19 vaccine (BNT162b2, mRNA-1273, ChAdOx1or BBIBP-CorV), we tested T cell responses and Spike-specific RBD-antibody titer, and neutralized antibody titer levels utilizing Spectral Flow cytometry, [...] Read more.
Background/Objectives: To evaluate how immune responses compare among ethnic groups approximately 2 years after receiving a third dose of COVID-19 vaccine (BNT162b2, mRNA-1273, ChAdOx1or BBIBP-CorV), we tested T cell responses and Spike-specific RBD-antibody titer, and neutralized antibody titer levels utilizing Spectral Flow cytometry, ELISA, and SARS-CoV-2 pseudotyped-based neutralization assays, respectively. Methods: Forty-four individuals from January–December 2023 were identified within the cohort and were classified into different ethnic backgrounds; Black (N = 13), Asian (N = 14), Caucasian (N = 17). We recognize that the “Asian” group includes diverse subpopulations with distinct genetic and environmental backgrounds, which could not be further stratified due to sample-size limitations. Spike-specific AIM+, CD4+, and CD8+ T cell responses were assessed and evaluated against SARS-CoV-2 variants, including the ancestral Wuhan, Delta, and multiple Omicron subvariants (B1.1529, BA2.86, BA.4/5, and XBB.1). Alongside we tested the RBD-IgG and neutralizing antibody titers against the ancestral Wuhan. Spearman’s correlation analysis was utilized to determine corelative relationships among the AIM+ and CD4+ T cell responses, as well as the RBD-IgG and neutralizing antibody titers. Results: Our results show robust and comparable RBD-IgG and neutralizing antibody titers across all groups, with a significant positive correlation between these two measurements. Significant differences were observed in T-cell activation, with Asian participants exhibiting lower frequencies of Spike-specific CD4+ T cells against SARS-CoV-2 Omicron subvariants and higher frequencies of cytokine-producing CD4+ T cells (TNF-α, IFN-γ, and IL-2) as compared to the Caucasian group. Breakthrough infection status was not fully controlled and may influence these findings. Conclusion: Despite a small sample size and potential confounding by natural infections within our long-time-span sampling, our data suggest persistent cellular and humoral immunity 2 years after vaccination across ethnicities, with notable differences in T cell activation and cytokine profile. These preliminary observations highlight the need for larger, more detailed studies that consider intra-ethnic diversity and hybrid immunity to better understand ethnic differences in COVID-19 vaccine responses. Full article
(This article belongs to the Special Issue 3rd Edition: Safety and Autoimmune Response to SARS-CoV-2 Vaccination)
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24 pages, 5995 KB  
Article
Aptamer Development for SARS-CoV-2 and Omicron Variants Using the Spike Protein Receptor Binding Domain as a Potential Diagnostic Tool and Therapeutic Agent
by Prasanna V. Shekar, Anuj Kumar, Nirmitee Mulgaonkar, Samneet Kashyap, Gourav Choudhir, Sandun Fernando and Sachin Rustgi
Biomolecules 2025, 15(6), 805; https://doi.org/10.3390/biom15060805 - 1 Jun 2025
Viewed by 1838
Abstract
Despite various methods for detecting and treating SARS-CoV-2, affordable and easily applicable solutions are still needed. Aptamers can potentially fill this gap. Here, we establish a workflow to identify aptamers that bind to the spike proteins of SARS-CoV-2, a process applicable to other [...] Read more.
Despite various methods for detecting and treating SARS-CoV-2, affordable and easily applicable solutions are still needed. Aptamers can potentially fill this gap. Here, we establish a workflow to identify aptamers that bind to the spike proteins of SARS-CoV-2, a process applicable to other targets as well. The spike protein is crucial for the virus’s entry into host cells. The aptamer development process for the spike protein’s receptor binding domain (RBD) begins with splitting the SARS-CoV-2’s genome into 40 nucleotide-long sequences, predicting their two-dimensional structure, and sorting based on the free energy. Selected oligomers undergo three-dimensional structure prediction and docking onto the viral spike protein’s RBD. Six RNA oligomers were identified as top candidates based on the RNA docking with the SARS-CoV-2 wild-type (WT) (Wuhan-Hu-1 strain) and Omicron variant BA.1 RBD and molecular dynamics simulations. Three oligomers also demonstrated strong predicted binding affinity with other SARS-CoV-2 variants, including BA.2, XBB.1.5, and EG.5, based on the protein–aptamer docking followed by stability evaluation using the MD simulations. The aptamer with the best fit for the spike protein RBD was later validated using biolayer interferometry. The process has resulted in identifying a single aptamer from a library of 29,000 RNA oligomers, which exhibited affinity in the submicromolar range and the potential to develop into a viral screen or therapeutic. Full article
(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)
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