Search Results (158)

Background/Objectives: Despite the lifting of the COVID-19 public health emergency, SARS-CoV-2 infections continue to be recorded worldwide. The continued prevalence of infection has been attributed to the ability of the virus to evade host immune responses, including neutralizing antibody-derived immunity. The vast majority of antibody escape mutations has been associated with the S1 subunit of the spike protein. The other region of the spike, the S2 subunit, is the most conserved region amongst coronaviruses. We hypothesized that S2-specific antibody levels are modest in vaccinated and SARS-CoV-2-infected patients, resulting in suboptimal neutralization of distant coronaviruses. Methods: Here, we analyzed S1- and S2-specific antibody levels in SARS-CoV-2-infected individuals, including a mixed cohort of those with and without immunosuppression and prior vaccination. Results: We found that S2-specific antibody responses were generally lower than S1-specific antibody responses. Intriguingly, Omicron-S1-specific antibody levels were higher than Wuhan-S1-specific antibody levels despite all vaccinated participants having received Wuhan-spike-based immunogens. This emphasizes the importance of the infecting variant and vaccine immunogen in the production of spike-targeting antibodies and associated hybrid immunity. Although S1-specific antibody levels were generally higher than their S2-specific counterparts, the correlation between neutralization and binding antibody levels was mostly higher in S2- compared with S1-specific responses. Conclusions: We conclude that S2-based immunogens are suitable for the induction of antibody-based immunity against novel SARS-CoV-2 variants but also against more distant coronaviruses, which would support a better protection for the immunocompromised as well as other vulnerable populations. Full article

The molecular basis for the distinct intestinal tropism of infectious bronchitis virus (IBV) strains remains poorly understood. This study identifies the S2 subunit of the spike glycoprotein as the critical determinant conferring duodenal tropism to the IBV CSL strain. Comparative pathogenesis in specific-pathogen-free (SPF) chicks revealed that the CSL strain achieved significantly higher viral titers in the duodenum compared to strains D90, PYG QX1, and XXX QX5. This duodenal replication was associated with severe epithelial inflammation, characterized by upregulation of pro-inflammatory cytokines (IL-6, IL-17A, IL-22, TNF-α, IFN-β, IFN-γ) and disruption of barrier integrity via downregulation of tight junction proteins (Occludin, Claudin-1, ZO-1). Crucially, reverse genetics using the non-enterotropic D90 backbone demonstrated that recombinant viruses carrying the CSL-S2 gene (rD90-ΔS/CSL and rD90-ΔS2/CSL), but not those carrying CSL-S1 (rD90-ΔS1/CSL), replicated efficiently and induced inflammation in the duodenum, phenocopying wild-type CSL. In contrast, renal tropism was independent of the S2 subunit. These findings establish the S2 subunit as both necessary and sufficient for IBV duodenal tropism, uncoupling it from renal pathogenicity. This identifies S2 as a prime molecular target for developing next-generation vaccines against intestinal IBV pathotypes. Full article

Background: Vaccines that stimulate systemic and mucosal immunity to a level required to prevent SARS-CoV-2 infection and transmission are an unmet need. Highly protective hepatitis B and human papillomavirus nanoparticle vaccines highlight the potential of multivalent nanoparticle vaccine platforms to provide enhanced immunity. Here, we report the construction and characterization of self-assembling 60-subunit icosahedral nanoparticle SARS-CoV-2 vaccines using the bacterial enzyme lumazine synthase (LuS). Methods and Results: Nanoparticles displaying prefusion-stabilized SARS-CoV-2 spike ectodomains fused to the surface-exposed amino terminus of LuS were designed using structure-guided approaches. Negative stain-electron microscopy studies of purified nanoparticles were consistent with self assembly into 60-mer nanoparticles displaying 20 spike trimers. After two intramuscular doses, these purified spike-LuS nanoparticles elicited significantly higher SARS-CoV-2 neutralizing activity than spike trimers in vaccinated mice. Furthermore, intramuscular DNA priming and intranasal boosting with a SARS-CoV-2 LuS nanoparticle vaccine stimulated mucosal IgA responses. Conclusion: These data identify LuS nanoparticles as highly immunogenic SARS-CoV-2 vaccine candidates and support the further development of this platform against SARS-CoV-2 and its emerging variants. Full article

(1) Background: The ongoing global health threat posed by SARS-CoV-2 requires reliable and accessible diagnostic tools, especially in resource-limited settings where RT-qPCR may be impractical. This study describes the development and validation of two enzyme-linked immunosorbent assays (ELISA) designed to detect anti-SARS-CoV-2 IgG antibodies employing recombinant S1 and S2 spike protein subunits. (2) Methods: The assays were optimized and validated using serum samples from 354 RT-qPCR-confirmed hospitalized patients and 337 pre-pandemic blood donors. (3) Results: The S1-based ELISA achieved a 52.8% sensitivity and a specificity of 93.5%, with an area under the ROC curve (AUC) of 71.6%. In contrast, the S2-based ELISA demonstrated superior diagnostic performance, with a sensitivity of 63.7%, a specificity of 99.7%, and an AUC of 83.1%. Cross-reactivity analysis using sera from individuals with unrelated infectious diseases confirmed the high specificity of the S2-ELISA. Time-stratified analysis revealed that sensitivity increased with time, peaking between 15 and 21 days post-symptom onset. Compared to commercial serological assays, the S2-ELISA demonstrated comparable or improved performance, particularly in specificity and diagnostic odds ratio. (4) Conclusions: The S2-ELISA offers a robust, highly specific, and operationally simple tool for serological detection of SARS-CoV-2 infection. Its strong diagnostic performance and accessibility make it well-suited for implementation in diverse epidemiological settings, particularly where molecular testing is limited. The development of affordable, validated serological assays such as this is critical for strengthening surveillance, understanding transmission dynamics, and informing public health responses. Full article

Background/Objectives: For viral entry into host cells, the spike (S) protein of coronavirus (CoV) uses its S1 domain to bind to the host receptor and S2 domain to mediate the fusion between virion and cellular membranes. The S1 domain acquired multiple mutations as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolved to give rise to Variant of Concerns (VOCs) but the S2 domain has limited changes. In particular, the stem helix in S2 did not change significantly and it is fairly well-conserved across multiple beta-CoVs. In this study, we generated a murine mAb 7B2 binding to the stem helix of SARS-CoV-2. Methods: MAb 7B2 was isolated from immunized mouse and its neutralization activity was evaluated using microneutralization, plaque reduction and cell–cell fusion assays. Bio-layer interferometry was used to measure binding affinity and AlphaFold3 was used to model the antibody–antigen interface. Results: MAb 7B2 has lower virus neutralizing and membrane block activities when compared to a previously reported stem helix-binding human mAb S2P6. Alanine scanning and AlphaFold3 modeling reveals that residues K1149 and D1153 in S form a network of polar interactions with the heavy chain of 7B2. Conversely, S2P6 binding to S is not affected by alanine substitution at K1149 and D1153 as indicated by the high ipTM scores in the predicted S2P6-stem helix structure. Conclusions: Our detailed characterization of the mechanism of inhibition of 7B2 reveals its distinctive binding model from S2P6 and yields insights on multiple neutralizing and highly conserved epitopes in the S2 domain which could be key components for pan-CoV vaccine development. Full article

The S1 subunit of the spike protein of avian infectious bronchitis virus (IBV) plays a crucial role in determining its host range and cell and tissue tropism. Following the continuous passage of IBV-EP3 through Vero cells over up to 65 generations, a total of 19 amino acid mutations accumulated in the S1 region of IBV-P65. To investigate the impact of these mutations on the adaptability of IBV to Vero cells, six recombinant viruses carrying either a subset or all of the identified mutations were constructed and obtained via a reverse genetics system. Analyses on the growth characteristics of these recombinant viruses and Western blot detection of the expression levels of their spike proteins indicated that the IBV mutant obtained by replacing the amino acid sequence from positions 179 to 323 in the S1 region of IBV-P65 with the corresponding segment from IBV-EP3 S1 significantly impaired viral growth and exhibited a lower replication efficiency in Vero cells, suggesting that five amino acid substitutions (T181I, I246T, F267C, T273I, Q296K) within this region could enhance the adaptation of IBV to Vero cells. Full article

Nanobodies, or single-domain antibodies (V_HHs) from camelid heavy-chain-only antibodies, offer significant advantages in therapeutic and diagnostic applications due to their small size and ability to bind cryptic protein epitopes inaccessible to conventional antibodies. In this study, we examined nanobodies specific to regions of the SARS-CoV-2 spike glycoprotein, including the receptor-binding domain (RBD), N-terminal domain (NTD), and subunit 2 (S2). Using flow virometry, a high-throughput technique for viral quantification, we achieved the efficient detection of pseudotyped viruses expressing the spike glycoprotein. RBD-targeting nanobodies showed the most effective staining, followed by NTD-targeting ones, while S2-specific nanobodies exhibited limited resolution. The simple genetic structure of nanobodies enables the creation of multimeric formats, improving binding specificity and avidity. Bivalent V_HH-Fc constructs (V_HHs fused to the Fc region of human IgG) outperformed monovalent formats in resolving viral particles from background noise. However, S2-specific monovalent V_HHs demonstrated improved staining efficiency, suggesting their smaller size better accesses restricted antigenic sites. Furthermore, direct staining of cell supernatants was possible without virus purification. This versatile nanobody platform, initially developed for antiviral therapy against SARS-CoV-2, can be readily adapted for flow virometry applications and other diagnostic assays. Full article

This study explores the role of intrinsically disordered regions (IDRs) in the SARS-CoV-2 proteome and their potential as targets for small-molecule drug discovery. Experimentally validated intrinsic disordered regions from the literature were utilized to assess the prediction of intrinsic disorder across a selection of SARS-CoV-2 proteins. The disorder propensities of proteins using four deep learning-based disorder prediction models: ADOPT, PONDR^®VLXT, PONDR^®VSL2, and flDPnn, were analyzed. ADOPT, VSL2, and VLXT identified a flexible linker (129–147), while VSL2 and VLXT predicted disorder in the Cu(II) binding region (163–167) of NSP1. ADOPT did not predict disordered regions in NSP11; however, VSL2 and VLXT identified disorder in the experimentally validated regions. The IDR in ORF3a is crucial for protein localization and immune modulation, affecting inflammatory pathways. VSL2 predicted significant disorder in the N-terminal domain (18–23), which aligns with experimental data (1–41), overlapping with the TRAF-binding motif, while ADOPT indicated high disorder in the C-terminal domain (255–275), consistent with VSL2 and flDPnn. All tools identified disorder in the N-terminal (1–68), central linker (181–248), and C-terminal (370–419) regions of the nucleocapsid (N) protein, suggesting flexibility and accuracy. The S2 subunit of the spike protein displayed more predicted disorder than the S1 subunit across ADOPT, VSL2, and flDPnn. These IDRs are essential for viral functions, like protein localization, immune modulation, receptor binding, and membrane fusion. This study highlights the importance of IDR in modulating key inflammatory pathways, suggesting that they could serve as promising targets for small-molecule drug development to combat COVID-19. Full article

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging zoonotic pathogen with different pathogenesis in humans and camels. The mechanisms behind the higher tolerance of camels to MERS-CoV infection are still unknown. Monocytes are innate myeloid cells that are able, depending on the local stimulation in their microenvironment, to differentiate into different functional subtypes of macrophages with an impact on the adaptive immune response. Several in vitro protocols have been used to induce the differentiation of monocyte-derived macrophages (MDMs) in human and several veterinary species. Such protocols are not available for camel species. In the present study, monocytes were separated from camel blood and differentiated in vitro in the presence of different stimuli into MDM. Camel MDMs generated in the presence of a combined stimulation of monocytes with LPS and GM-CSF resulted in the development of an M1 macrophages phenotype with increased abundance of the antigen-presentation receptor MHCII molecules and a decreased expression of the scavenger receptor CD163. The expression pattern of the cell markers CD163, CD14, CD172a, CD44, and CD9 on MDM generated in the presence of the MERS-CoV S1 protein revealed similarity with M-CSF-induced MDM, suggesting the potential of the MERS-CoV S1 protein to induce an M2 macrophages phenotype. Similarly to the effect of M-CSF, MERS-CoV-S protein-induced MDMs showed enhanced phagocytosis activity compared to non-polarized or LPS/GM-CSF-polarized MDMs. Collectively, our study represents the first report on the in vitro generation of monocyte-derived macrophages (MDMs) in camels and the characterization of some phenotypic and functional properties of camel MDM under the effect of M1 and M2 polarizing stimuli. In addition, the results suggest a polarizing effect of the MERS-CoV S1 protein on camel MDMs, developing an M2-like phenotype with enhanced phagocytosis activity. To understand the clinical relevance of these in vitro findings on disease pathogenesis and camel immune response toward MERS-CoV infection, further studies are required. Full article

Background/Objectives: Long-term studies on the immune response following multiple doses of SARS-CoV-2 mRNA vaccines remain limited. Methods: Secondary analyses of data from a cohort of non-immunocompromised subjects who received two doses of BNT162b2 (primary vaccination) and a booster with mRNA-1273 nine months later. Antibodies targeting the receptor-binding domain of the S1 subunit of the SARS-CoV-2 spike (anti-RBD) were measured at eight time points during follow-up; the SARS-CoV-2-specific T cell response was measured 16 and 25 months after primary vaccination using an interferon-γ release assay. Results: During the 9-month follow up period after primary vaccination and before the mRNA-1273 booster, anti-RBD were significantly higher at all time points in subjects with documented SARS-CoV-2 infection before the first study time point (previously infected subjects; n = 50) compared to naïve subjects (n = 208; p < 0.05). During a 16-month follow up period following the mRNA-1273 booster, anti-RBD were lower at all time points in previously infected subjects (n = 21) compared to naïve subjects (n = 109), although the differences were non-significant. Breakthrough SARS-CoV-2 infections increased over time in both groups, particularly after the mRNA-1273 booster. Most participants had a persistent SARS-CoV-2 specific T cell response regardless of prior infection. Conclusions: These findings suggest a modulating effect of previous SARS-CoV-2 infection on the humoral immune response to mRNA vaccination, a non-durable hybrid immunity following mRNA vaccination in previously infected subjects, and attenuation of the humoral immune response (immune damping) after repeated exposure to SARS-CoV-2 antigens through mRNA vaccination and/or infection. Full article

Background. The pathogenic coronaviruses (CoVs) MERS-CoV and SARS-CoV-2, which are responsible for the MERS outbreak and the COVID-19 pandemic, respectively, continue to infect humans, with significant adverse outcomes. There is a continuing need to develop mucosal vaccines against these respiratory viral pathogens to prevent entry and replication at mucosal sites. The receptor-binding domain (RBD) of the CoV spike (S) protein is a critical vaccine target, and glycan masking is a unique approach for designing subunit vaccines with improved neutralizing activity. Methods. We evaluated the efficacy of mucosal immunity, broad neutralizing activity, and cross-protection afforded by a combined glycosylated mucosal subunit vaccine encoding the RBDs of the original SARS-CoV-2 strain (SARS2-WT-RBD), the Omicron-XBB.1.5 variant (SARS2-Omi-RBD), and MERS-CoV (MERS-RBD). Results. Intranasal administration of the three-RBD protein cocktail induced effective, durable IgA and systemic IgG antibodies specific for the S protein of these CoVs, thereby neutralizing infection by pseudotyped SARS-CoV-2-WT, Omicron-XBB.1.5, and MERS-CoV. The mucosal vaccine cocktail protected immunized mice from challenge with SARS-CoV-2 Omicron-XBB.1.5 and MERS-CoV, leading to a significant reduction in the viral titers in the lungs. By contrast, the individual glycosylated RBD proteins only induced such immune responses and neutralizing antibodies against either SARS-CoV-2 or MERS-CoV, protecting against subsequent challenge with either SARS-CoV-2 or MERS-CoV; they did not provide simultaneous protection against both CoVs. Conclusions. This study describes a unique strategy for designing efficacious mucosal subunit vaccines that induce durable mucosal immunity, cross-neutralizing activity, and cross-protection against SARS-CoV-2 and MERS-CoV, highlighting the potential for the design of mucosal vaccines against other pathogens. Full article

Porcine epidemic diarrhea virus (PEDV) is a major pathogen that causes serious economic losses to the swine industry. To aid PEDV clinical diagnosis and vaccine development, sensitive and precise serological methods are demanded for rapid detection of (neutralizing) antibodies. Aiming for the development of a novel virus-free hemagglutination inhibition (HI) assay, the N-terminal region of the PEDV S1 subunit, encompassing the sialic acid-binding motif, was first expressed as an Fc-fusion protein with a C-terminal Spy Tag (S1^0A-Spy). The S1^0A-Spy protein was then presented on SpyCatcher-mi3 nanoparticles, forming virus-like particles designated S1^0A-NPs. Electron microscopy and dynamic light scattering analysis confirmed its topology, and the hemagglutination assay showed that S1^0A-NPs can efficiently agglutinate red blood cells. The HI assay based on S1^0A-NPs was then validated with PEDV-positive and -negative samples. The results showed that the HI assay had high specificity for the detection of PEDV antibodies. Next, a total of 253 clinical serum samples were subjected to the HI testing along with virus neutralization (VN) assay. The area under the receiver operating characteristic curve with VN was 0.959, and the kappa value was 0.759. Statistical analysis of the results indicated that the HI titers of the samples tested exhibited high consistency with the VN titers. Taken together, a novel virus-free HI assay based on the multivalent display of a chimeric PEDV spike protein upon self-assembling nanoparticles was established, providing a new approach for PEDV serological diagnosis. Full article

Fusarium graminearum is recognized as the pathogen responsible for wheat head blight. It produces deoxynivalenol (DON) during infection, which endangers human health. DON biosynthesis occurs within toxisomes in the endoplasmic reticulum (ER). In eukaryotes, the ER membrane protein complex (EMC) is critical for the ER’s normal operation. However, the specific role of the EMC in F. graminearum remains poorly understood. In this study, six EMC subunits (FgEmc1-6) were identified in F. graminearum, and all of them were localized to the toxisomes. Our results demonstrate that the EMC is indispensable for vegetative growth and asexual and sexual reproduction, which are the fundamental life processes of F. graminearum. Importantly, EMC deletion led to reduced virulence in wheat spikes and petioles. Further investigation revealed that in ΔFgemc1-6, the expression of trichothecene (TRI) genes is decreased, the biosynthesis of lipid droplets (LDs) is diminished, toxisome formation is impaired, and DON production is reduced. Additionally, defects in the formation of the infection cushion were observed in ΔFgemc1-6. In conclusion, the EMC is involved in regulating growth and virulence in F. graminearum. This study enhances our understanding of the EMC functions in F. graminearum and offers valuable insights into potential targets for managing wheat head blight. Full article

Increasing nitrogen and planting density can enhance crop yield, but it can reduce lodging resistance due to decreased lignin content. There is an urgent need to find feasible measures to balance these conflicting factors. We conducted a two-year field experiment in Tai’an, Shandong Province, China, evaluated SN23 (lodging resistant) and SN16 (lodging sensitive), under three nitrogen applications (120 kg/ha, N1; 240 kg/ha, N2; 360 kg/ha, N3) and four planting densities (75 plants/m², D1; 225 plants/m², D2; 375 plants/m², D3; 525 plants/m², D4), with N2D2 as the control, and measured lodging resistance related indexes and yield. N2D3 (SN23) increased internode length by 0.40 cm, reduced fresh weight by 0.09 g, resulting in a bending moment reduction of 0.39 g/cm. Lignin, cellulose, and hemicellulose decreased by 18.27, 16.48, and 16.22 mg/g DW, while S and G lignin subunits decreased by 118.09 and 127.34 μg/g DW, and H subunit increased by 23.59 μg/g DW. Eventually, the breaking strength was reduced by 1.74 g/cm resulting in a reduction of 0.09 in the lodging resistance index. The yield reached 10.17 t/ha due to an increase in spike number by 100.33 plants/m², achieving an optimal balance between yield and lodging resistance in this experiment. This study provides a viable solution for balancing lodging resistance and yield in winter wheat. Full article

Background: This study addresses a particular aspect of the biological behavior of the Spike subunit S1 of SARS-CoV-2. Researchers observed S1 acting freely in the human organism during and after COVID-19 and vaccination. One of its properties is that it interacts one-to-one with human proteins. S1 interacts with 12 specific human proteins in the liver. Methods: We used these proteins as seeds to extract their functional relationships from the human proteome through enrichment. The interactome representing the set of metabolic activities in which they are involved shows several molecular processes (KEGG), including some linked to HBV (hepatitis B) and HCC (hepatocellular carcinoma) with many genes/proteins involved. Reports show that, in some COVID patients, HBV reactivated or progressed to cancer. Results: We analyzed the interactome with several approaches to understand whether the two pathologies have independent progressions or a common progression. All our efforts consistently showed that the molecular processes involving both HBV and HCC are significantly present in all approaches we used, making it difficult to extract any useful information about their fate. Through BioGRID, we extracted experimental data in vivo but derived it from model cell systems. The lack of patient data in STRING results prevents diagnosis or prediction of real disease progression; therefore, we can consider them “aseptic” model data. Conclusion: The interactome tells us that genes involved in HCC and HVB-related pathways have the potential to activate disease processes. We can consider them as a gold standard. It is the comparison with similar molecular interactions found in individual human phenotypes that shows us whether the phenotype favors or hinders their progression. This also suggests how to use these features. These sets of proteins constitute a molecular “toolkit”. In fact, if we compare them with similar molecular sets of the patient, they will provide us with information on the level of the phenotypic state that is driving the disease. The information derived from the composition of an entire group of proteins is broader and more detailed than a single marker. Therefore, these protein compositions can serve as a reference system with which doctors can compare specific cases for personalized molecular medicine diagnoses. Full article