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The recent coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has exerted considerable impact on global health. To prepare for rapidly mutating viruses and for the forthcoming pandemic, effective therapies targeting the critical stages of the viral life cycle need to be developed. Viruses are dependent on the interaction between the receptor-binding domain (RBD) of the viral Spike (S) protein (S-RBD) and the angiotensin-converting enzyme 2 (ACE2) receptor to efficiently establish infection and the following replicate. Targeting this interaction provides a promising strategy to inhibit the entry process of the virus, which in turn has both preventive and therapeutic effects. In this study, we developed a robust and straightforward assay based on the Yeast-Two Hybrid system (Y2H) for identifying inhibitors targeting the S-RBD-ACE2 interaction of SARS-CoV-2. Through high-throughput screening, two compounds were identified as potential entry inhibitors. Among them, IMB-1C was superior in terms of pseudovirus entry inhibition and toxicity. It could bind to both ACE2 and S-RBD and induce conformational change in the S-RBD+ACE2 complex. This is the first study to verify the feasibility of utilizing the Y2H system to discover potent SARS-CoV-2 inhibitors targeting the receptor recognition stage. This approach may also be applied in the discovery of other virus receptor recognition inhibitors. [ABSTRACT FROM AUTHOR]

Coronaviruses continue to disrupt health and economic productivity worldwide. Porcine epidemic diarrhea virus (PEDV) is a devastating swine disease and SARS-CoV-2 is the latest coronavirus to infect the human population. Both viruses display a similar spike protein on the surface that is a target of vaccine development. Despite the availability of commercial vaccines for both viruses, there is still a high occurrence of infections and a great need for enhanced efficacy and lower costs. We previously produced the PEDV spike protein (S) using transgenic maize, enabling a low-cost supply of the vaccine candidate. In this study, we (1) test orally delivered PEDV vaccine candidates in pigs to optimize the mucosal immune response; (2) generate the SARS-CoV-2 S1 protein in maize; and (3) perform structural characterization of the S1 protein for PEDV and SARS-CoV-2. We demonstrated high expression levels in maize of the S1 subunit of the SARS-CoV-2 spike protein, both with and without fusion to the heat-labile enterotoxin B (LTB) subunit. We found that the LTB fusion protein from both coronaviruses preferentially assembles into higher molecular weight multimers, consistent with the formation of trimers. For PEDV, administering the spike protein fused to LTB to young pigs elicited a higher level of mucosal IgAs compared to maize grain containing the S1 protein alone or controls. This suggests that fusing the coronavirus spike protein with LTB may provide better protection. [ABSTRACT FROM AUTHOR]

The ongoing global pandemic caused by the SARS-CoV-2 virus has demanded the urgent search for effective therapeutic interventions. In response, our research aimed at identifying natural products (NPs) with potential inhibitory effects on the entry of the SARS-CoV-2 spike (S) protein into host cells. Utilizing the Protein Data Bank Japan (PDBJ) and BindingDB databases, we isolated 204 S-glycoprotein sequences and conducted a clustering analysis to identify similarities and differences among them. We subsequently identified 33,722 binding molecules (BMs) by matching them with the sequences of 204 S-glycoproteins and compared them with 52,107 secondary metabolites (SMs) from the KNApSAcK database to identify potential inhibitors. We conducted docking and drug-likeness property analyses to identify several SMs with potential as drug candidates based on binding energy (BE), no Lipinski's rule violation (LV), psychochemical properties within the pink area of the bioavailability radar, and a bioavailability score (BAS) not less than 0.55. Fourteen SMs were predicted through computational analysis as potential candidates for inhibiting the three major types of S proteins. Our study provides a foundation for further experimental validation of these compounds as potential therapeutic agents against SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Introduction: Vaccine platforms such as viral vectors and mRNA can accelerate vaccine development in response to newly emerging pathogens, as demonstrated during the COVID-19 pandemic. However, the differential effects of platform and antigen insert on vaccine immunogenicity remain incompletely understood. Innate immune responses induced by viral vector vaccines are suggested to have an adjuvant effect for subsequent adaptive immunity. Integrating data on both innate and adaptive immunity, systems vaccinology approaches can improve the understanding of vaccine-induced immune mechanisms. Methods: Two vaccine candidates against SARS-CoV-2, both based on the viral vector Modified Vaccinia virus Ankara (MVA) and encoding the native (MVA-SARS-2-S) or prefusion-stabilized spike protein (MVA-SARS-2-ST), were evaluated in phase 1 clinical trials (ClinicalTrials.gov: NCT04569383, NCT04895449). Longitudinal dynamics of innate and early adaptive immune responses induced by vaccination in SARS-CoV-2-naïve individuals were analyzed based on transcriptome and flow cytometry data, in comparison to the licensed ChAd and mRNA vaccines. Results: Compared to MVA-SARS-2-S, MVA-SARS-2-ST (encoding the prefusion-stabilized spike protein) induced a stronger transcriptional activation early after vaccination, as well as higher virus neutralizing antibodies. Positive correlations were observed between innate and adaptive immune responses induced by a second MVA-SARS-2-ST vaccination. MVA-, ChAd- and mRNA-based vaccines induced distinct immune signatures, with the overall strongest transcriptional activation as well as monocyte and circulating T follicular helper (cTFH) cell responses induced by ChAd. Discussion: Our findings suggest a potential impact of the spike protein conformation not only on adaptive but also on innate immune responses. As indicated by positive correlations between several immune parameters induced by MVA-SARS-2-ST, the distinct transcriptional activation early after vaccination may be linked to the induction of classical monocytes and activation of cTFH1 cells, which may in turn result in the superior adaptive immunogenicity of MVA-SARS-2-ST, compared to MVA-SARS-2-S. Overall, our data demonstrate that both the vaccine platform and antigen insert can affect innate immune responses and subsequent vaccine immunogenicity in humans. [ABSTRACT FROM AUTHOR]

The goal of the next‐generation COVID‐19 vaccine is to provide rapid respiratory tract protection with a single dose. Circulating antibodies do not protect the olfactory mucosa from viral infection, necessitating localized mucosal immunization. Live attenuated vesicular stomatitis virus (VSVMT)‐based COVID‐19 vaccines effectively stimulate mucosal immunity in animals, though safety concerns remain, particularly in immunocompromised populations. A viral vector capable of single‐cycle replication may face less stringent regulatory requirements. A replication‐defective VSVMT is developed with its G protein replaced by a SARS‐CoV‐2 spike protein (S) mutant, where residues K986 and V987 are substituted by prolines (S2P). This studies show that single‐cycle VSVMT encoding Omicron subvariant S2P (VSVMT‐S2P) is safe in both healthy and immunocompromised animals treated with cyclophosphamide (CP). Significant antibody and T‐cell responses against the spike protein are observed in VSVMT‐S2P vaccinated healthy animals. Intramuscular VSVMT‐S2P administration induces neutralizing antibody responses comparable to those from replication‐competent VSVMT‐S. In immunocompromised animals, lower and delayed immune responses are observed. Thus, single‐cycle M‐protein mutated VSV offers a safe and effective platform for SARS‐CoV‐2 immunogen delivery. Remarkably, replication‐competent VSVMT‐S caused no pathogenicity and elicited potent mucosal immunity via intranasal administration, highlighting its potential as a mucosal COVID‐19 vaccine. [ABSTRACT FROM AUTHOR]

COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) had an adverse effect globally because it caused a global pandemic with several million deaths. This virus possesses spike protein that is cleaved or activated by Furin-like protease enzymes occurring by mammalian lung or respiratory cells to enter the mammalian body. The addition of the Furin cleavage site in SARS-CoV-2 makes it a more infectious and emerging virus than its ancestor's viruses. Phylogenetic relationships of coronavirus spike proteins have analyzed and mapped Furin recognition motif on the tree using bioinformatics tools such as GTEx, KEGG, GO, NCBI, PolyPhen-2, SNAP2, PANTHER, Hidden Markov Models (Fathmm), Phd-single-nucleotide polymorphism (SNP), I-TASSER, Modpred, Phobius, SIFT, iPTREE-STAB, and PROVEAN. During this study, it has been found that in certain regions, Furin SNPs have some relation with the susceptibility to SARS-CoV-2. Whereas in other regions, the effects are very negligible. Finally, our study demonstrates that Furin SNPs have a strong relationship with susceptibility to SARS-CoV-2. As it helps to cleave the spike protein of the virus, thus it can be targeted to inhibit at a particular site to prevent the SARS-CoV-2 from the entrance into the body. [ABSTRACT FROM AUTHOR]

Human endogenous retroviruses (HERVs) are genomic fragments integrated into human DNA from germline infections by exogenous retroviruses that threatened primates early in their evolution and are inherited vertically in the germline. So far, HERVs have been studied in the context of extensive immunopathogenic, neuropathogenic and even oncogenic effects within their host. In particular, in our paper, we elaborate on the aspects related to the possible correlation of transposable HERV elements' activation and SARS-CoV-2 spike protein's presence in cells of COVID-19 patients or upon COVID-19 vaccination with implications for natural and adaptive immunity. In particular, the release of cytokines TNF-α, IL-1β and IL-6 occurs in such cases and plays a notable role in sustaining chronic inflammation. Moreover, well-known interindividual variations of HERVs might partially account for the interpersonal variability of COVID-19 symptoms or unwanted events post-vaccination. Accordingly, further studies are required to clarify the SARS-CoV-2 spike protein's role in triggering HERVs. [ABSTRACT FROM AUTHOR]

Renal cell carcinoma (RCC) is the most common form of kidney cancer, known for its immune evasion and resistance to chemotherapy. Evidence indicates that the SARS-CoV-2 virus may worsen outcomes for RCC patients, as well as patients with diminished renal function. Evidence suggests that the SARS-CoV-2 virus may exacerbate outcomes in RCC patients and those with impaired renal function. This study explored the unidirectional effects of RCC cells and the SARS-CoV-2 spike protein (S protein) on human renal proximal tubule epithelial cells (RPTECs) using a microphysiological approach. We co-cultured RCC cells (Caki-1) with RPTEC and exposed them to the SARS-CoV-2 S protein under dynamic 3D conditions. The impact on metabolic activity, gene expression, immune secretions, and S protein internalization was evaluated. The SARS-CoV-2 S protein was internalized by RPTEC but poorly interacted with RCC cells. RPTECs exposed to RCC cells and the S protein exhibited upregulated expression of genes involved in immunogenic pathways, particularly those related to antigen processing and presentation via the major histocompatibility complex I (MHCI). Additionally, increased TNF-α secretion suggested a pro-inflammatory response. Metabolic shifts toward glycolysis were observed in RCC co-culture, while the presence of the S protein led to minor changes. The presence of RCC cells amplified the immune-modulatory effects of the SARS-CoV-2 S protein on the renal epithelium, potentially exacerbating renal inflammation and fostering tumor-supportive conditions. These findings suggest that COVID-19 infections can impact renal function in the presence of kidney cancer. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 infection is associated with long-lasting neurological symptoms, although the underlying mechanisms remain unclear. Using optical clearing and imaging, we observed the accumulation of SARS-CoV-2 spike protein in the skull-meninges-brain axis of human COVID-19 patients, persisting long after viral clearance. Further, biomarkers of neurodegeneration were elevated in the cerebrospinal fluid from long COVID patients, and proteomic analysis of human skull, meninges, and brain samples revealed dysregulated inflammatory pathways and neurodegeneration-associated changes. Similar distribution patterns of the spike protein were observed in SARS-CoV-2-infected mice. Injection of spike protein alone was sufficient to induce neuroinflammation, proteome changes in the skull-meninges-brain axis, anxiety-like behavior, and exacerbated outcomes in mouse models of stroke and traumatic brain injury. Vaccination reduced but did not eliminate spike protein accumulation after infection in mice. Our findings suggest persistent spike protein at the brain borders may contribute to lasting neurological sequelae of COVID-19. [Display omitted] • SARS-CoV-2 spike protein persists in the skull-meninges-brain axis in COVID-19 patients • Spike protein is sufficient to induce brain pathological and behavioral changes in mice • Spike protein enhances brain vulnerability and exacerbates neurological damage in mice • mRNA vaccines reduce, but do not eliminate, the spike burden SARS-CoV-2 infection can lead to long-lasting neurological sequelae, but underlying mechanisms are unclear. Rong et al. report that SARS-CoV-2 spike protein persists in the skull-meninges-brain axis, inducing inflammation, neurodegeneration-related changes, and increasing the brain's vulnerability to further injury. [ABSTRACT FROM AUTHOR]

Coronaviruses (CoVs) share key genomic elements critical for viral replication, suggesting the feasibility of developing therapeutics with efficacy across different viruses. In a previous work, we demonstrated the antiviral activity of the antipsychotic drug lurasidone against both SARS-CoV-2 and HCoV-OC43. In this study, our investigations on the mechanism of action of lurasidone suggested that the drug exhibits antiviral activity by targeting the papain-like protease (PL-Pro) of both viruses, and the Spike protein of SARS-CoV-2, thereby hampering both the entry and the viral replication. In vitro assays demonstrate that lurasidone significantly reduces viral load in infected cells, showing that the drug is a promising candidate for further development as a dual-action antiviral, offering a potential new strategy in the fight against COVID-19 and other coronavirus-related diseases. [ABSTRACT FROM AUTHOR]

We report the case of an 84‐year‐old male patient who was transferred to our hospital because of impaired consciousness and high fever, and died about 10 weeks after his fourth "coronavirus disease 2019" (COVID‐19) vaccination. Autopsy revealed acute ischemic change with microhemorrhage and perivascular T‐cell infiltration in the thalamus, pons, and cerebellum, which were considered to be related to neurological symptoms. There were dilatation of the right ventricle, accumulation of pleural effusion, and ascites, suggesting right heart failure. Although the patient had a negative COVID‐19 polymerase chain reaction test, immunohistochemical analysis for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) antigens (spike and nucleocapsid proteins) was performed to identify the cause of death. Surprisingly, only SARS‐CoV‐2 spike protein was detected in the thalamus, pons, and pituitary and adrenal glands. The presence of SARS‐CoV‐2 spike protein might have been due to vaccination rather than viral infection, because no SARS‐CoV‐2 nucleocapsid protein was detected. The spike protein in the central nervous system might have been related to the acute ischemic change, and that in the pituitary and adrenal glands may have been associated with right heart failure, possibly through dysfunction of the renin‐angiotensin‐aldosterone system. [ABSTRACT FROM AUTHOR]

The Coronavirus Disease (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2), highlighted significant gaps in our understanding of the virus’s molecular structure, its biological properties, and the interactions between viral proteins and host biological systems, which have underscored the critical need for further research in this area. Coagulation disorders, particularly those leading to thromboinflammation, have been linked to severe complications in COVID-19 cases. The occurrence of thromboinflammation has likewise been corroborated in cases of both Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). In this study, we investigated the protein-protein interactions between the SARS-CoV-2 spike protein and fibrinogen, a glycoprotein that plays a crucial role in blood coagulation. Molecular docking analysis revealed key interactions between the β and γ subunits of fibrinogen and the spike protein. The findings suggest that these interactions may contribute to the understanding of the coagulation disorders observed in COVID-19 patients. This study provides insights into the molecular mechanisms underlying these disorders and identifies potential targets for the development of therapeutic interventions. [ABSTRACT FROM AUTHOR]

Background: Although treatments using thermal water have yielded beneficial effects in respiratory tract infections, the effects of thermal water under experimental conditions similar to those triggered by SARS-CoV-2 have yet to be evaluated. This study aimed to assess whether thermal water could interfere with the interaction between SARS-CoV-2 and host cells and influence inflammatory factors. Methods: Human nasal epithelial primary cells (HNEpCs) were stimulated with SARS-CoV-2 spike protein in the presence or absence of thermal water or tap water. Cell viability, cytokine concentration, ACE2 and TMPRSS2 levels, and ACE2 activity were determined in the cell cultures. Results: Exposure of HNEpCs to spike protein increased IL-6, IL-8, and IL-1β production, with decreased production observed in the presence of thermal water at an optimal dose. Treatment of cells with tap water did not affect cytokine release in unstimulated or spike-stimulated cells. Spike-protein-stimulated HNEpCs showed reduced levels of ACE2, which were partially restored only in the presence of thermal water. Spike protein did not affect the TMPRSS2 levels of the cell lysates. Stimulation with spike protein induced an increase in the concentration of both receptors in the supernatants, while treatment with thermal water reduced TMPRSS2 levels in both the cells and supernatants. Stimulation with spike protein increased ACE2 activity, which was reduced with thermal water. Conclusions: This study shows the regulatory effects of mineral-rich thermal water on spike-protein-induced pro-inflammatory cytokine production and the amount and activity of receptors mainly involved in viral entry, suggesting a potential use of this treatment as a support therapy for SARS-CoV-2 infection of the upper respiratory tract. [ABSTRACT FROM AUTHOR]

Background/Objectives: While post-acute COVID-19 syndrome is well known and extensively studied, the post-acute COVID vaccination syndrome (PACVS) is a more recent nosological entity that is poorly defined at the immunopathological level, although it shares many symptoms with the sequelae of viral infections. Methods: This single-center retrospective study reports a case series of 17 subjects vaccinated with mRNA or adenoviral vector vaccines who were healthy before vaccination and had never been infected with SARS-CoV-2 but who presented with symptoms similar to PACVS for a median time of 20 months (min 4, max 32). The medical records of all patients referred to our outpatient clinic over a one-year period were retrospectively analyzed. Results: In this group, serological tests showed that, in addition to positivity for anti-spike protein antibodies, a high percentage of subjects were positive for antibodies against G protein-coupled receptors and molecules involved in the response to SARS-CoV-2. In a panel of 16 autoantibodies tested, a few were positively associated with some of the symptoms reported by patients: anti-ATR1 with lymphadenopathy and/or tonsillitis; anti-ACE2 with skin symptoms such as ecchymosis, skin oedema, and rash; anti-MAS1 with widespread burning sensation; and anti-STAB1 with skin oedema and rash. Anti-ADRA2A were negatively associated with memory loss and/or mental fog. ACE2 correlated with the serum levels of anti-S antibodies, supporting the hypothesis of an anti-idiotype mechanism in the immunopathogenesis of PACVS. Conclusions: This exploratory analysis suggests that the levels of autoantibodies directed against ACE2, and probably also MAS1 and STAB1, may serve as biomarkers for PACVS. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants harboring mutations in the structural protein, especially in the receptor binding domain (RBD) of spike protein, have raised concern about potential immune escape. The spike protein of SARS-CoV-2 plays a vital role in infection and is an important target for neutralizing antibodies. The mutations that occur in the structural proteins, especially in the spike protein, lead to changes in the virus attributes of transmissibility, an increase in disease severity, a notable reduction in neutralizing antibodies generated and thus a decreased response to vaccines and therapy. The observed multiple mutations in the RBD of the spike protein showed immune escape because it increases the affinity of spike protein binding with the ACE-2 receptor of host cells and increases resistance to neutralizing antibodies. Cytotoxic T-cell responses are crucial in controlling SARS-CoV-2 infections from the infected tissues and clearing them from circulation. Cytotoxic T cells efficiently recognized the infected cells and killed them by releasing soluble mediator's perforin and granzymes. However, the overwhelming response of T cells and, subsequently, the overproduction of inflammatory mediators during severe infections with SARS-CoV-2 may lead to poor outcomes. This review article summarizes the impact of mutations in the spike protein of SARS-CoV-2, especially mutations of RBD, on immunogenicity, immune escape and vaccine-induced immunity, which could contribute to future studies focusing on vaccine design and immunotherapy. [ABSTRACT FROM AUTHOR]

Abstract The spread of SARS-CoV-2 to animals has the potential to evolve independently. In this study, we distinguished several sentinel animal species and genera for monitoring the re-emergence of COVID-19 or the new outbreak of COVID-19-like disease. We analyzed SARS-CoV-2 genomic data from human and nonhuman mammals in the taxonomic hierarchies of species, genus, family and order of their host. We find that SARS-CoV-2 carried by domestic dog (Canis lupus familiaris), domestic cat (Felis catus), mink (Neovison vison), and white-tailed deer (Odocoileus virginianus) cluster closely to human-origin viruses and show no differences in the majority of amino acids, but have the most positively selected sites and should be monitored to prevent the re-emergence of COVID-19 caused by novel variants of SARS-CoV-2. Viruses from the genera Panthera (especially lion (Panthera leo)), Manis and Rhinolophus differ significantly from human-origin viruses, and long-term surveillance should be undertaken to prevent the future COVID-19-like outbreaks. Investigation of the variation dynamics of sites 142, 501, 655, 681 and 950 within the S protein may be necessary to predict the novel animal SARS-CoV-2 variants.

In order to clarify the pre-exist immunity background of different human coronaviruses (HCoV), this study investigated the positive rate of spike (S) protein antibodies of HCoV, including HCoV- severe acute respiratory syndrome (SARS) −associated coronavirus (SARS-CoV-1), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Middle East respiratory syndrome coronavirus (MERS-CoV), HCoV-229E, HCoV-NL63, HCoV-HKU1 and HCoV-OC43, before and after the Coronavirus Disease 2019 (COVID-19) outbreak. We utilized pseudotyped virus-based neutralization assays (PBNA) or enzyme-linked immunosorbent assays (ELISA) to detect antibody levels against HCoV in serum samples collected in 2009–2010 and 2023. The PBNA results showed that neutralizing antibodies against SARS-CoV-1 and the MERS-CoV were negative. In the serum samples from 2009 to 2010, neutralizing antibodies against SARS-CoV-2 (D614G) were negative, whereas in the serum samples from 2023, 73 samples (73 %) showed neutralizing reactions with the SARS-CoV-2 D614G strain, 96 samples (96 %) with the BA.5 strain, and 91 samples (91 %) with the BF.7 strain. Among pre-COVID-19 samples, 33 % (33/100) showed neutralizing reactions with HCoV-229E and 63 % (63/100) with HCoV-NL63. Among post-COVID-19 samples, 50 % (50/100) showed neutralizing reactions with HCoV-229E and 49 % (49/100) with HCoV-NL63. Due to the different receptors of alpha coronavirus genus compared to other beta coronavirus genus, neutralizing antibodies against HCoV-OC43 and HCoV-HKU1 virus cannot be detected by constructing corresponding pseudotyped virus. Binding antibodies against HCoV-OC43 and HCoV-HKU1 virus were detected using ELISA. The results revealed that among pre-COVID-19 samples, 83 % (83/100) and 45 % (45/100) had binding activity with HCoV-OC43 and HCoV-HKU1, respectively. Among post-COVID-19 samples, 100 % (100/100) and 81 % (81/100) had binding activity with HCoV-OC43 and HCoV-HKU1, respectively.

Cardiac injury is common in hospitalized coronavirus disease 2019 (COVID-19) patients and cardiac abnormalities have been observed in a significant number of recovered COVID-19 patients, portending long-term health issues for millions of infected individuals. To better understand how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, CoV-2 for short) damages the heart, it is critical to fully comprehend the biology of CoV-2 encoded proteins, each of which may play multiple pathological roles. For example, CoV-2 spike glycoprotein (CoV-2-S) not only engages angiotensin converting enzyme II (ACE2) to mediate virus infection but also directly activates immune responses. In this work, the goal is to review the known pathological roles of CoV-2-S in the cardiovascular system, thereby shedding lights on the pathogenesis of COVID-19 related cardiac injury.

Abstract Frequent RNA virus mutations raise concerns about evolving virulent variants. The purpose of this study was to investigate genetic variation in salmonid alphavirus-3 (SAV3) over the course of an experimental infection in Atlantic salmon and brown trout. Atlantic salmon and brown trout parr were infected using a cohabitation challenge, and heart samples were collected for analysis of the SAV3 genome at 2-, 4- and 8-weeks post-challenge. PCR was used to amplify eight overlapping amplicons covering 98.8% of the SAV3 genome. The amplicons were subsequently sequenced using the Nanopore platform. Nanopore sequencing identified a multitude of single nucleotide variants (SNVs) and deletions. The variation was widespread across the SAV3 genome in samples from both species. Mostly, specific SNVs were observed in single fish at some sampling time points, but two relatively frequent (i.e., major) SNVs were observed in two out of four fish within the same experimental group. Two other, less frequent (i.e., minor) SNVs only showed an increase in frequency in brown trout. Nanopore reads were de novo clustered using a 99% sequence identity threshold. For each amplicon, a number of variant clusters were observed that were defined by relatively large deletions. Nonmetric multidimensional scaling analysis integrating the cluster data for eight amplicons indicated that late in infection, SAV3 genomes isolated from brown trout had greater variation than those from Atlantic salmon. The sequencing methods and bioinformatics pipeline presented in this study provide an approach to investigate the composition of genetic diversity during viral infections.

Background: Coronavirus disease 2019 (COVID-19) vaccination has been shown to elicit both humoral (antibody) and cell-mediated (T-cell) immune responses. This study aimed to characterize and compare the QuantiFERON severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and anti-SARS-CoV-2 antibody responses in vaccinated and unvaccinated COVID-19 patients, as well as vaccinated healthy controls (HCs). Methods: A total of 96 COVID-19 patients (68 vaccinated with Sinopharm and 15 with AstraZeneca), 13 unvaccinated COVID-19 patients, and 16 vaccinated HCs (8 Sinopharm and 8 AstraZeneca) were included. Serum antibodies against the SARS-CoV-2 spike (S1) protein and nucleocapsid (N) protein were measured by enzyme-linked immunosorbent assay. T-cell responses were evaluated using the QuantiFERON assay against three SARS-CoV-2 viral antigens (Ag1, Ag2, and Ag3). Results: There were no significant differences in S1 antibody levels between COVID-19 patients (vaccinated or unvaccinated) and HCs. However, 100% of unvaccinated COVID-19 patients had anti-N antibodies, which was significantly higher than the AstraZeneca-vaccinated group. T-cell responses did not differ significantly between vaccinated and unvaccinated patients or between vaccinated patients and HCs. Vaccination with Sinopharm induced higher levels of total N antibodies and greater interferon-gamma release against the viral antigens compared to the other groups. Conclusions: Vaccination, especially with Sinopharm, induced robust humoral (N antibodies) and cellular (T-cell) immune responses in COVID-19 patients. The findings highlight the importance of vaccination in eliciting a comprehensive immune response against SARS-CoV-2, even in the context of prior infection.

Recognising the fact that the SARS-CoV-2 spike glycoprotein is the most crucial protein for the virus's attachment to surfaces and subsequent infection, we carried out massive all-atom molecular dynamics studies of the conformational states of S-protein in solvents of various pH values, ranging from pH = 1 through pH = 11. Our studies found that: (1) The S-protein's structural deviation measured in the backbone at pH = 1 is 185% higher than that of pH = 7, and most of this overall deviation occurs at the receptor-binding domain and N-terminal domain. (2) Structural changes are also observed at both pH = 3 and pH = 11, albeit to a lesser extent than at pH = 1. (3) Changes, as measured by various metrics at pH = 5, pH = 7 and pH = 9, are insignificant. Such a high degree of structural tolerance of the S-protein at these pH values corroborates indirectly with in vitro observations that the virus retains significant infectivity over a wide range of pH. The multiscale structural analyses pinpoint the critical regions that are responsible for the S-protein's structural deviations. [ABSTRACT FROM AUTHOR]

The continued emergence of deadly human coronaviruses from animal reservoirs highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq), we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryoelectron microscopy (cryo-EM) structure of 54043-5 bound to the prefusion S2 subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses in vitro , including antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit. [Display omitted] • 50 cross-reactive coronavirus spike antibodies were isolated from human donors • 54043-5 binds spikes from multiple betacoronaviruses • Structural analysis of 54043-5 defines a conserved epitope at the apex of S2 • Fc attenuation confers neutralization-independent, protective phenotypes in mice Johnson et al. identify antibody 54043-5, a non-neutralizing antibody that broadly targets betacoronavirus spike proteins. 54043-5 targets a highly conserved epitope at the apex of the prefusion S2 subunit and elicits Fc-mediated immune functions. An Fc-knockout variant of 54043-5 protects mice from disease, suggesting additional considerations for developing antibody-based interventions. [ABSTRACT FROM AUTHOR]

Amidst the global pandemic caused by the SARS-CoV-2 virus, researchers are actively studying its evolution and impact. This research delves into the spike protein of the SARS-CoV-2 Delta variant, using advanced computational methods to analyze mutations and their effects. By examining mutations and their evolutionary connections in the spike protein using data from databases, the study aims to gain insights into the virus's behavior. To gauge the stability of the spike protein variants, we used various methods. We predicted protein sequence disorders using PONDR. We also used the I-Mutant v2.0 bioinformatics tool to assess how mutations affected stability. We then performed functional studies using Protparam and NetPhos to analyze the consequences of these mutations. These analyses identified several key mutations in the spike protein, especially the D614G substitution. This polar-to-nonpolar amino acid change was particularly noteworthy. Our research identified significant mutations in the spike protein of the Delta Indian variant of SARS-CoV-2, including: T19R, E156G, L452R, T478K, P681R, and D950N. Deletions occurred at positions Y145, F157, and R158. Analysis showed increased phosphorylation of the spike protein, hinting at potential regulation by these mutations. Using structural modeling by Spdbv tool, we found that mutations within the Receptor-Binding Domain (RBD) region reduced protein stability. This study enhances our understanding of the mutations and their impact on the function of the Delta Indian variant's spike protein. Our research explores how mutations in the SARS-CoV-2 virus affect how its proteins work and stay stable. By understanding these effects, we can lay the foundation for future studies that design treatments specifically for new SARS-CoV-2 variants. In summary, our work shows that SARS-CoV-2 is constantly evolving, making it crucial to keep track of changes and keep researching to help guide health policies. [ABSTRACT FROM AUTHOR]

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes coronavirus disease 2019 (COVID‐19) and has been related to more than 7 million deaths globally since 2019. The association of high levels of IL‐6 with severe cases led to the early evaluation of the anti‐IL6 inhibitor tocilizumab as a potential treatment, which unfortunately failed to improve survival in many trials. Moreover, little is known about the development of COVID‐19 sequelae, and biomarkers are needed to understand and anticipate these processes. Because extracellular vesicles (EVs) play an important role in viral infection and immune response, they could potentially serve as predictive and prognostic biomarkers. We isolated EVs from 39 patients with severe COVID‐19, from which 29 received tocilizumab and 10 were considered controls. Blood samples, which were collected at hospitalisation before treatment, at Day 7, and Day 15 during follow‐up, were assessed by immunoblot for longitudinal expression of spike (S) and nucleocapsid (N) proteins. Dynamic expression was calculated and compared with clinicopathological and experimental variables. Expression of EV S was validated by immunogold and imaging flow‐cytometry, revealing an enrichment in CD9+ EVs. As a result, decreasing expression of EV viral proteins was observed in patients treated with tocilizumab. Moreover, higher increase in EV S was observed in patients with lower antibody response, hyperfibrinogenemia, lower respiratory function, higher blood pressure and shorter outcomes. These findings lay the foundation for future studies characterizing the role of EVs in multiorgan assessment and identifying biomarkers in patients with severe COVID‐19 and possible long COVID. [ABSTRACT FROM AUTHOR]

Covid-19, an infectious disease caused by the novel respiratory virus Sars-Cov-2, was declared a pandemic by the WHO in December 2019. Its clinical spectrum ranges from asymptomatic to Acute Respiratory Distress Syndrome (ARDS). This pandemic has forced health systems to adapt quickly to improve diagnostics, patient care and implement vaccination. Three years after the virus appeared, acquired immunity and vaccines have changed the trajectory of the pandemic, reducing the transmission and severity of illnesses associated with Sars-Cov-2. Although vaccines offer strong protection against severe forms of Covid-19, hospitalizations and mortality, the continued circulation of the virus, exacerbated by mutations in its spike protein, highlights the importance of maintaining vaccination programs. The evolution of the immune response against Sars-Cov-2 remains poorly characterized. For its evaluation, a prospective study was carried out at the laboratory of CHU Hassan 2 in Fez to study the kinetics of the level of anti-Sars-Cov-2 antibodies in hospital staff, before and after vaccination. [ABSTRACT FROM AUTHOR]