SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Issue 4 - Impact of air pollution on COVID-19 mortality and morbidity: An epidemiological and mechanistic review

Air pollution is a major global environment and health concern. Recent studies have suggested an association between air pollution and COVID-19 mortality and morbidity. In this context, a close association between increased levels of air pollutants such as particulate matter ≤2.5 to 10 µM, ozone and nitrogen dioxide and SARS-CoV-2 infection, hospital admissions and mortality due to COVID 19 has been reported. Air pollutants can make individuals more susceptible to SARS-CoV-2 infection by inducing the expression of proteins such as angiotensin converting enzyme (ACE)2 and transmembrane protease, serine 2 (TMPRSS2) that are required for viral entry into the host cell, while causing impairment in the host defence system by damaging the epithelial barrier, muco-ciliary clearance, inhibiting the antiviral response and causing immune dysregulation. The aim of this review is to report the epidemiological evidence on impact of air pollutants on COVID 19 in an up-to-date manner, as well as to provide insights on in vivo and in vitro mechanisms.

The characterization of technical design of a virus-like structure (VLS) nanodelivery system as vaccine candidate against SARS-CoV-2 variants

The constant mutation of SARS-CoV-2 has led to the continuous appearance of viral variants and their pandemics and has improved the development of vaccines with a broad spectrum of antigens to curb the spread of the virus. The work described here suggested a novel vaccine with a virus-like structure (VLS) composed of combined mRNA and protein that is capable of stimulating the immune system in a manner similar to that of viral infection. This VLS vaccine is characterized by its ability to specifically target dendritic cells and/or macrophages through S1 protein recognition of the DC-SIGN receptor in cells, which leads to direct mRNA delivery to these innate immune cells for activation of robust immunity with a broad spectrum of neutralizing antibodies and immune protective capacity against variants. Research on its composition characteristics and structural features has suggested its druggability. Compared with the current mRNA vaccine, the VLS vaccine was identified as having no cytotoxicity at its effective application dosage, while the results of safety observations in animals revealed fewer adverse reactions during immunization.

Translating animal models of SARS-CoV-2 infection to vascular, neurological and gastrointestinal manifestations of COVID-19

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initiated a global pandemic resulting in an estimated 775 million infections with over 7 million deaths, it has become evident that COVID-19 is not solely a pulmonary disease. Emerging evidence has shown that, in a subset of patients, certain symptoms - including chest pain, stroke, anosmia, dysgeusia, diarrhea and abdominal pain - all indicate a role of vascular, neurological and gastrointestinal (GI) pathology in the disease process. Many of these disease processes persist long after the acute disease has been resolved, resulting in 'long COVID' or post-acute sequelae of COVID-19 (PASC). The molecular mechanisms underlying the acute and systemic conditions associated with COVID-19 remain incompletely defined. Appropriate animal models provide a method of understanding underlying disease mechanisms at the system level through the study of disease progression, tissue pathology, immune system response to the pathogen and behavioral responses. However, very few studies have addressed PASC and whether existing models hold promise for studying this challenging problem. Here, we review the current literature on cardiovascular, neurological and GI pathobiology caused by COVID-19 in patients, along with established animal models of the acute disease manifestations and their prospects for use in PASC studies. Our aim is to provide guidance for the selection of appropriate models in order to recapitulate certain aspects of the disease to enhance the translatability of mechanistic studies.

Glucose-regulated protein 94 (Grp94/gp96) in viral pathogenesis: Insights into its role and therapeutic potentials

Glucose-regulated protein 94 (Grp94/gp96) is endoplasmic reticulum (ER) resident form of the 90 kDa heat shock protein 90 (Hsp90) that is responsible for folding, maturation and stabilization of more than 400 client proteins. Grp94 has been implicated for various diseases including metastatic cancer, primary open-angle glaucoma, and infectious diseases. In fact, Grp94 plays critical roles in different stages of viral infection cycle. It chaperones receptor proteins and viral glycoproteins that are necessary for viral entry and replication. Beyond its role in protein homeostasis, Grp94 modulates host cellular processes such as apoptosis and immune responses, which are often exploited by viruses to sustain infection. This work provides an overview of the roles of Grp94 in viral pathogenesis across various viruses and its involvement in immune modulation with the development of Grp94-selective inhibitors and their potential as anti-viral therapeutics.

The potential of metal-organic framework MIL-101(Al)-NH2 in the forefront of antiviral protection of cells via interaction with SARS-CoV-2 spike RBD protein and their antibacterial action mediated with hypericin and photodynamic treatment

The global pandemic of SARS-CoV-2 has highlighted the necessity for innovative therapeutic solutions. This research presents a new formulation utilising the metal-organic framework MIL-101(Al)-NH2, which is loaded with hypericin, aimed at addressing viral and bacterial challenges. Hypericin, recognised for its antiviral and antibacterial efficacy, was encapsulated to mitigate its hydrophobicity, improve bioavailability, and utilise its photodynamic characteristics. The MIL-101(Al)-NH2 Hyp complex was synthesised, characterised, and evaluated for its biological applications for the first time. The main objective of this study was to demonstrate the multimodal potential of such a construct, in particular the effect on SARS-CoV-2 protein levels and its interaction with cells. Both in vitro and in vivo experiments demonstrated the effective transport of hypericin to cells that express ACE2 receptors, thereby mimicking mechanisms of viral entry. In addition, hypericin found in the mitochondria showed selective phototoxicity when activated by light, leading to a decrease in the metabolic activity of glioblastoma cells. Importantly, the complex also showed antibacterial efficacy by selectively targeting Gram-positive Staphylococcus epidermidis compared to Gram-negative Escherichia coli under photodynamic therapy (PDT) conditions. To our knowledge, this study was the first to demonstrate the interaction between hypericin, MIL-101(Al)-NH2 and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, which inhibits cellular uptake and colocalises with ACE2-expressing cells. Therefore, the dual functionality of the complex - targeting the viral RBD and the antibacterial effect via PDT - emphasises its potential to mitigate complications of viral infections, such as secondary bacterial infections. In summary, these results suggest that MIL-101(Al)-NH2 Hyp is a promising multifunctional therapeutic agent for antiviral and antibacterial applications, potentially contributing to the improvement of COVID-19 treatment protocols and the treatment of co-infections.

Developing Zika virus-transduced hACE2 expression models for severe acute respiratory syndrome coronavirus 2 infection in vitro and in vivo

To address the human ACE2 dependence for SARS-CoV-2 infection, this study presents a novel strategy for generating ZIKV-hACE2 single-round infectious particles (SRIPs) by incorporating the hACE2 gene into a Zika virus (ZIKV) mini-replicon. SARS-CoV-2 SRIP infection was significantly enhanced in HEK293T cells pre-infected with ZIKV-hACE2, as evidenced by increased cytopathic effects and elevated mRNA and protein levels of the SARS-CoV-2 nucleocapsid (N) protein. A mouse model was also developed with this approach to investigate SARS-CoV-2 infection. Immunohistochemical and real-time RT-PCR analyses confirmed the presence of the SARS-CoV-2 N protein in the lungs of mice injected with ZIKV-hACE2 SRIPs, indicating successful infection. The mouse model displayed COVID-19-like pathological changes, including increased macrophages in BALF, severe lung damage, and elevated pro-inflammatory cytokines (IL-6 and IL-1β). These features mimic severe COVID-19 cases in humans. Additionally, treatment with nirmatrelvir resulted in a 6.2-fold reduction in viral load and a marked decrease in N protein levels. Overall, this ZIKV mini-replicon-mediated hACE2 expression model, both in vitro and in vivo, is a valuable tool for studying SARS-CoV-2 infection and evaluating therapeutic interventions. The mouse model's pathological features further underscore its relevance for in vivo research on SARS-CoV-2.

Role of membrane proximal actin regulators in SARS-CoV-2 spike-induced cell-cell fusion

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein has the ability to induce multinucleated syncytia via cell-cell fusion, which is thought to be related to the pathogenesis of the coronavirus disease 2019 (COVID-19). However, the mechanism by which spike protein regulates cell fusion remains unclear. Given the close correlation between cell-cell fusion and membrane protrusions, we investigated the role of membrane-proximal actin regulators in spike-induced cell fusion. We found that while Rac-Arp2/3 dependent branched actin polymerization is required for spike-mediated cell fusion, RhoA dependent actomyosin contractility has an inhibitory effect on fusion. In addition, plasma membrane tension regulated by membrane-cortex attachment plays a negative role in spike-dependent cell fusion. Furthermore, we identified several BAR proteins, which couple membrane curvature with actin dynamics, involved in spike-induced syncytia formation. Our study suggests that these actin regulators could be promising targets for inhibiting SARS-CoV-2 spike protein-induced syncytia formation.

Human-genetic variants associated with susceptibility to SARS-CoV-2 infection

SARS-CoV-2, the third major coronavirus of the 21st century, causing COVID-19 disease, profoundly impacts public health and workforces worldwide. Identifying individuals at heightened risk of SARS-CoV-2 infection is crucial for targeted interventions and preparedness. This study investigated 35 SNVs within viral infection-associated genes in SARS-CoV-2 patients and uninfected controls from the Basque Country (March 2020-July 2021). Its primary aim was to uncover genetic markers indicative of SARS-CoV-2 susceptibility and explore genetic predispositions to infection. Association analyses revealed previously unreported associations between SNVs and susceptibility. Haplotype analyses uncovered novel links between haplotypes and susceptibility, surpassing individual SNV associations. Descriptive modelling identified key susceptibility factors, with rs11246068-CC (IFITM3), rs5742933-GG (ORMDL1), rs35337543-CG (IFIH1), and GGGCT (rs2070788, rs2298659, rs17854725, rs12329760, rs3787950) variation in TMPRSS2 emerging as main infection-susceptibility indicators for a COVID-19 pandemic situation. These findings underscore the importance of integrated SNV and haplotype analyses in delineating susceptibility to SARS-CoV-2 and informing proactive prevention strategies. The genetic markers profiled in this study offer valuable insights for future pandemic preparedness.

Synthesis of 3'-modified xylofuranosyl nucleosides bearing 5'-silyl or -butyryl groups and their antiviral effect against RNA viruses

D-xylofuranosyl nucleoside analogues bearing alkylthio and glucosylthio substituents at the C3'-position were prepared by photoinitiated radical-mediated hydrothiolation reactions from the corresponding 2',5'-di-O-silyl-3'-exomethylene uridine. Sequential desilylation and 5'-O-butyrylation of the 3'-thiosubstituted molecules produced a 24-membered nucleoside series with diverse substitution patterns, and the compounds were evaluated for their in vitro antiviral activity against three dangerous human RNA viruses, SARS-CoV-2, SINV and CHIKV. Eight compounds exhibited SARS-CoV-2 activity with low micromolar EC50 values in Vero E6 cells, and two of them also inhibited virus growth in human Calu cells. The best anti-SARS-CoV-2 activity was exhibited by 2',5'-di-O-silylated 3'-C-alkylthio nucleosides. Twelve compounds showed in vitro antiviral activity against CHIKV and fourteen against SINV with low micromolar EC50 values, with the 5'-butyryl-2'-silyl-3'-alkylthio substitution pattern being the most favorable against both viruses. In the case of the tested nucleosides, removal of the 2'-O-silyl group completely abolished the antiviral activity of the compounds against all three viruses. Overall, the most potent antiviral agent was the disilylated 3'-glucosylthio xylonucleoside, which showed excellent and specific antiviral activity against SINV with an EC50 value of 3 μM and no toxic effect at the highest tested concentration of 120 μM.

Defining diverse spike-receptor interactions involved in SARS-CoV-2 entry: Mechanisms and therapeutic opportunities

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped RNA virus that caused the Coronavirus Disease 2019 (COVID-19) pandemic. The SARS-CoV-2 Spike glycoprotein binds to angiotensin converting enzyme 2 (ACE2) on host cells to facilitate viral entry. However, the presence of SARS-CoV-2 in nearly all human organs - including those with little or no ACE2 expression - suggests the involvement of alternative receptors. Recent studies have identified several cellular proteins and molecules that influence SARS-CoV-2 entry through ACE2-dependent, ACE2-independent, or inhibitory mechanisms. In this review, we explore how these alternative receptors were identified, their expression patterns and roles in viral entry, and their impact on SARS-CoV-2 infection. Additionally, we discuss therapeutic strategies aimed at disrupting these virus-receptor interactions to mitigate COVID-19 pathogenesis.

Membrane Protein of SARS-CoV-2 Promotes the Production of CXCL10 and Apoptosis of Myocardial Cells

SARS-CoV-2 infections directly or indirectly cause unconscionable vascular events, significantly increasing the morbidity and mortality of COVID-19. Biomarkers associated with cardiac injury often elevate in individuals with COVID-19. Cytokine storm is a mechanism underlying myocardial cell injury caused by SARS-CoV-2 infections. Cell apoptosis in AC16 cells overexpressing structural and helper proteins of SARS-CoV-2 was detected by Western blot, MTT and TUNEL assay. The M protein was determined to play the most pronounced role in inducing apoptosis. Transcriptome sequencing on AC16 cells overexpressing the M protein was performed to screen differentially expressed genes (DEGs), which were further subjected to the gene set enrichment analysis. The regulatory effect of CXCL10 on cell apoptosis of AC16 cells overexpressing M protein was finally explored. Overexpression of M protein significantly increased the Bax/Bcl-2 and cleaved caspase-3/caspase-3(CC3/C3) ratios and the percentage of TUNEL-positive cells in AC16 cells, while markedly reducing cell viability. CXCL10 was the most prominent DEG in AC16 cells overexpressing M protein. Knockdown of CXCL10 partially reversed the increases in the Bax/Bcl-2 and cleaved caspase-3/caspase-3 ratios, the percentage of TUNEL-positive cells, as well as the release of pro-inflammatory cytokines in AC16 cells overexpressing M protein. The M protein of SARS-CoV-2 triggers the production of CXCL10 and apoptosis of myocardial cells.

Multiple exposures to SARS-CoV-2 Spike enhance cross-reactive antibody-dependent cellular cytotoxicity against SARS-CoV-1

Vaccination or infection by SARS-CoV-2 elicits a protective immune response against severe outcomes. It has been reported that SARS-CoV-2 infection or vaccination elicits cross-reactive antibodies against other betacoronaviruses. While plasma neutralizing capacity was studied in great detail, their Fc-effector functions remain understudied. Here, we analyzed Spike recognition, neutralization and antibody-dependent cellular cytotoxicity (ADCC) against D614G, a recent Omicron subvariant of SARS-CoV-2 (JN.1) and SARS-CoV-1. Plasma from individuals before their first dose of mRNA vaccine, and following their second, third and sixth doses were analyzed. Despite poor neutralization activity observed after the second and third vaccine doses, ADCC was readily detected. By the sixth dose, individuals could neutralize and mediate ADCC against JN.1 and SARS-CoV-1. Since previous reports have shown that Fc-effector functions were associated with survival from acute infection, these results suggest that ADCC could help in combating future SARS-CoV-2 variants as well as closely related coronaviruses.

Organs on chips: fundamentals, bioengineering and applications

Human body constitutes unique biological system containing specific fluid mechanics and biomechanics. Traditional cell culture techniques of 2D and 3D do not recapitulate these specific natures of the human system. In addition, they lack the spatiotemporal conditions of representing the cells. Moreover, they do not enable the study of cell-cell interactions in multiple cell culture platforms. Therefore, establishing biological system of dynamic cell culture was of great interest. Organs on chips systems were fabricated proving their concept to mimic specific organs functions. Therefore, it paves the way for validating new drugs and establishes mechanisms of emerging diseases. It has played a key role in validating suitable vaccines for Coronavirus disease (COVID-19). Herein, the concept of organs on chips, fabrication methodology and their applications are discussed.

Anti-SARS-CoV-2 and anticancer properties of triptolide and its derived carbonized nanomaterials

The COVID-19 pandemic remains an ongoing global health threat, yet effective treatments are still lacking. This has led to a high demand for complementary/alternative medicine, such as Chinese herbal medicines for curbing the COVID-19 pandemic. Given the dual anticancer and antiviral activities of many herbal drugs, they may hold a multifaceted potential to tackle both cancer and SARS-CoV-2. Triptolide is the major bioactive compound isolated from Tripterygium wilfordii Hook F (TwHF), a traditional Chinese medicinal herb recognized for its beneficial pharmacological properties in many diseases, including cancer and viral infection. However, its application in the clinic has been greatly limited due to its toxicity and poor water solubility. Here, from a screen of a natural compound library of Chinese Pharmacopoeia, we identified triptolide as a top candidate to inhibit cell entry of SARS-CoV-2. We demonstrated that triptolide robustly blocked viral entry at nanomolar concentrations in cellular models, with broad range activity against emerging Omicron variants of SARS-CoV-2. Mechanistically, triptolide disrupted the interaction of SARS-CoV-2 spike protein with its receptor ACE2. Furthermore, we synthesized water-soluble, triptolide-derived carbon quantum dots. Compared to triptolide, these highly biocompatible nanomaterials exhibited prominent antiviral capabilities against Omicron variants of SARS-CoV-2 with less cytotoxicity. Finally, we showed that triptolide-derived carbonized materials excelled in their anticancer properties compared to triptolide and Minnelide, a water-soluble analog of triptolide. Together, our results provide a rationale for the potential development of triptolide-carbonized derivatives as a promising antiviral candidate for the current pandemic and future outbreaks, as well as anticancer agents.

Decoding post-mortem infection dynamics of SARS-CoV-2, IAV and RSV: New insights for public health and emerging infectious diseases management

OBJECTIVES

The persistence and infectivity of respiratory viruses in cadavers remain poorly characterized, posing significant biosafety risks for forensic and healthcare professionals. This study systematically evaluates the post-mortem stability and transmission potential of SARS-CoV-2, influenza A virus (IAV), and respiratory syncytial virus (RSV) under varying environmental conditions, providing critical insights into viral kinetics.

METHODS

To assess the post-mortem stability of SARS-CoV-2, tissue samples were collected from infected cadavers at 4 ℃, room temperature (RT, 20-22 ℃), and 37 ℃ over a predetermined timeframe. Viral kinetics were analyzed using quantitative assays, while histopathology and immunohistochemistry characterized tissue-specific distribution. Additionally, comparative analyses were conducted both in vitro and in cadaveric tissues to characterize the survival dynamics of IAV and RSV under identical conditions.

RESULTS

SARS-CoV-2 exhibited prolonged post-mortem infectivity, persisting for up to 5 days at RT and 37 ℃ and over 7 days at 4 ℃, with the highest risk of transmission occurring within the first 72 h at RT and 24 h at 37 ℃. In contrast, RSV remained viable for 1-2 days, while IAV persisted for only a few hours post-mortem. Viral decay rates were temperature-dependent and varied across tissues, demonstrating distinct post-mortem survival kinetics.

CONCLUSIONS

This study presents the first comprehensive analysis of viral persistence in cadavers, revealing prolonged SARS-CoV-2 stability compared to IAV and RSV. These findings underscore the need for enhanced post-mortem biosafety protocols to mitigate occupational exposure risks in forensic and clinical settings. By elucidating viral decay dynamics across environmental conditions, this research establishes a critical foundation for infection control strategies, informing biosafety policies for emerging respiratory pathogens.

YIPF5 is an essential host factor for porcine epidemic diarrhea virus double-membrane vesicle formation

Porcine epidemic diarrhea virus (PEDV) is a major coronavirus in swine, causing substantial economic losses in the industry. To deepen our understanding of the PEDV-host cell interactions, we performed whole-genome CRISPR/Cas9 screens on porcine IPEC-J2 and IPI-2I cell lines to identify key host factors essential for PEDV infection. Our study identified the Yip family 5 (YIPF5) protein as a critical host factor, where its knockout suppressed PEDV infection by specifically affecting the virus replication stage. YIPF5 interacts with viral non-structural protein (nsp) 3, 4, and 6, facilitating the formation of double-membrane vesicles (DMVs), essential for replication organelle biogenesis. The knockout of YIPF5 interferes with the interaction between nsp3 and nsp4, consequently impacting the formation of DMVs mediated by these proteins. These findings establish YIPF5 as a key host factor involved in DMV formation during PEDV infection, highlighting its potential as a therapeutic target.

IMPORTANCE

Coronaviruses pose serious health threats to both humans and animals. Identifying host genes critical for porcine epidemic diarrhea virus (PEDV) infection can uncover new therapeutic targets and enhance our understanding of coronavirus pathogenesis. In this study, we conducted genome-scale CRISPR/Cas9 screens in two porcine cell lines (IPEC-J2 and IPI-2I) and identified YIPF5 as an essential host factor for PEDV replication. Our results demonstrate that YIPF5 plays a pivotal role in the formation of PEDV-induced double-membrane vesicles (DMVs), which are crucial for viral replication. These findings shed new light on the molecular mechanisms of PEDV and suggest YIPF5 as a therapeutic target.

Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules

Machine learning (ML) techniques have become powerful tools in both industrial and academic settings. Their ability to facilitate analysis of complex data and generation of predictive insights is transforming how scientific problems are approached across a wide range of disciplines. In this tutorial, we present a cursory introduction to three widely used ML techniques─logistic regression, random forest, and multilayer perceptron─applied toward analyzing molecular dynamics (MD) trajectory data. We employ our chosen ML models to the study of the SARS-CoV-2 spike protein receptor binding domain interacting with the receptor ACE2. We develop a pipeline for processing MD simulation trajectory data and identifying residues that significantly impact the stability of the complex.

Host susceptibilities and entry processes of SARS-CoV-2 Omicron variants using pseudotyped viruses carrying spike protein

The zoonotic potential has been well studied for SARS-CoV-2 and its earlier variants, but the information for Omicron variants and SARS-CoV is lacking. In this study, we generated lentivirus-based pseudoviruses carrying spike protein (S) of SARS-CoV-2, parental and Omicron variants including BA.1.1, BA.4/5, XBB.1 and JN.1 to assess the entry into cells expressing human or animal ACE2 including dogs, cats and white-tailed deer. Using these pseudoviruses, along with pseudoviruses carrying S of MERS-CoV and SARS-CoV, we assessed the protease processing of these various S through western blotting, entry/inhibition assays, and fusion assays. The results showed that overall, pseudotyped viruses carrying each S of SARS-CoV-2 Omicron strains efficiently entered cells expressing human or animal ACE2 comparably (BA.1.1 and JN.1) or better (BA.4/5 and XBB.1) than those with parental strain. In addition, the entries of pseudotyped viruses carrying S of SARS-CoV were also efficient the cells expressing human or animal ACE2. The presence of TMPRSS2 significantly increased the entry of all tested pseudoviruses including those with S of MERS-CoV, SARS-CoV and SARS-CoV-2, with BA.1.1, JN1, and XBB.1 Omicron having the largest fold increase. When cathepsin inhibitors were examined to assess their inhibitory effects on entry of parental and Omicron variants, they were significantly less effective in the entry of Omicron variants compared to parent strain, suggesting Omicron strains do not depend on the endosomal route compared to parental strain.

Engineered cell membrane-based nano therapies fight infectious diseases

Infectious diseases continue to present significant global public health challenges, with pathogens such as bacteria and viruses posing substantial threats to human health. Conventional therapeutic approaches face several limitations, including the rising prevalence of drug resistance, suboptimal targeting, and adverse side effects, which collectively complicate clinical management. Cell membrane vesicles (MVs), characterized by their natural biocompatibility and outstanding drug delivery capabilities, have emerged as a promising platform for addressing these challenges in the treatment of infectious diseases. To further augment the therapeutic potential of MVs, engineering modifications have been extensively employed to enhance their functionality and efficacy. This review provides a comprehensive overview of the production and modification techniques associated with MVs, emphasizing recent advancements in the development of engineered membrane vesicles (EMVs) as versatile nanoplatforms for combating infectious diseases. Additionally, the clinical prospects and existing challenges of EMVs are critically analyzed, and recommendations are proposed to guide future research and facilitate their clinical translation into practical applications in combating infective disease.

Immune evasion, infectivity, and membrane fusion of the SARS-CoV-2 JN.1 variant

SARS-CoV-2 undergoes continuous mutations during transmission, resulting in a variety of Omicron subvariants. Currently, SARS-CoV-2 BA.2.86 and its descendants JN.1, KP.2, KP.1.1 have been identified as the primary variants spreading globally. These emerging Omicron variants have increased transmissibility, potentially elevating the risk of viral reinfection in the population. However, the biological characteristics of newly-emerged Omicron subvariants in infecting host cells remain unclear. In this study, we assessed the neutralization effect of BA.2.86 and its descendant JN.1, as well as D614G, BA.2, BA.4/5, XBB.1.5, EG.5.1, HV.1, HK.3, JD.1.1 and JG.3 on convalescent sera obtained from individuals infected with BA.5 or XBB.1.5 strain. We evaluated the biological characteristics of variants spike proteins by measuring viral infectivity, affinity for receptors, and membrane fusion. Compared to XBB-related subvariants, BA.2.86 exhibited a diminished immune escape response, but JN.1 displayed a markedly augmented immune escape capability, which was closely related to its rapid transmission. BA.2.86 was less infectious in susceptible cells, while the JN.1 variant exhibited relatively high infectivity. Notably, BA.2.86 and JN.1 exhibited low fusion activity in 293 T-ACE2 cells, but relatively high fusogenicity in transmembrane protease serine 2 (TMPRSS2) overexpression cells. This study explored the evolutionary characteristics of emerging Omicron subvariants in host adaptation, and provided new strategies for the prevention and treatment of coronavirus disease 2019 (COVID-19).

SerpinB3/Protease Activated Receptor-2 Axis Is Essential for SARS CoV-2 Infection

Recent research has proposed several host factors required for SARS-CoV-2 infection and involved in the inflammatory response. Among these, members of the human serpin family and PAR2 have been suggested to play a relevant role. As it has been shown that one of the multiple activities of protease inhibitor SerpinB3 is the activation of PAR2, we have modulated the expression of these two molecules on both human bronchial and hepatic cells and assessed cell surface Spike binding and SARS-CoV-2 infectivity. Our findings indicate that both SerpinB3 and PAR2 play a pivotal role in viral infection and downregulate the expression of interferon-γ, a cytokine with a well-known antiviral effect. These results underscore the potential of the SerpinB3-PAR2 axis as a target for antiviral therapy and provide support for addressing serpins as targets for this purpose.

Role of N-linked glycosylation sites in human ACE2 in SARS-CoV-2 and hCoV-NL63 infection

Angiotensin-converting enzyme 2 (ACE2) is a transmembrane protein known for its physiological role in the renin-angiotensin system that also serves as a receptor for entry of SARS-CoV-1, SARS-CoV-2, and the seasonal human coronavirus NL63 (hCoV-NL63). ACE2 contains seven N-linked glycosylation sites. Molecular simulation and binding analyses suggest that some of them are involved in the interaction with the Spike (S) proteins of hCoVs, but their relevance in S-mediated fusion and viral entry is poorly investigated. To address this, we determined the impact of all seven N-linked glycosylation sites in ACE2 on S-mediated SARS-CoV-2 and hCoV-NL63 infection as well as cell-to-cell fusion. We found that all mutant ACE2 proteins are expressed and localized at the cell surface, albeit ACE2 lacks all glycans at decreased levels. On average, changes in T92I, N322A, and N690A, as well as combined mutation of all N-linked glycosylation sites increased endocytic VSVpp infection mediated by early HU-1 as well as Omicron BA.2, BA.5, and XBB.1.5 SARS-CoV-2 S proteins. In comparison, only the lack of glycan at N322 in ACE2 enhanced syncytia formation and only in the case of HU-1 and XBB.1.5 S proteins. Changes in N90A, T92I, and N322A increased infection by the early SARS-CoV-2 HU-1 strain about twofold to threefold but had lesser effects on infection by genuine Omicron variants. Despite reduced cell surface expression of ACE2, elimination of all N-linked glycosylation sites usually enhanced SARS-CoV-2 infection via the endocytic pathway while having little effect on entry at the cell surface in the presence of TMPRSS2. Our results provide insights into the role of N-linked glycans in the ability of human ACE2 (hACE2) to serve as receptors for coronavirus infection.

IMPORTANCE

Several human coronaviruses use angiotensin-converting enzyme 2 (ACE2) as a primary receptor for infection of human cells. ACE2 is glycosylated at seven distinct positions, and the role of glycans for the entry of SARS-CoV-2 and hCoV-NL63 into their target cells is incompletely understood. Here, we examined the impact of individual and combined mutations in hACE2 glycosylation sites on Spike-mediated VSV-pseudoparticle and genuine SARS-CoV-2 and hCoV-NL63 infection and cell-to-cell fusion. Our results provide new information on the role of glycans in hACE2 for infection by highly pathogenic and seasonal coronaviruses.

Syntaxin-6 restricts SARS-CoV-2 infection by facilitating virus trafficking to autophagosomes

Despite the diminishing global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus continues to circulate and undergo mutations, posing ongoing challenges for public health. A comprehensive understanding of virus entry mechanisms is crucial for managing new epidemic strains. However, the cellular processes post-endocytosis remain largely unexplored. This study employs proximity labeling to examine proteins near ACE2 post-viral infection and identified syntaxin-6 (STX6) as a factor that inhibits SARS-CoV-2 infection by impeding the endocytic release of the virus. SARS-CoV-2 infection enhances early endosome recruitment of STX6. STX6 appears to hinder the maturation of viral particles-laden early endosomes into late endosomes, from which the virus could escape. Instead, it promotes the trafficking of the virus toward the autophagy-lysosomal degradation pathway. STX6 exhibits a broad-spectrum effect against various SARS-CoV-2 variants and several other viruses that enter via endocytosis. We report for the first time the function of STX6 as a restrictive factor in viral infection.IMPORTANCEVirus entry is the first step of the virus life cycle, and the exploitation of the endo-lysosome pathway for cellular entry by viruses has been well documented. Meanwhile, the intrinsic defense present within cells interferes with virus entry. We identified STX6 as a host restriction factor for viral entry by facilitating the virus trafficking to the autophagy-lysosomal degradation pathway. Notably, STX6 exhibits broad-spectrum antiviral activity against diverse severe acute respiratory syndrome coronavirus 2 variants and other viruses employing endocytosis for entry.

Targeting USP22 to promote K63-linked ubiquitination and degradation of SARS-CoV-2 nucleocapsid protein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) generally hijacks the cellular machinery of host cells for survival. However, how SARS-CoV-2 employs the host's deubiquitinase to facilitate virus replication remains largely unknown. In this study, we identified the host deubiquitinase USP22 as a crucial regulator of the expression of SARS-CoV-2 nucleocapsid protein (SARS-CoV-2 NP), which is essential for SARS-CoV-2 replication. We demonstrated that SARS-CoV-2 NP proteins undergo ubiquitination-dependent degradation in host cells, while USP22 interacts with SARS-CoV-2 NP and downregulates K63-linked polyubiquitination of SARS-CoV-2 NP, thereby protecting SARS-CoV-2 NP from degradation. Importantly, we further revealed that sulbactam, an antibiotic, can reduce USP22 protein levels, eventually promoting the degradation of SARS-CoV-2 NP in vitro and in vivo. This study reveals the mechanism by which SARS-CoV-2-encoded NP protein employs host deubiquitinase for virus survival and provides a potential strategy to fight against SARS-CoV-2 infection.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (SARS-CoV-2 NP) plays a pivotal role in viral infection by binding to viral RNA, stabilizing the viral genome, and promoting replication. However, the interactions between SARS-CoV-2 NP and host intracellular proteins had not been elucidated. In this study, we provide evidence that SARS-CoV-2 NP interacts with the deubiquitinase USP22 in host cells, which downregulates SARS-CoV-2 NP ubiquitination. This reduction in ubiquitination effectively prevents intracellular degradation of SARS-CoV-2 NP, thereby enhancing its stability, marking USP22 as a potential target for antiviral strategies. Additionally, our findings indicate that sulbactam significantly decreases the protein levels of USP22, thereby reducing SARS-CoV-2 NP levels. This discovery suggests a novel therapeutic pathway in which sulbactam could be repurposed as an antiviral agent, demonstrating how certain antibiotics might contribute to antiviral treatment. This work thus opens avenues for drug repurposing and highlights the therapeutic potential of targeting host pathways to inhibit viral replication.

Shared host genetic landscape of respiratory viral infection

Respiratory viruses represent a major global health burden. Although these viruses have different life cycles, they may depend on common host genetic factors, which could be targeted by broad-spectrum host-directed therapies. We used genome-wide CRISPR screens and advanced data analytics to map a network of host genes that support infection by nine human respiratory viruses [influenza A virus, parainfluenza virus, human rhinovirus, respiratory syncytial virus, human coronavirus (HCoV)-229E, HCoV-NL63, HCoV-OC43, Middle East respiratory syndrome-related coronavirus, and severe acute respiratory syndrome-related coronavirus 2]. We explored shared pathways using knowledge graphs to inform on pharmacological targets. We selected and validated STT3A/B proteins of the N-oligosaccharyltransferase complex as host targets of broad-spectrum antiviral small molecules. Our work highlights the commonalities of viral host genetic dependencies and the feasibility of using this information to develop broad-spectrum antiviral agents.

The comprehensive transcriptomic atlas of porcine immune tissues and the peripheral blood mononuclear cell (PBMC) immune dynamics reveal core immune genes

BACKGROUND

Viral diseases have profoundly influenced the sustainable development of the swine farming industry. With the development of genomics technology, the combination of transcriptome, genetic variation, immune response, and QTL mapping data to illustrate the interactions between pathogen and host immune system, will be an effective tool for identification of disease resistance genes in pigs. The immune system of an organism is the source of disease resistance in livestock, consisting of various immune tissues, as well as the immune cells and cytokines they produced. However, comprehensive systematic studies on transcriptome of porcine immune tissues are still rare. Poly(I:C), as a viral mimic, is commonly used to study immune responses of the body during viral infections, and serves as a valuable tool for investigating immune mechanisms in swine.

RESULTS

WGCNA analysis identified core immune genes across six immune tissues (bone marrow, jejunum, lymph node, PBMC, spleen, thymus) in Landrace pigs, which are also crucial for the development of PBMCs. The examination of the changes in the proportion of immune cells during three developmental stages (1-month-old, 4-month-old, 7-month-old) shows a shift from innate immunity to humoral immunity. By integrating different epigenetic genomics datasets, we identified several core immune genes and their causal variants, including IFI44, IFIT5, EIF2AK2 and others, which are closely related to immune development and response. Functional validation studies reveal that the IFI44 gene acts as a negative regulator of the antiviral response; its inhibition effect significantly reduced Poly(I:C)-induced cell necrosis, while enhancing apoptosis to combat viral infections.

CONCLUSION

Our study elucidated the fundamental transcriptional program in porcine immune tissues and the immunodynamics underlying development of PBMCs, identifying many core immune genes, including IFI44, which plays a critical negative regulator role in the antiviral response, providing valuable insights for breeding programs aimed at enhancing pig disease resistance.

The age-dependent neuroglial interaction with peripheral immune cells in coronavirus-induced neuroinflammation with a special emphasis on COVID-19

Neurodegenerative diseases are chronic progressive disorders that impair memory, cognition, and motor functions, leading to conditions such as dementia, muscle weakness, and speech difficulties. Aging disrupts the stringent balance between pro- and anti-inflammatory cytokines, increasing neuroinflammation, which contributes to neurodegenerative diseases. The aging brain is particularly vulnerable to infections due to a weakened and compromised immune response and impaired integrity of the blood-brain barrier, allowing pathogens like viruses to trigger neurodegeneration. Coronaviruses have been linked to both acute and long-term neurological complications, including cognitive impairments, psychiatric disorders, and neuroinflammation. The virus can induce a cytokine storm, damaging the central nervous system (CNS) and worsening existing neurological conditions. Though its exact mechanism of neuroinvasion remains elusive, evidence suggests it disrupts the blood-brain barrier and triggers immune dysregulation, leading to persistent neurological sequelae in elderly individuals. This review aims to understand the interaction between the peripheral immune system and CNS glial cells in aged individuals, which is imperative in addressing coronavirus-induced neuroinflammation and concomitant neurodegeneration.

Neurotoxic Implications of Human Coronaviruses in Neurodegenerative Diseases: A Perspective from Amyloid Aggregation

Human coronaviruses (HCoVs) include seven species: HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, MERS-CoV, SARS-CoV-1, and SARS-CoV-2. The last three, classified as Betacoronaviruses, are highly transmissible and have caused severe pandemics. HCoV infections primarily affect the respiratory system, leading to symptoms such as dry cough, fever, and breath shortness, which can progress to acute respiratory failure and death. Beyond respiratory effects, increasing evidence links HCoVs to neurological dysfunction. However, distinguishing direct neural complications from preexisting disorders, particularly in the elderly, remains challenging. This study examines the association between HCoVs and neurodegenerative diseases like Alzheimer disease, Parkinson disease, Lewy body dementia, amyotrophic lateral sclerosis, and Creutzfeldt-Jakob disease. It also presents the long-term neurological effects of HCoV infections and their differential impact across age groups and sexes. A key aspect of this study is the investigation of the sequence and structural similarities between amyloidogenic and HCoV spike proteins, which can provide insights into potential neuropathomechanisms.

Molecular Insight into the Role of Vitamin D in Immune-Mediated Inflammatory Diseases

In the last decades, it has become increasingly evident that the role of vitamin D extends beyond the regulation of calcium homeostasis and the maintenance of bone health. A significant extraskeletal function of vitamin D is its role in modulating the immune system, particularly highlighted in the context of immune-mediated inflammatory diseases, where correlations between vitamin D status and genetic variations in the vitamin D receptor have been observed about the incidence and severity of these conditions. Additionally, different studies have reported the existence of immunomodulatory effects of vitamin D, particularly the effects of vitamin D on dendritic cell function, maturation, cytokine production, and antigen presentation, and that its deficiency may be associated with a sub-inflammatory state. In this sense, different clinical trials have been conducted to assess the therapeutic efficacy of vitamin D in different immune-mediated inflammatory disorders, including asthma, atopic dermatitis (AD), rheumatoid arthritis (RA), psoriasis, thyroid diseases, infectious diseases, and systemic lupus erythematosus (SLE). This review will provide a comprehensive overview of the current understanding of the molecular mechanisms underlying vitamin D's immunomodulatory properties, its role, and innovative therapeutic applications in patients with immune-mediated inflammatory diseases.

Formulation and In-Vitro Testing of Nebulized Camostat Mesylate Loaded Nanoliposomes for the Treatment of SARS-CoV- 2 Infection

COVID- 19, caused by the coronavirus SARS-CoV- 2, has arisen as a global health epidemic, claiming the lives of millions of people throughout the world. Combating the pandemic has involved developing and approving vaccines and antiviral products. Camostat Mesylate (Camo) is a TMPRSS2 inhibitor that inhibits virus-cell membrane fusion and, thereby, viral multiplication. Significant limitations of using oral Camo include the limited amount of Camo reaching the site of action, lungs, side effects due to distribution to all tissues, and enzymatic breakdown in the gut. This investigation aims to develop self-administrable and patient-compliant extended-release Camo-loaded pegylated nanoliposomes (Camo-pegNLs) for delivering Camo directly to the lungs, thereby enabling faster onset of action and overcoming limitations of oral Camo delivery. We developed the Camo-pegNLs were composed of 1,2-dipalmitoyl-sn-glycerol- 3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycerol- 3-phosphoethanolamine (DOPE-PEG, MW2000) and cholesterol using the ethanol injection technique and syringe pump. The NLs were characterized for their particle size, polydispersity index (PDI), and zeta potential using Malvern Zetasizer. The assay, unentrapped Camo using Vivaspin 500 ultrafilter (10 kDa) and in-vitro release were determined. The Camo content was analyzed using a validated HPLC method. The aerodynamic properties of Camo-pegNLs were determined using a Westech Andersen Cascade Impactor (ACI) at 28.3L/min and a pneumatic jet nebulizer. The antiviral effect of Camo-pegNLs was assessed in Vero cells expressing TMPRSS2 and infected with SARS-CoV- 2. Camo-pegNLs suspension showed size of 167.50 ± 0.90 nm, zeta potential of 0.48 ± 0.04 mV, and PDI of 0.07 ± 0.01. The quantity of entrapped Camo was found to be 44.86 ± 1.35%w/v, and the drug loading was 27.41 ± 0.04%w/w. The Camo-pegNL- 2 had an extended release of up to 24 h, MMAD of 4.295 ± 0.1 µm, GSD of 1.915 ± 0.064, and FPF of 42.01% ± 6.90. Camo-pegNLs showed a significant antiviral effect on Vero cells compared to no treatment group (p < 0.01). An efficacious nebulized Camo-pegNLs suspension product was successfully developed for direct lung delivery to Camo-pegNLs to treat the SARS-CoV- 2 infection.

Identification and targeting of regulators of SARS-CoV-2-host interactions in the airway epithelium

The impact of SARS-CoV-2 in the lung has been extensively studied, yet the molecular regulators of host-cell programs hijacked by the virus in distinct human airway epithelial cell populations remain poorly understood. Some of the reasons include overreliance on transcriptomic profiling and use of nonprimary cell systems. Here we report a network-based analysis of single-cell transcriptomic profiles able to identify master regulator (MR) proteins controlling SARS-CoV-2-mediated reprogramming in pathophysiologically relevant human ciliated, secretory, and basal cells. This underscored chromatin remodeling, endosomal sorting, ubiquitin pathways, as well as proviral factors identified by CRISPR assays as components of the viral-host response in these cells. Large-scale drug perturbation screens revealed 11 candidate drugs able to invert the entire MR signature activated by SARS-CoV-2. Leveraging MR analysis and perturbational profiles of human primary cells represents an innovative approach to investigate pathogen-host interactions in multiple airway conditions for drug prioritization.

Revisiting Pathogen Exploitation of Clathrin-Independent Endocytosis: Mechanisms and Implications

Endocytosis is a specialized transport mechanism in which the cell membrane folds inward to enclose large molecules, fluids, or particles, forming vesicles that are transported within the cell. It plays a crucial role in nutrient uptake, immune responses, and cellular communication. However, many pathogens exploit the endocytic pathway to invade and survive within host cells, allowing them to evade the immune system and establish infection. Endocytosis can be classified as clathrin-mediated (CME) or clathrin-independent (CIE), based on the mechanism of vesicle formation. Unlike CME, which involves the formation of clathrin-coated vesicles that bud from the plasma membrane, CIE does not rely on clathrin-coated vesicles. Instead, other mechanisms facilitate membrane invagination and vesicle formation. CIE encompasses a variety of pathways, including caveolin-mediated, Arf6-dependent, and flotillin-dependent pathways. In this review, we discuss key features of CIE pathways, including cargo selection, vesicle formation, routes taken by internalized cargo, and the regulatory mechanisms governing CIE. Many viruses and bacteria hijack host cell CIE mechanisms to facilitate intracellular trafficking and persistence. We also revisit the exploitation of CIE by bacterial and viral pathogens, highlighting recent discoveries in entry mechanisms, intracellular fate, and host-pathogen interactions. Understanding how pathogens manipulate CIE in host cells can inform the development of novel antimicrobial and immunomodulatory interventions, offering new avenues for disease prevention and treatment.

LL-37 Inhibits TMPRSS2-Mediated S2' Site Cleavage and SARS-CoV-2 Infection but Not Omicron Variants

Continual evolution of SARS-CoV-2 spike drives the emergence of Omicron variants that show increased spreading and immune evasion. Understanding how the variants orientate themselves towards host immune defence is crucial for controlling future pandemics. Herein, we demonstrate that human cathelicidin LL-37, a crucial component of innate immunity, predominantly binds to the S2 subunit of SARS-CoV-2 spike protein, occupying sites where TMPRSS2 typically binds. This binding impedes TMPRSS2-mediated priming at site S2' and subsequent membrane fusion processes. The mutation N764K within S2 subunit of Omicron variants reduces affinity for LL-37 significantly, thereby diminishing binding capacity and inhibitory effects on membrane fusion. Moreover, the early humoral immune response enhanced by LL-37 is observed in mice against SARS-CoV-2 spike but not Omicron BA.4/5 spike. These findings reveal the mechanism underlying interactions amongst LL-37, TMPRSS2 and SARS-CoV-2 and VOCs, and highlight the distinct mutation for Omicron variants to evade the fusion activity inhibition by host innate immunity.

Integrating multiplex PCR in fever clinics for acute respiratory pathogen-specific diagnosis

The epidemiological patterns of respiratory tract infections (RTIs) have experienced substantial changes due to the influence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a particular focus on acute respiratory infections (ARIs). Challenges in early diagnosis, inadequate triage strategies, and the inappropriate use of antimicrobials or antivirals have compounded the difficulties in accurately diagnosing and managing ARIs in the post-pandemic context. This study aimed to investigate the efficacy of fever clinics equipped with nucleic acid testing capabilities in the precise triage of ARIs. In a cohort of 604 individuals presenting with symptoms of ARIs, we utilized real-time reverse transcription polymerase chain reaction (RT-PCR) technology available in the fever clinic to perform nucleic acid testing for SARS-CoV-2, influenza A virus (Flu A), influenza B virus (Flu B), respiratory syncytial virus, adenovirus, human rhinovirus, and Mycoplasma pneumoniae. Subsequently, statistical methods were employed to analyze the distribution and types of ARIs associated with these pathogens. In fever clinics, most patients presenting with respiratory pathogen infections were diagnosed with non-SARS-CoV-2 respiratory pathogens, with a higher incidence noted among pediatric patients compared to adults. In contrast, SARS-CoV-2 primarily affected the adult population and was linked to more severe clinical outcomes. Consequently, the swift triage of patients exhibiting ARI symptoms in a fever clinic equipped with nucleic acid testing enables the rapid identification and precise treatment of pathogens. This approach alleviates patient discomfort and enhances the efficiency of healthcare resource utilization.

Lyophilized MSC-EVs attenuates COVID-19 pathogenesis by regulating the JAK/STAT pathway

BACKGROUND

The JAK/STAT signaling pathway plays a crucial role in the release of interferons (IFNs) and the proinflammatory response during SARS-CoV-2 infection, contributing to the cytokine storm characteristic of severe COVID-19 cases. STAT3, a key protein in this pathway, has been implicated in promoting inflammation, making its inhibition a potential therapeutic strategy to mitigate disease severity. Mesenchymal Stem Cell-derived Extracellular Vesicles (MSC-EVs), enriched with immunomodulatory and antiviral miRNAs, offer a promising therapeutic approach by modulating gene expression and regulating inflammatory responses. This study investigates the ability of Lyophilized MSC-EVs to inhibit the JAK/STAT pathway, highlighting their potential application in COVID-19 management.

METHODS

Male Syrian hamsters were used as an experimental model, housed under controlled laboratory conditions. SARS-CoV-2 (hCoV-19/Egypt/NRC-03/2020) was propagated in Vero E6 cells, and viral titers were determined using plaque assays. Hamsters were intranasally challenged with the virus and treated intraperitoneally with 0.5 mL of lyophilized human Wharton's jelly-derived MSC-extracellular vesicles (MSC-EVs). Histopathological evaluations were performed on lung tissues using H&E, Masson's trichrome, and immunohistochemical staining. Morphometric analyses were conducted to assess lung injury and fibrosis. Western blotting was employed to evaluate protein expression. All procedures adhered to ethical and biosafety guidelines.

RESULTS

The administration of MSC-EVs significantly upregulated the expression levels of miRNA-146a, miRNA-124, miRNA-155, miRNA-29b, miRNA-7, miRNA-145 and miRNA-18a compared to their levels in the COVID-19 group, suggesting a targeted release of miRNA-cargo from the MSC-EVs into the lung tissue of the animals. MSC-EVs impaired the activation of the STAT3/STAT1 signaling pathway and reduced the cytokine storm and coagulopathy associated with COVID-19.

CONCLUSIONS

These findings suggest that MSC-EVs have the potential to effectively mitigate the pathogenesis of COVID-19 by targeting the JAK/STAT signaling pathway. Further research is needed to fully understand the mechanisms underlying the therapeutic effects of MSC-EVs and their clinical application in combating the COVID-19 pandemic.

Trypstatin as a Novel TMPRSS2 Inhibitor with Broad-Spectrum Efficacy against Corona and Influenza Viruses

Respiratory viruses, such as SARS-CoV-2 and influenza, exploit host proteases like TMPRSS2 for entry, making TMPRSS2 a prime antiviral target. Here, the identification and characterization of Trypstatin, a 61-amino acid Kunitz-type protease inhibitor derived from human hemofiltrate are reported. Trypstatin inhibits TMPRSS2 and related proteases with high potency, exhibiting half-maximal inhibitory concentration values in the nanomolar range, comparable to the small molecule inhibitor camostat mesylate. In vitro assays demonstrate that Trypstatin effectively blocks spike-driven entry of SARS-CoV-2, SARS-CoV-1, MERS-CoV, and hCoV-NL63, as well as hemagglutinin-mediated entry of influenza A and B viruses. In primary human airway epithelial cultures, Trypstatin significantly reduces SARS-CoV-2 replication and retained activity in the presence of airway mucus. In vivo, intranasal administration of Trypstatin to SARS-CoV-2-infected Syrian hamsters reduces viral titers and alleviates clinical symptoms. These findings highlight Trypstatin's potential as a broad-spectrum antiviral agent against TMPRSS2-dependent respiratory viruses.

Antiviral activity against HSV-1 of triterpene saponins from Anagallis arvensis is related tothe fusion-inhibitory activity of desglucoanagalloside B

The identification of antiviral natural products as new lead structures has become a major task in medical science. Especially saponins have gained high interest for their antiviral activity. Antiviral effects of the saponin-containing plant Anagallis arvensis, widely used in traditional medicine, have been described, while mode of action or detailed phytochemical and functional investigations are still missing. A saponin enriched extract (AAS) from the aerial material of A. arvensis was characterized in detail by LC-HRMS, indicating the presence of a complex mixture of triterpene saponins and flavonoid glycosides. Plaque assays with Herpes simplex virus 1 (HSV-1) on Vero cells indicated strong inhibition of viral spread after infection of the host cells, resulting in reduced plaque size. The strongest effect was achieved by treating host cells post infection, which points towards an interference with the viral post-entry step. Using a specific HSV-1 fusion assay, AAS was shown to inhibit HSV-1 glycoprotein-mediated cell fusion at >2 μg/mL. Bioassay-guided fractionation of AAS yielded one active subfraction, which significantly reduced HSV-1 plaque size on Vero cells. The membrane-fusion inhibiting effect was correlated to the presence of desglucoanagalloside B 9. Interestingly, this compound was also detected in relevant amounts in herbal preparations from traditional medicine, which again could rationalize the use of A. arvensis as antiviral remedy in folk medicine. Relevant antiviral activity against SARS-CoV-2 was not detected.

Vitamin D status in children with mild, moderate, or severe confirmed COVID-19: systematic-review and meta-analysis

Background

Vitamin D acts as a pro-hormone with a wide range of beneficial effects. It is reported that vitamin D deficiency is a risk factor for COVID-19 severity in children. In the present study, we decided to assess 25 hydroxy (OH) vitamin D status in children with mild, moderate, or severe confirmed COVID-19 and also compare them with those of a healthy control group using existing data.

Methods

Relevant studies were extracted using online international databases including Scopus, Science Direct, PubMed, Web of Science, ProQuest, and Google Scholar search engine between Jan 2019 and 2024. The quality of all papers is determined by the NOS checklist. Heterogeneity between the results of primary studies was evaluated with the I-square index. Egger's test, funnel plot, and sensitivity analysis were applied. The statistical analysis was done using Stata version 17.

Results

In 12 documents, the status of vitamin D was examined between case and control groups. By combining the results of these studies using random effect model, the standardized mean difference (SMD) vitamin D level in the COVID-19 children compared to the control group was estimated to be -0.88 (98% CI: -1.24, -0.51), which was statistically significant. In the present study, the odd ratio of vitamin D deficiency and vitamin D disorder (insufficiency and deficiency) in children with moderate COVID-19 compared to asymptomatic children with COVID-19 were estimated to be 3.58 (1.10, 11.63) and 2.52 (0.99, 6.41) respectively which was higher than in asymptomatic children with COVID-19. In addition, vitamin D deficiency and vitamin D disorder in children with moderate COVID-19 compared to the children with mild COVID-19 were estimated to be 2.12 (0.90, 4.98) and 1.82 (0.78, 4.22) respectively, which was higher than in children with mild COVID-19. Also, vitamin D deficiency and vitamin D disorder in children with mild COVID-19 compared to asymptomatic children with COVID-19 were estimated to be 2.02 (0.60, 6.78) and 1.64 (0.53, 5.07) respectively, which was higher than in asymptomatic children.

Conclusions

Combining the results of these studies, the effect size of the relationship between vitamin D and COVID-19 in children is significant. During the COVID-19 pandemic (except for the Omicron peak), children were less affected by the severity of COVID-19. The standardized mean difference (SMD) vitamin D level in children with COVID-19 was significantly 0.88 units lower than the control group. Also, the odds ratio of moderate COVID-19 in children with vitamin D deficiency was significantly 3.58 times higher than in asymptomatic children with COVID-19.

A Novel Antiviral Therapeutic Platform: Anchoring IFN-β to the Surface of Infectious Virions Equips Interferon-Evasive Virions with Potent Antiviral Activity

The COVID-19 pandemic highlighted the need for new therapeutic strategies to counter emerging pathogenic viruses. Herein, we introduce a novel fusion protein platform that enables antiviral targeting of distinct viral species based on host receptor specificity. Proof-of-concept studies focused on the human coronavirus NL63, which shares specificity for the ACE2 host receptor with the pandemic SARS-CoV and SARS-CoV-2 species. This antiviral fusion protein combines IFN-β with the soluble extracellular domain of ACE2 (IFNβ-ACE2). Both domains retained predicted bioactivities in that the IFN-β domain exhibited potent antiproliferative activity and the ACE2 domain exhibited full binding to the transmembrane SARS-CoV-2 Spike protein. In virus-washed (virus-targeted) and non-washed in vitro infection systems, we showed that the pool of IFNβ-ACE2 targeted to the virion surface had superior antiviral activity against NL63 compared to soluble ACE2, IFN-β, or the unlinked combination of ACE2 and IFN-β. The pool of IFNβ-ACE2 on the virion surface exhibited robust antiviral efficacy based on the preemptive targeting of antiviral IFN-β activity to the proximal site of viral infection. In conclusion, virus-targeted IFN-β places interferon optimally and antecedent to viral infection to constitute a new antiviral strategy.

Determinants of susceptibility to SARS-CoV-2 infection in murine ACE2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes angiotensin-converting enzyme 2 (ACE2) as a receptor to enter host cells, and primary receptor recognition of the spike protein is a major determinant of the host range of SARS-CoV-2. Since the emergence of SARS-CoV-2, a considerable number of variants have emerged. However, the determinants of host tropism of SARS-CoV-2 remain elusive. We conducted infection assays with chimeric recombinant SARS-CoV-2 carrying the spike protein from 10 viral variants, assessing their entry efficiency using mammalian ACE2 orthologs from species that have close contact with humans. We found that only murine ACE2 exhibited different susceptibilities to infection with the SARS-CoV-2 variants. Moreover, we revealed that the mutation N501Y in the viral spike protein has a crucial role in determining the infectivity of cells expressing murine ACE2 and of mice in vivo. Next, we identified six amino acid substitutions at 24, 30, 31, 82, 83, and 353 in murine ACE2 that allowed for viral entry of the variants to which murine ACE2 was previously resistant. Furthermore, we showed that ACE2 from a species closely related to mice, Mus caroli, is capable of supporting entry of the viral variants that could not use murine ACE2. These results suggest that few ACE2 orthologs have different susceptibility to infection with SARS-CoV-2 variants as observed for murine ACE2. Collectively, our study reveals critical amino acids in ACE2 and the SARS-CoV-2 spike protein that are involved in the host tropism of SARS-CoV-2, shedding light on interspecies susceptibility to infection.IMPORTANCESARS-CoV-2 can infect many species besides humans, leading to the evolution of the virus and adaptation to other animal hosts, which could trigger a new COVID-19 wave. The SARS-CoV-2 spike protein utilizes ACE2 as a receptor for entry into host cells. The interaction of ACE2 with the spike protein determines the host range of SARS-CoV-2. In this study, using chimeric viruses carrying the spike protein of SARS-CoV-2 variants to infect cells expressing different ACE2 orthologs from species humans come in close contact with, we confirmed murine ACE2 alone showed different susceptibility to the variants. We identified residues in murine ACE2 and the viral spike that restrict viral entry. Furthermore, an ACE2 ortholog from a species genetically close to mice mediated entry of SARS-CoV-2 variants incapable of infecting mice. This research highlights the uniquely limited susceptibility of mice to different SARS-CoV-2 variants and provides invaluable insights into the host tropism of SARS-CoV-2.

IFITM proteins are key entry factors for porcine epidemic diarrhea coronavirus

Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that poses a substantial threat to the global swine industry. However, our current understanding of the host factors crucial for PEDV infection remains limited. To identify these host factors, we conducted a genome-wide CRISPR/Cas9 gene knockout screen using a PEDV-permissive cell line. Our results indicate that the endogenous expression of human interferon-inducible transmembrane protein 3 (IFITM3) enhances PEDV entry and replication. Silencing or eliminating endogenous IFITM3 in Huh7 cells significantly suppressed PEDV entry, whereas reintroducing IFITM3 partially restored susceptibility to PEDV. Overexpression of human IFITM3 or IFITM2, but not IFITM1, in Huh7.5 cells substantially increased PEDV entry and replication. Importantly, our results suggest that human IFITM3 influences PEDV entry at a later stage. Furthermore, the overexpression of porcine IFITM1 significantly enhanced PEDV infection in LLC-PK1 cells, whereas the overexpression of porcine IFITM2/3 did not produce similar effects. Notably, removing the C-terminal 15 amino acids of porcine IFITM2/3 resulted in increased PEDV entry. Coimmunoprecipitation analyses showed that all IFITMs interacted with the PEDV S1 protein, indicating a direct role in the viral entry process. Additionally, porcine IFITM1 colocalized with the PEDV S protein at the cell nuclear periphery and enhanced PEDV infection in porcine small intestinal organoids. Overall, our results suggest that IFITMs are critical in facilitating PEDV entry into cells. Targeting IFITMs may provide a promising strategy for controlling PEDV transmission and developing interventions to mitigate the virus's impact on the swine industry.

IMPORTANCE

Understanding the mechanisms underlying porcine epidemic diarrhea virus (PEDV) infection is vital for addressing its significant impact on the swine industry. This study reveals that interferon-inducible transmembrane (IFITM) proteins, particularly human IFITM3 and porcine IFITM1, play crucial roles in facilitating PEDV entry and replication. By elucidating these molecular interactions, the research highlights the potential of IFITMs as therapeutic targets for managing PEDV infections and paves the way for antiviral strategies. Moreover, this research extends beyond PEDV management, underscoring the critical role of host factors in controlling the spread of pathogenic coronaviruses.

A Rare Case of Small Bowel Ulceration Induced by COVID-19

Background

COVID-19 can affect multiple organ systems beyond the respiratory tract, including the gastrointestinal tract, where gastrointestinal symptoms include nausea, vomiting, diarrhea, abdominal pain, and even serious manifestations such as ulcers, perforation, or gastrointestinal bleeding.

Case Presentation

We report a case of a 45-year-old male patient with small bowel ulcers caused by chronic COVID-19 infection. Initially presenting with fever and transient unconsciousness, he developed ischemic necrosis and required a mid-thigh amputation. Despite treatment with anti-infection therapy, extracorporeal membrane oxygenation, and continuous renal replacement therapy, he experienced persistent abdominal pain and gastrointestinal bleeding. Imaging and colonoscopy confirmed partial small bowel obstruction and inflammation. After treatment with methylprednisolone and enteral nutrition, his symptoms improved. However, he suffered a gastrointestinal perforation requiring emergency surgery and later underwent a successful stoma reversal. The patient was subsequently discharged with improvement and was discharged with a primary diagnosis of "enterostomal status, perforation of small intestinal ulcer, viral myocarditis, COVID-19 infection, and post right lower extremity amputation". During the past year of follow-up, the patient has not experienced any recurrence of abdominal pain or rectal bleeding.

Conclusion

Although coronavirus pneumonia combined with small bowel ulcers is rare, it requires emergency treatment and has a high mortality rate. This case highlighted the severe gastrointestinal complications induced by COVID-19 infection and the effectiveness of comprehensive management strategies.

Structural basis of TMPRSS11D specificity and autocleavage activation

Transmembrane Protease, Serine-2 (TMPRSS2) and TMPRSS11D are human proteases that enable SARS-CoV-2 and Influenza A/B virus infections, but their biochemical mechanisms for facilitating viral cell entry remain unclear. We show these proteases spontaneously and efficiently cleave their own zymogen activation motifs, activating their broader protease activity on cellular substrates. We determine TMPRSS11D co-crystal structures with a native and an engineered activation motif, revealing insights into its autocleavage activation and distinct substrate binding cleft features. Leveraging this structural data, we develop nanomolar potency peptidomimetic inhibitors of TMPRSS11D and TMPRSS2. We show that a broad serine protease inhibitor that underwent clinical trials for TMPRSS2-targeted COVID-19 therapy, nafamostat mesylate, was rapidly cleaved by TMPRSS11D and converted to low activity derivatives. In this work, we develop mechanistic insights into human protease viral tropism and highlight both the strengths and limitations of existing human serine protease inhibitors, informing future drug discovery efforts targeting these proteases.

Receptor Binding for the Entry Mechanisms of SARS-CoV-2: Insights from the Original Strain and Emerging Variants

Since its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, giving rise to multiple variants that have significantly altered the trajectory of the COVID-19 pandemic. These variants have resulted in multiple waves of the pandemic, exhibiting characteristic mutations in the spike (S) protein that may have affected receptor interaction, tissue tropism, and cell entry mechanisms. While the virus was shown to primarily utilize the angiotensin-converting enzyme 2 (ACE2) receptor and host proteases such as transmembrane serine protease 2 (TMPRSS2) for entry into host cells, alterations in the S protein have resulted in changes to receptor binding affinity and use of alternative receptors, potentially expanding the virus's ability to infect different cell types or tissues, contributing to shifts in clinical presentation. These changes have been linked to variations in disease severity, the emergence of new clinical manifestations, and altered transmission dynamics. In this paper, we overview the evolving receptor utilization strategies of SARS-CoV-2, focusing on how mutations in the S protein may have influenced viral entry mechanisms and clinical outcomes across the ongoing pandemic waves.

Effects of COVID-19 on the contrast sensitivity

There are significant gaps in understanding the extent of the damage caused by COVID-19, with few publications examining its link to contrast sensitivity function (CSF). The aim of the present study was to evaluate CSF at low, medium, and high spatial frequencies in individuals with and without a history of COVID-19. Thirty adults, both male and female, aged between 18 and 49 years, participated in the study, 15 with a history of COVID-19 and 15 without. CSF was measured using Metropsis software (version 11) and vertical sine-wave gratings with spatial frequencies ranging from 0.2 to 19.8 cycles per degree (cpd). The results indicated COVID-19-related changes in CSF at spatial frequencies of 6.1 (U=36.00; P=0.003; r=-0.55), 13.2 (U=29.00; P=0.001; r=-0.61), 15.9 (U=17.00; P=0.001; r=-0.70), and 19.8 cpd (U=13.00; P=0.001; r=-0.73). The observed decrease in CSF within specific spatial frequency bands suggested that the visual system of individuals exposed to COVID-19 required higher contrast levels to detect high spatial frequencies. This psychophysical finding indicated that COVID-19 altered the functioning of the visual system and likely affected the neural mechanisms responsible for processing high spatial frequencies.

Dexamethasone disrupts intracellular pH homeostasis to delay coronavirus infectious bronchitis virus cell entry via sodium hydrogen exchanger 3 activation

Coronavirus entry into host cells enables the virus to initiate its replication cycle efficiently while evading host immune response. Cell entry is intricately associated with pH levels in the cytoplasm or endosomes. In this study, we observed that the sodium hydrogen exchanger 3 (Na+/H+ exchanger 3 or NHE3), which is strongly activated by dexamethasone (Dex) to promote cell membrane Na+/H+ exchange, was critical for cytoplasmic and endosomal acidification. Dex activates NHE3, which increases intracellular pH and blocks the initiation of coronavirus infectious bronchitis virus (IBV) negative-stranded genomic RNA synthesis. Also, Dex antiviral effects are relieved by the glucocorticoid receptor (GR) antagonist RU486 and the NHE3 selective inhibitor tenapanor. These results show that Dex antiviral effects depend on GR and NHE3 activities. Furthermore, Dex exhibits remarkable dose-dependent inhibition of IBV replication, although its antiviral effects are constrained by specific virus and cell types. To our knowledge, this is the first report to show that Dex helps suppress the entry of coronavirus IBV into cells by promoting proton leak pathways, as well as by precisely tuning luminal pH levels mediated by NHE3. Disrupted cytoplasmic pH homeostasis, triggered by Dex and NHE3, plays a crucial role in impeding coronavirus IBV replication. Therefore, cytoplasmic pH plays an essential role during IBV cell entry, probably assisting viruses at the fusion and/or uncoating stages. The strategic modulation of NHE3 activity to regulate intracellular pH could provide a compelling mechanism when developing potent anti-coronavirus drugs.IMPORTANCESince the outbreak of coronavirus disease 2019, dexamethasone (Dex) has been proven to be the first drug that can reduce the mortality rate of coronavirus patients to a certain extent, but its antiviral effect is limited and its underlying mechanism has not been fully clarified. Here, we comprehensively evaluated the effect of Dex on coronavirus infectious bronchitis virus (IBV) replication and found that the antiviral effect of Dex is achieved by regulating sodium hydrogen exchanger 3 (NHE3) activity through the influence of glucocorticoid receptor on cytoplasmic pH or endosome pH. Dex activates NHE3, leading to an increase in intracellular pH and blocking the initiation of negative-stranded genomic RNA synthesis of coronavirus IBV. In this study, we identified the mechanism by which glucocorticoids counteract coronaviruses in cell models, laying the foundation for the development of novel antiviral drugs.

The LDL receptor related protein 1 (LRP1) facilitates ACE2-mediated endocytosis of SARS-CoV2 spike protein-containing pseudovirions

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, employs the viral spike (S) protein to associate with host cells. While angiotensin-converting enzyme 2 (ACE2) is a major receptor for the SARS-CoV-2 spike protein, evidence reveals that other cellular receptors may also contribute to viral entry. We interrogated the role of the low-density lipoprotein receptor-related protein 1 (LRP1) in the involvement of SARS-CoV-2 viral entry. Employing surface plasmon resonance studies, we demonstrated high affinity binding of the trimeric SARS-CoV-2 spike protein to purified LRP1. Further, we observed high affinity interaction of the SARS-CoV-2 spike protein with other low-density lipoprotein receptor (LDLR) family members as well, including LRP2 and the very low-density lipoprotein receptor (VLDLR). Binding of the SARS-CoV-2 spike protein to LRP1 was mediated by its receptor binding domain (RBD). Several LRP1 ligands require surface exposed lysine residues for their interaction with LRP1, and chemical modification of lysine residues on the RBD with sulfo-NHS-acetate ablated binding to LRP1. Using cellular model systems, we demonstrated that cells expressing LRP1, but not those lacking LRP1, rapidly internalized purified 125I-labeled S1 subunit of the SARS-CoV-2 spike protein. LRP1-mediated internalization of the 125I-labeled S1 subunit was enhanced in cells expressing ACE2. By employing pseudovirion particles containing a murine leukemia virus core and luciferase reporter that express the SARS-CoV-2 spike protein on their surface, we confirmed that LRP1 facilitates ACE2-mediated psuedovirion endocytosis. Together, these data implicate LRP1, and perhaps other LDLR family members as host factors for SARS-CoV-2 infection.

Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors

E-64 is an irreversible cysteine protease inhibitor prominently used in chemical biology and drug discovery. Here we uncover a nonribosomal peptide synthetase-independent biosynthetic pathway for E-64, which is widely conserved in fungi. The pathway starts with epoxidation of fumaric acid to the warhead (2S,3S)-trans-epoxysuccinic acid with an Fe(II)/α-ketoglutarate-dependent oxygenase, followed by successive condensation with an L-amino acid by an adenosine triphosphate grasp enzyme and with an amine by the fungal example of amide bond synthetase. Both amide bond-forming enzymes display notable biocatalytic potential, including scalability, stereoselectivity toward the warhead and broader substrate scopes in forming the amide bonds. Biocatalytic cascade with these amide bond-forming enzymes generated a library of cysteine protease inhibitors, leading to more potent cathepsin inhibitors. Additionally, one-pot reactions enabled the preparative synthesis of clinically relevant inhibitors. Our work highlights the importance of biosynthetic investigation for enzyme discovery and the potential of amide bond-forming enzymes in synthesizing small-molecule libraries.

Advances in COVID-19 Therapeutics: Exploring the role of lectins and protease inhibitors

The rapid global spread of SARS-CoV-2 has demanded innovative approaches to treatment and prevention. This article reviews the current landscape of COVID-19 therapeutics and vaccines, emphasizing the role of biotechnological products, particularly lectins and protease inhibitors. SARS-CoV-2, a single-stranded RNA virus, infects host cells via its spike (S) protein, which binds to the angiotensin-converting enzyme 2 (ACE2) receptor. This interaction is facilitated by host proteases like TMPRSS2, which are critical for viral entry. Treatments for COVID-19 primarily focus on antiviral drugs, anti-inflammatory agents, and monoclonal antibodies. Protease inhibitors that target viral enzymes like Mpro and PLpro have demonstrated potential. Additionally, vaccines, including mRNA-based, DNA-based, and those using viral vectors or inactivated viruses, are essential for preventing new infections. Lectins, proteins that bind specifically to carbohydrates, have emerged as potential antiviral agents. They can impede viral entry by binding to glycoproteins on the virus's surface or modulate immune responses. Studies indicate that lectins like cyanovirin-N and griffithsin exhibit significant antiviral activity against SARS-CoV-2. While most of the research on these biotechnological products is still in preclinical or early stages, their potential for treating and preventing COVID-19 is substantial. Further investigation and clinical trials are crucial to validate their efficacy and safety. This article underscores the need for continued exploration of novel therapeutic strategies to combat the evolving COVID-19 pandemic. However, the review is limited by the scarcity of clinical data on these products, highlighting the need for translational research.

Therapeutic Approaches for COVID-19: A Review of Antiviral Treatments, Immunotherapies, and Emerging Interventions

The coronavirus disease 2019 (COVID-19) global health crisis, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has presented unprecedented challenges to global healthcare systems, leading to rapid advances in treatment development. This review comprehensively examines the current therapeutic approaches for managing COVID-19, including direct-acting antivirals, immunomodulators, anticoagulants, and adjuvant therapies, as well as emerging and experimental approaches. Direct-acting antivirals target various stages of the viral life cycle, offering specific intervention points, while immunomodulators aim to modulate the host's immune response, reducing disease severity. Anticoagulant therapies address the coagulopathy frequently observed in severe cases, and adjuvant treatments provide supportive care to improve overall outcomes. We also explore the challenges and limitations of implementing these treatments, such as drug resistance, variable patient responses, and access to therapies, especially in resource-limited settings. The review also discusses future perspectives, including the potential of next-generation vaccines, personalized medicine, and global collaboration in shaping future COVID-19 treatment paradigms. Continuous innovation, combined with an integrated and adaptable approach, will be crucial to effectively managing COVID-19 and mitigating the impact of future pandemics.